From sorench at gmail.com  Wed Apr  1 00:31:47 2009
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 1 Apr 2009 15:31:47 +1100
Subject: [MINC-users] mritoself
Message-ID: <d6e2d6550903312131x7d946d83p33bb0864965d5343@mail.gmail.com>

Hi,
 I think this one has been raised before a while ago.
When mritoself is called on a target and source with identical base names
the resulting transformation is erroneous so this is a silent error.
Eg. mritoself -nothreshold -far dateA/FLAIR.mnc dateB/FLAIR.mnc my.xfm
will create an incorrect xfm.

How about changing this in the next release?
It seems to be the two calls to crop that utilize the same tmp folder with
the original basenames, thereby overwriting the first file.

($source_cropped, $source_crop, $source_subsample)=
   &Crop ($SourceBase, $Source, "crop",
          $GuessCrop, $GuessSubsample, \@Subsample, \@Crop);
($target_cropped, $target_crop, $target_subsample) =
   &Crop ($TargetBase, $Target, "crop",
          $GuessCrop, $GuessSubsample, \@Subsample, \@Crop);

I would think changing crop to cropS and cropT respectively should take care
of it but hopefully someone can doublecheck.



Cheers
Soren

From a.janke at gmail.com  Wed Apr  1 07:20:15 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 1 Apr 2009 22:20:15 +1100
Subject: [MINC-users] mritoself
In-Reply-To: <d6e2d6550903312131x7d946d83p33bb0864965d5343@mail.gmail.com>
References: <d6e2d6550903312131x7d946d83p33bb0864965d5343@mail.gmail.com>
Message-ID: <d747ed50904010420w465bb021rd5d9a3b430b88fdd@mail.gmail.com>

2009/4/1 Soren Christensen <sorench at gmail.com>:
> ?I think this one has been raised before a while ago.
> How about changing this in the next release?

Thanks for reminding me Soren, I have added this to the mni_autoreg
CVS. TThere is a new release imminent with this package so you will
see it in there.


Thanks again.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


From a.janke at gmail.com  Wed Apr  1 07:45:48 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 1 Apr 2009 22:45:48 +1100
Subject: [MINC-users] Classify
In-Reply-To: <3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca>
References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca> 
	<A01ACA50-D5BB-43D6-ADA6-1AAF961F09A2@bic.mni.mcgill.ca>
	<3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca>
Message-ID: <d747ed50904010445g49cc595bie0729947b06ec9fb@mail.gmail.com>

2009/3/31 Jon Erik Ween <jween at klaru-baycrest.on.ca>:
> May I trouble the list with another question? (Guess I'll do so
> anyhow...)

Hi Jon,

No images... (the list wont accept them)  Can you put them up
somewhere on the web instead?


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From jween at klaru-baycrest.on.ca  Wed Apr  1 10:29:53 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 1 Apr 2009 10:29:53 -0400
Subject: [MINC-users] compiling dyld, 32, 64?
In-Reply-To: <7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca>
References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
	<20090306142234.N2730@mrs.mni.mcgill.ca>
	<1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca>
	<7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca>
Message-ID: <376755ED-4DF7-43B6-B680-F1767B4DD243@klaru-baycrest.on.ca>

I am indeed respecting which minc file format to use with the  
different tool versions. Still, I can't touch the screen location of  
the command interface apart from issuing commands Move it around the  
scree a little and it stops responding.

Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.



On 30-Mar-09, at 5:01 PM, Dale Einarson wrote:

> Hi all,
>   I haven't seen this bug yet but just in case...  Do note that there
> are both minc1 and minc2 version of Display in that tarball...
>
> minc1   mni/bin/display
> minc2   bic/bin/Display
>
>
> Cheers!
> dale
>
>
>
> On 30-Mar-09, at 4:23 PM, Jon Erik Ween wrote:
>
>> Alex
>>
>> I noticed some odd behavior with the 64 bit OSS X version of Display:
>> If I move Display's  "keyboard" function-controller window, it stops
>> responding to mouse clicks and keyboard strokes. As long as I lave it
>> alone, everything seems to work well. Is that odd?
>>
>> Jon
>>
>> Soli Deo Gloria
>>
>> Jon Erik Ween, MD, MS
>> Scientist, Kunin-Lunenfeld Applied Research Unit
>> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
>> Assistant Professor, Dept. of Medicine, Div. of Neurology
>>   University of Toronto Faculty of Medicine
>>
>> Kimel Family Building, 6th Floor, Room 644
>> Baycrest Centre
>> 3560 Bathurst Street
>> Toronto, Ontario M6A 2E1
>> Canada
>>
>> Phone: 416-785-2500 x3648
>> Fax: 416-785-2484
>> Email: jween at klaru-baycrest.on.ca
>>
>>
>> Confidential: This communication and any attachment(s) may contain
>> confidential or privileged information and is intended solely for the
>> address(es) or the entity representing the recipient(s). If you have
>> received this information in error, you are hereby advised to destroy
>> the document and any attachment(s), make no copies of same and inform
>> the sender immediately of the error. Any unauthorized use or
>> disclosure of this information is strictly prohibited.
>>
>>
>>
>> On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote:
>>
>>> On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote:
>>>>
>>>> Sadly I have had to do such ugly hacks as,
>>>> HDF
>>>> 	perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile
>>>> */
>>>> Makefile */*/Makefile */*/*/Makefile
>>>>
>>>> LIBTOOL
>>>> 	perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool
>>>> 	perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool
>>>
>>> The following configure line is what I used combined with the
>>> libtool hack
>>> I mentionned:
>>>
>>> ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch
>>> x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local
>>>
>>> Alex
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From jween at klaru-baycrest.on.ca  Wed Apr  1 10:55:03 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 1 Apr 2009 10:55:03 -0400
Subject: [MINC-users] Classify
In-Reply-To: <d747ed50904010445g49cc595bie0729947b06ec9fb@mail.gmail.com>
References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca>
	<A01ACA50-D5BB-43D6-ADA6-1AAF961F09A2@bic.mni.mcgill.ca>
	<3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca>
	<d747ed50904010445g49cc595bie0729947b06ec9fb@mail.gmail.com>
Message-ID: <5587D58B-3469-439C-AE69-C89E003305AB@klaru-baycrest.on.ca>

Dear list

Sorry about the pics. They can be found at:   http://www.klaru-baycrest.on.ca/index.php?section=969

I figured out that the mask option in classify specifies which voxels  
you WANT to classify (for us in the lesion world, we generally think  
of a mask for those things you DON'T want to include, ie: The stuff  
that will mess up the algorithm). So, the 3DT1 volume I want to  
classify (with lesion mask overlaid and in tal space) is given in  
Picture1. (You'll notice that the registration is not great, I get  
some of the lesion in the ventricle! Any hints as to how to optimize  
the registration with mritotal would be appreciated!).

Running  classify -clobber -user_mask_value 0 -tagfile tags.tag -mask  
14017_083005_combo_lbl2_tal.mnc 14017_083005_3dvol_tal.mnc  
14017_083005_3dvol_cls.mnc

gives me the result you see in Picture2. Lesioned whitematter is  
classified as grey matter and grey matter seems to be way over  
represented.

So, I figured out one way to go around this: Subtract the lesion mask  
from the volume BEORE running classify. The result of this is in  
Picture3. Here, we don't have the problem with lesion being classified  
as grey matter, but normal grey still seems over represented.

Questions:

1) How to optimize the classification so the grey matter is more  
representative of that seen visually on the 3DT1 (particularly the  
cortical ribbon)?

2) When setting tag points in your tag file to feed classify, setting  
paint label value in "Display" to "0" (for background) you don't seem  
to record anything. One work-around I did was to set the value to "4"  
and then edit the tagfile back to "0". Is this normal behavior or am I  
doing something wrong?

3) Saving the tagfile in "Display" gives you a bit different format  
(which classify doesn't like)  compared to the tagfile in ../mni/share/ 
classify/ntags_1000_bg.tag

Display "save labels .tag":  -82 -109 108 1 1 1
/mni/share/classify/ntags_1000_bg.tag:  -82 -109 108 "1"

Am I using the wrong function here?

4) Once I get a classified volume (and I have flair lesion and 3DT1  
lesion in separate masks) how do I calculate volumes? I can't seem to  
find the functions that do this, though suspect they are in minmath or  
minccalc somewhere.

Thanks for all the help!

Cheers


Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.



On 1-Apr-09, at 7:45 AM, Andrew Janke wrote:

> 2009/3/31 Jon Erik Ween <jween at klaru-baycrest.on.ca>:
>> May I trouble the list with another question? (Guess I'll do so
>> anyhow...)
>
> Hi Jon,
>
> No images... (the list wont accept them)  Can you put them up
> somewhere on the web instead?
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From acveilleux at mrs.mni.mcgill.ca  Wed Apr  1 11:26:12 2009
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Wed, 1 Apr 2009 11:26:12 -0400
Subject: [MINC-users] compiling dyld, 32, 64?
In-Reply-To: <376755ED-4DF7-43B6-B680-F1767B4DD243@klaru-baycrest.on.ca>;
	from jween@klaru-baycrest.on.ca on Wed, Apr 01, 2009 at
	10:29:53AM -0400
References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
	<20090306142234.N2730@mrs.mni.mcgill.ca>
	<1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca>
	<7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca>
	<376755ED-4DF7-43B6-B680-F1767B4DD243@klaru-baycrest.on.ca>
Message-ID: <20090401112612.F30839@mrs.mni.mcgill.ca>

Out of curiosity, what OS X version are you using and what hardware
(including video card)?

Alex

On Wed, Apr 01, 2009 at 10:29:53AM -0400, Jon Erik Ween wrote:
> From: Jon Erik Ween <jween at klaru-baycrest.on.ca>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Date: Wed, 1 Apr 2009 10:29:53 -0400
> X-Mailer: Apple Mail (2.930.3)
> Subject: Re: [MINC-users] compiling dyld, 32, 64?
> 
> I am indeed respecting which minc file format to use with the  
> different tool versions. Still, I can't touch the screen location of  
> the command interface apart from issuing commands Move it around the  
> scree a little and it stops responding.
> 
> Jon
> 
> Soli Deo Gloria
> 
> Jon Erik Ween, MD, MS
> Scientist, Kunin-Lunenfeld Applied Research Unit
> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
> Assistant Professor, Dept. of Medicine, Div. of Neurology
>      University of Toronto Faculty of Medicine
> 
> Kimel Family Building, 6th Floor, Room 644
> Baycrest Centre
> 3560 Bathurst Street
> Toronto, Ontario M6A 2E1
> Canada
> 
> Phone: 416-785-2500 x3648
> Fax: 416-785-2484
> Email: jween at klaru-baycrest.on.ca
> 
> 
> Confidential: This communication and any attachment(s) may contain  
> confidential or privileged information and is intended solely for the  
> address(es) or the entity representing the recipient(s). If you have  
> received this information in error, you are hereby advised to destroy  
> the document and any attachment(s), make no copies of same and inform  
> the sender immediately of the error. Any unauthorized use or  
> disclosure of this information is strictly prohibited.
> 
> 
> 
> On 30-Mar-09, at 5:01 PM, Dale Einarson wrote:
> 
> > Hi all,
> >   I haven't seen this bug yet but just in case...  Do note that there
> > are both minc1 and minc2 version of Display in that tarball...
> >
> > minc1   mni/bin/display
> > minc2   bic/bin/Display
> >
> >
> > Cheers!
> > dale
> >
> >
> >
> > On 30-Mar-09, at 4:23 PM, Jon Erik Ween wrote:
> >
> >> Alex
> >>
> >> I noticed some odd behavior with the 64 bit OSS X version of Display:
> >> If I move Display's  "keyboard" function-controller window, it stops
> >> responding to mouse clicks and keyboard strokes. As long as I lave it
> >> alone, everything seems to work well. Is that odd?
> >>
> >> Jon
> >>
> >> Soli Deo Gloria
> >>
> >> Jon Erik Ween, MD, MS
> >> Scientist, Kunin-Lunenfeld Applied Research Unit
> >> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
> >> Assistant Professor, Dept. of Medicine, Div. of Neurology
> >>   University of Toronto Faculty of Medicine
> >>
> >> Kimel Family Building, 6th Floor, Room 644
> >> Baycrest Centre
> >> 3560 Bathurst Street
> >> Toronto, Ontario M6A 2E1
> >> Canada
> >>
> >> Phone: 416-785-2500 x3648
> >> Fax: 416-785-2484
> >> Email: jween at klaru-baycrest.on.ca
> >>
> >>
> >> Confidential: This communication and any attachment(s) may contain
> >> confidential or privileged information and is intended solely for the
> >> address(es) or the entity representing the recipient(s). If you have
> >> received this information in error, you are hereby advised to destroy
> >> the document and any attachment(s), make no copies of same and inform
> >> the sender immediately of the error. Any unauthorized use or
> >> disclosure of this information is strictly prohibited.
> >>
> >>
> >>
> >> On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote:
> >>
> >>> On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote:
> >>>>
> >>>> Sadly I have had to do such ugly hacks as,
> >>>> HDF
> >>>> 	perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g' Makefile
> >>>> */
> >>>> Makefile */*/Makefile */*/*/Makefile
> >>>>
> >>>> LIBTOOL
> >>>> 	perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool
> >>>> 	perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool
> >>>
> >>> The following configure line is what I used combined with the
> >>> libtool hack
> >>> I mentionned:
> >>>
> >>> ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch
> >>> x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local
> >>>
> >>> Alex
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From jween at klaru-baycrest.on.ca  Wed Apr  1 12:13:21 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 1 Apr 2009 12:13:21 -0400
Subject: [MINC-users] compiling dyld, 32, 64?
In-Reply-To: <20090401112612.F30839@mrs.mni.mcgill.ca>
References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
	<20090306142234.N2730@mrs.mni.mcgill.ca>
	<1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca>
	<7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca>
	<376755ED-4DF7-43B6-B680-F1767B4DD243@klaru-baycrest.on.ca>
	<20090401112612.F30839@mrs.mni.mcgill.ca>
Message-ID: <F81E8800-2EC9-4630-AE2B-CB8EC607C86B@klaru-baycrest.on.ca>

Alex


OS X v10.5.6

Model Name:	Mac Pro
   Model Identifier:	MacPro3,1
   Processor Name:	Quad-Core Intel Xeon
   Processor Speed:	3 GHz
   Number Of Processors:	2
   Total Number Of Cores:	8
   L2 Cache (per processor):	12 MB
   Memory:	10 GB
   Bus Speed:	1.6 GHz
   Boot ROM Version:	MP31.006C.B05
   SMC Version:	1.25f4
   Serial Number:	G890409VXYL

NVIDIA GeForce 8800 GT:

   Chipset Model:	NVIDIA GeForce 8800 GT
   Type:	Display
   Bus:	PCIe
   Slot:	Slot-1
   PCIe Lane Width:	x16
   VRAM (Total):	512 MB
   Vendor:	NVIDIA (0x10de)
   Device ID:	0x0602
   Revision ID:	0x00a2
   ROM Revision:	3233
   Displays:
Cinema:
   Resolution:	1680 x 1050
   Depth:	32-bit Color
   Core Image:	Hardware Accelerated
   Main Display:	Yes
   Mirror:	Off
   Online:	Yes
   Quartz Extreme:	Supported
   Rotation:	Supported
Cinema:
   Resolution:	1680 x 1050
   Depth:	32-bit Color
   Core Image:	Hardware Accelerated
   Mirror:	Off
   Online:	Yes
   Quartz Extreme:	Supported
   Rotation:	Supported



Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.



On 1-Apr-09, at 11:26 AM, Alexandre CARMEL-VEILLEUX wrote:

> Out of curiosity, what OS X version are you using and what hardware
> (including video card)?
>
> Alex
>
> On Wed, Apr 01, 2009 at 10:29:53AM -0400, Jon Erik Ween wrote:
>> From: Jon Erik Ween <jween at klaru-baycrest.on.ca>
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Date: Wed, 1 Apr 2009 10:29:53 -0400
>> X-Mailer: Apple Mail (2.930.3)
>> Subject: Re: [MINC-users] compiling dyld, 32, 64?
>>
>> I am indeed respecting which minc file format to use with the
>> different tool versions. Still, I can't touch the screen location of
>> the command interface apart from issuing commands Move it around the
>> scree a little and it stops responding.
>>
>> Jon
>>
>> Soli Deo Gloria
>>
>> Jon Erik Ween, MD, MS
>> Scientist, Kunin-Lunenfeld Applied Research Unit
>> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
>> Assistant Professor, Dept. of Medicine, Div. of Neurology
>>     University of Toronto Faculty of Medicine
>>
>> Kimel Family Building, 6th Floor, Room 644
>> Baycrest Centre
>> 3560 Bathurst Street
>> Toronto, Ontario M6A 2E1
>> Canada
>>
>> Phone: 416-785-2500 x3648
>> Fax: 416-785-2484
>> Email: jween at klaru-baycrest.on.ca
>>
>>
>> Confidential: This communication and any attachment(s) may contain
>> confidential or privileged information and is intended solely for the
>> address(es) or the entity representing the recipient(s). If you have
>> received this information in error, you are hereby advised to destroy
>> the document and any attachment(s), make no copies of same and inform
>> the sender immediately of the error. Any unauthorized use or
>> disclosure of this information is strictly prohibited.
>>
>>
>>
>> On 30-Mar-09, at 5:01 PM, Dale Einarson wrote:
>>
>>> Hi all,
>>>  I haven't seen this bug yet but just in case...  Do note that there
>>> are both minc1 and minc2 version of Display in that tarball...
>>>
>>> minc1   mni/bin/display
>>> minc2   bic/bin/Display
>>>
>>>
>>> Cheers!
>>> dale
>>>
>>>
>>>
>>> On 30-Mar-09, at 4:23 PM, Jon Erik Ween wrote:
>>>
>>>> Alex
>>>>
>>>> I noticed some odd behavior with the 64 bit OSS X version of  
>>>> Display:
>>>> If I move Display's  "keyboard" function-controller window, it  
>>>> stops
>>>> responding to mouse clicks and keyboard strokes. As long as I  
>>>> lave it
>>>> alone, everything seems to work well. Is that odd?
>>>>
>>>> Jon
>>>>
>>>> Soli Deo Gloria
>>>>
>>>> Jon Erik Ween, MD, MS
>>>> Scientist, Kunin-Lunenfeld Applied Research Unit
>>>> Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
>>>> Assistant Professor, Dept. of Medicine, Div. of Neurology
>>>>  University of Toronto Faculty of Medicine
>>>>
>>>> Kimel Family Building, 6th Floor, Room 644
>>>> Baycrest Centre
>>>> 3560 Bathurst Street
>>>> Toronto, Ontario M6A 2E1
>>>> Canada
>>>>
>>>> Phone: 416-785-2500 x3648
>>>> Fax: 416-785-2484
>>>> Email: jween at klaru-baycrest.on.ca
>>>>
>>>>
>>>> Confidential: This communication and any attachment(s) may contain
>>>> confidential or privileged information and is intended solely for  
>>>> the
>>>> address(es) or the entity representing the recipient(s). If you  
>>>> have
>>>> received this information in error, you are hereby advised to  
>>>> destroy
>>>> the document and any attachment(s), make no copies of same and  
>>>> inform
>>>> the sender immediately of the error. Any unauthorized use or
>>>> disclosure of this information is strictly prohibited.
>>>>
>>>>
>>>>
>>>> On 6-Mar-09, at 2:22 PM, Alexandre CARMEL-VEILLEUX wrote:
>>>>
>>>>> On Fri, Mar 06, 2009 at 01:46:00PM -0500, Dale Einarson wrote:
>>>>>>
>>>>>> Sadly I have had to do such ugly hacks as,
>>>>>> HDF
>>>>>> 	perl -pi -e 's/-O2 -g x86_64 -arch/-g -O2 -arch x86_64/g'  
>>>>>> Makefile
>>>>>> */
>>>>>> Makefile */*/Makefile */*/*/Makefile
>>>>>>
>>>>>> LIBTOOL
>>>>>> 	perl -pi -e 's/-fno-builtin/-arch x86_64 -fno-builtin/g' libtool
>>>>>> 	perl -pi -e 's/-dynamiclib/-dynamiclib -arch x86_64/g' libtool
>>>>>
>>>>> The following configure line is what I used combined with the
>>>>> libtool hack
>>>>> I mentionned:
>>>>>
>>>>> ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch
>>>>> x86_64 -m64" --with-szlib=yes --with-zlib=yes --prefix=/usr/local
>>>>>
>>>>> Alex
>>>>> _______________________________________________
>>>>> MINC-users at bic.mni.mcgill.ca
>>>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>>
>>>>
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From acveilleux at mrs.mni.mcgill.ca  Wed Apr  1 12:39:50 2009
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Wed, 1 Apr 2009 12:39:50 -0400
Subject: [MINC-users] compiling dyld, 32, 64?
In-Reply-To: <F81E8800-2EC9-4630-AE2B-CB8EC607C86B@klaru-baycrest.on.ca>;
	from jween@klaru-baycrest.on.ca on Wed, Apr 01, 2009 at
	12:13:21PM -0400
References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
	<20090306142234.N2730@mrs.mni.mcgill.ca>
	<1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca>
	<7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca>
	<376755ED-4DF7-43B6-B680-F1767B4DD243@klaru-baycrest.on.ca>
	<20090401112612.F30839@mrs.mni.mcgill.ca>
	<F81E8800-2EC9-4630-AE2B-CB8EC607C86B@klaru-baycrest.on.ca>
Message-ID: <20090401123950.J30839@mrs.mni.mcgill.ca>

Interestingly, I've only every tried this software on macs with ATI adapters,
I don't know if that has any effects.

If you create a new normal user with a completely stock profile (and .cshrc,
.bashrc, .profile, etc.) do you still have the problem? Use no extra library,
fink or anything else (none should be required if everything is installed
in /usr/local).

Alex

On Wed, Apr 01, 2009 at 12:13:21PM -0400, Jon Erik Ween wrote:
> 
[snip]
> NVIDIA GeForce 8800 GT:
[snip]

Alex

From jween at klaru-baycrest.on.ca  Wed Apr  1 14:17:10 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 1 Apr 2009 14:17:10 -0400
Subject: [MINC-users] compiling dyld, 32, 64?
In-Reply-To: <20090401123950.J30839@mrs.mni.mcgill.ca>
References: <04CAF529-3FC6-4EA8-A5C0-7EF81E5521C6@bic.mni.mcgill.ca>
	<20090306142234.N2730@mrs.mni.mcgill.ca>
	<1AE3E552-EEFF-4351-BA67-81AF54C8A983@klaru-baycrest.on.ca>
	<7F295845-9A64-4539-9612-EAA13D1844BF@bic.mni.mcgill.ca>
	<376755ED-4DF7-43B6-B680-F1767B4DD243@klaru-baycrest.on.ca>
	<20090401112612.F30839@mrs.mni.mcgill.ca>
	<F81E8800-2EC9-4630-AE2B-CB8EC607C86B@klaru-baycrest.on.ca>
	<20090401123950.J30839@mrs.mni.mcgill.ca>
Message-ID: <C600C1EB-F118-4AC3-9686-14FEE8F3A55E@klaru-baycrest.on.ca>

Seems to work better with the "clean" user! I guess I'm pointing to  
some odd library or something. I thought I had gotten rid of the fink  
dependencies, but maybe not. I'll check it out.

Thanks

Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.



On 1-Apr-09, at 12:39 PM, Alexandre CARMEL-VEILLEUX wrote:

> Interestingly, I've only every tried this software on macs with ATI  
> adapters,
> I don't know if that has any effects.
>
> If you create a new normal user with a completely stock profile  
> (and .cshrc,
> .bashrc, .profile, etc.) do you still have the problem? Use no extra  
> library,
> fink or anything else (none should be required if everything is  
> installed
> in /usr/local).
>
> Alex
>
> On Wed, Apr 01, 2009 at 12:13:21PM -0400, Jon Erik Ween wrote:
>>
> [snip]
>> NVIDIA GeForce 8800 GT:
> [snip]
>
> Alex
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From m.bahri at ulg.ac.be  Sat Apr  4 09:27:48 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Sat, 04 Apr 2009 15:27:48 +0200
Subject: [MINC-users] Minc-2 installation problems
Message-ID: <49D76054.3060909@ulg.ac.be>

Dear all,

I have a problem with minc-2.0.17 installation (make command fails). Any 
one have an idea how I can solve that?
I use linux (Fedora 9, 64-bit).

libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
-I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
-I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
-MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
-o libsrc/hdf_convenience.o
libsrc/hdf_convenience.c: In function ?hdf_id_add?:
libsrc/hdf_convenience.c:83: erreur: too few arguments to function 
?H5Gopen2?
libsrc/hdf_convenience.c: In function ?hdf_var_add?:
libsrc/hdf_convenience.c:185: erreur: too few arguments to function 
?H5Dopen2?
libsrc/hdf_convenience.c: In function ?hdf_put_dimorder?:
libsrc/hdf_convenience.c:621: erreur: too few arguments to function 
?H5Acreate2?
libsrc/hdf_convenience.c: In function ?hdf_set_length?:
libsrc/hdf_convenience.c:928: erreur: too few arguments to function 
?H5Acreate2?
libsrc/hdf_convenience.c: In function ?hdf_attput?:
libsrc/hdf_convenience.c:1106: erreur: too few arguments to function 
?H5Dcreate2?
libsrc/hdf_convenience.c:1110: attention : transtypage vers un pointeur 
depuis un entier de taille diff?rente
libsrc/hdf_convenience.c:1110: erreur: incompatible type for argument 2 
of ?H5Aiterate2?
libsrc/hdf_convenience.c:1110: erreur: incompatible type for argument 3 
of ?H5Aiterate2?
libsrc/hdf_convenience.c:1110: erreur: too few arguments to function 
?H5Aiterate2?
libsrc/hdf_convenience.c:1189: erreur: too few arguments to function 
?H5Acreate2?
libsrc/hdf_convenience.c: In function ?hdf_vardef?:
libsrc/hdf_convenience.c:1384: erreur: too few arguments to function 
?H5Dcreate2?
libsrc/hdf_convenience.c: In function ?hdf_copy_attr?:
libsrc/hdf_convenience.c:2043: attention : transtypage d'un pointeur 
vers un entier de taille diff?rente
libsrc/hdf_convenience.c:2060: erreur: too few arguments to function 
?H5Acreate2?
libsrc/hdf_convenience.c: In function ?hdf_open_dsets?:
libsrc/hdf_convenience.c:2122: erreur: too few arguments to function 
?H5Gopen2?
libsrc/hdf_convenience.c:2133: erreur: too few arguments to function 
?H5Dopen2?
libsrc/hdf_convenience.c: In function ?hdf_open?:
libsrc/hdf_convenience.c:2209: erreur: too few arguments to function 
?H5Dopen2?
libsrc/hdf_convenience.c:2240: erreur: too few arguments to function 
?H5Dopen2?
libsrc/hdf_convenience.c:2248: erreur: too few arguments to function 
?H5Dopen2?
libsrc/hdf_convenience.c:2259: erreur: too few arguments to function 
?H5Gopen2?
libsrc/hdf_convenience.c:2265: erreur: too few arguments to function 
?H5Gopen2?
libsrc/hdf_convenience.c: In function ?hdf_create?:
libsrc/hdf_convenience.c:2299: erreur: too few arguments to function 
?H5Gcreate2?
libsrc/hdf_convenience.c:2303: erreur: too few arguments to function 
?H5Gcreate2?
libsrc/hdf_convenience.c:2308: erreur: too few arguments to function 
?H5Gcreate2?
libsrc/hdf_convenience.c:2313: erreur: too few arguments to function 
?H5Gcreate2?
libsrc/hdf_convenience.c:2318: erreur: too few arguments to function 
?H5Gcreate2?
make[2]: *** [libsrc/hdf_convenience.lo] Erreur 1
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.17 ?
make[1]: *** [all-recursive] Erreur 1
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.17 ?
make: *** [all] Erreur 2


Thanks a lot in advance,
Best regards,

Mohamed

From claude at bic.mni.mcgill.ca  Sat Apr  4 10:20:28 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Sat, 4 Apr 2009 10:20:28 -0400
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D76054.3060909@ulg.ac.be>
Message-ID: <200904041420.n34EKS6S006300@grumio.bic.mni.mcgill.ca>

Hi,

> I have a problem with minc-2.0.17 installation (make command fails). Any 
> one have an idea how I can solve that?
> I use linux (Fedora 9, 64-bit).
>
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
> -o libsrc/hdf_convenience.o
> libsrc/hdf_convenience.c: In function ?hdf_id_add?:
> libsrc/hdf_convenience.c:83: erreur: too few arguments to function 
> ?H5Gopen2?
> libsrc/hdf_convenience.c: In function ?hdf_var_add?:
> libsrc/hdf_convenience.c:185: erreur: too few arguments to function 

I haven't seen this problem, but here is an idea.

Which version of HDF5 have you installed? minc2 has been tested
with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would suggest
to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I recall,
5-1.8.X is not 100% compatible with previous versions.

The problem may be different too, but making sure you are using
a compatible version of HDF5 is the first step.

Yours,

Claude
 

From m.bahri at ulg.ac.be  Sat Apr  4 11:12:10 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Sat, 04 Apr 2009 17:12:10 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <200904041420.n34EKS6S006300@grumio.bic.mni.mcgill.ca>
References: <200904041420.n34EKS6S006300@grumio.bic.mni.mcgill.ca>
Message-ID: <49D778CA.1090805@ulg.ac.be>

Hi Claude,

Thank you for your answer. I tried to use HDF5-1.6.6 instead of 
hdf5-1.8.2 but now I have errors with HDF5.
I use the following command lines:

1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/ 
--with-zlib=/usr/local/ --enable-fortran --enable-cxx
2) make

===============================================

g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE 
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
-I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o .libs/H5PropList.lo
H5PropList.cpp: In member function 'std::string 
H5::PropList::getClassName() const':
H5PropList.cpp:428: error: 'free' was not declared in this scope
make[3]: *** [H5PropList.lo] Erreur 1
make[3]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++/src ?
make[2]: *** [lib] Erreur 1
make[2]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++ ?
make[1]: *** [lib] Erreur 1
make[1]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6 ?
make: *** [all] Erreur 2
=======================================================

Thanks a lot,
Mohamed

Claude LEPAGE a ?crit :
> Hi,
>
>   
>> I have a problem with minc-2.0.17 installation (make command fails). Any 
>> one have an idea how I can solve that?
>> I use linux (Fedora 9, 64-bit).
>>
>> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
>> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
>> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
>> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
>> -o libsrc/hdf_convenience.o
>> libsrc/hdf_convenience.c: In function ?hdf_id_add?:
>> libsrc/hdf_convenience.c:83: erreur: too few arguments to function 
>> ?H5Gopen2?
>> libsrc/hdf_convenience.c: In function ?hdf_var_add?:
>> libsrc/hdf_convenience.c:185: erreur: too few arguments to function 
>>     
>
> I haven't seen this problem, but here is an idea.
>
> Which version of HDF5 have you installed? minc2 has been tested
> with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would suggest
> to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I recall,
> 5-1.8.X is not 100% compatible with previous versions.
>
> The problem may be different too, but making sure you are using
> a compatible version of HDF5 is the first step.
>
> Yours,
>
> Claude
>  
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From claude at bic.mni.mcgill.ca  Sat Apr  4 13:22:43 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Sat, 4 Apr 2009 13:22:43 -0400
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D778CA.1090805@ulg.ac.be>
Message-ID: <200904041722.n34HMhAn012610@grumio.bic.mni.mcgill.ca>

Hi,

> Thank you for your answer. I tried to use HDF5-1.6.6 instead of 
> hdf5-1.8.2 but now I have errors with HDF5.
> I use the following command lines:
>
> 1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/ 
> --with-zlib=/usr/local/ --enable-fortran --enable-cxx
> 2) make

Here is how I compile HDF5-1.6.6 in 64 bits Linux:

./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} -fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
make 
make install

--disable-shared is optional
no need to fuss about fortran (not needed by minc2)

By the way, which compiler are you using? It looks like your C++
compiler does not like the code. Strange...

gcc --version

minc2 may compile with gcc 4.2+, but not all MNI tools do (yet).

Claude


> ===============================================
>
> g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE 
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
> -I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o .libs/H5PropList.lo
> H5PropList.cpp: In member function 'std::string 
> H5::PropList::getClassName() const':
> H5PropList.cpp:428: error: 'free' was not declared in this scope
> make[3]: *** [H5PropList.lo] Erreur 1
> make[3]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++/src ?
> make[2]: *** [lib] Erreur 1
> make[2]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++ ?
> make[1]: *** [lib] Erreur 1
> make[1]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6 ?
> make: *** [all] Erreur 2
> =======================================================
>
> Thanks a lot,
> Mohamed
>
> Claude LEPAGE a ?crit :
> > Hi,
> >
> >   
> >> I have a problem with minc-2.0.17 installation (make command fails). Any 
> >> one have an idea how I can solve that?
> >> I use linux (Fedora 9, 64-bit).
> >>
> >> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
> >> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> >> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
> >> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
> >> -o libsrc/hdf_convenience.o
> >> libsrc/hdf_convenience.c: In function ?hdf_id_add?:
> >> libsrc/hdf_convenience.c:83: erreur: too few arguments to function 
> >> ?H5Gopen2?
> >> libsrc/hdf_convenience.c: In function ?hdf_var_add?:
> >> libsrc/hdf_convenience.c:185: erreur: too few arguments to function 
> >>     
> >
> > I haven't seen this problem, but here is an idea.
> >
> > Which version of HDF5 have you installed? minc2 has been tested
> > with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would suggest
> > to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I recall,
> > 5-1.8.X is not 100% compatible with previous versions.
> >
> > The problem may be different too, but making sure you are using
> > a compatible version of HDF5 is the first step.
> >
> > Yours,
> >
> > Claude
> >  
> >   
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >   
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From m.bahri at ulg.ac.be  Sun Apr  5 05:55:42 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Sun, 05 Apr 2009 11:55:42 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <200904041722.n34HMhAn012610@grumio.bic.mni.mcgill.ca>
References: <200904041722.n34HMhAn012610@grumio.bic.mni.mcgill.ca>
Message-ID: <49D8801E.9040807@ulg.ac.be>

Hi Claude,

I tried with your command line and it gave me the following error:

-----------------------------------------------------------------------------------------------------------
[root at localhost hdf5-1.6.6]# ./configure --disable-shared 
--prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} 
-fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for sizeof hsize_t and hssize_t... large
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-4.3.0
checking for config ./config/site-specific/host-localhost.localdomain... no
checking for config ./config/site-specific/host-localdomain... no
checking for gcc... gcc
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.
------------------------------------------------------------------------------------------------------
As compiler I use gcc 4.3 (gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8).
I also attached the config.log if this could give information about my 
problem.

Thank you very much for your help

Best regards
Mohamed





Claude LEPAGE a ?crit :
> Hi,
>
>   
>> Thank you for your answer. I tried to use HDF5-1.6.6 instead of 
>> hdf5-1.8.2 but now I have errors with HDF5.
>> I use the following command lines:
>>
>> 1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/ 
>> --with-zlib=/usr/local/ --enable-fortran --enable-cxx
>> 2) make
>>     
>
> Here is how I compile HDF5-1.6.6 in 64 bits Linux:
>
> ./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} -fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
> make 
> make install
>
> --disable-shared is optional
> no need to fuss about fortran (not needed by minc2)
>
> By the way, which compiler are you using? It looks like your C++
> compiler does not like the code. Strange...
>
> gcc --version
>
> minc2 may compile with gcc 4.2+, but not all MNI tools do (yet).
>
> Claude
>
>
>   
>> ===============================================
>>
>> g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE 
>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
>> -I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o .libs/H5PropList.lo
>> H5PropList.cpp: In member function 'std::string 
>> H5::PropList::getClassName() const':
>> H5PropList.cpp:428: error: 'free' was not declared in this scope
>> make[3]: *** [H5PropList.lo] Erreur 1
>> make[3]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++/src ?
>> make[2]: *** [lib] Erreur 1
>> make[2]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++ ?
>> make[1]: *** [lib] Erreur 1
>> make[1]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6 ?
>> make: *** [all] Erreur 2
>> =======================================================
>>
>> Thanks a lot,
>> Mohamed
>>
>> Claude LEPAGE a ?crit :
>>     
>>> Hi,
>>>
>>>   
>>>       
>>>> I have a problem with minc-2.0.17 installation (make command fails). Any 
>>>> one have an idea how I can solve that?
>>>> I use linux (Fedora 9, 64-bit).
>>>>
>>>> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
>>>> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
>>>> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
>>>> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
>>>> -o libsrc/hdf_convenience.o
>>>> libsrc/hdf_convenience.c: In function ?hdf_id_add?:
>>>> libsrc/hdf_convenience.c:83: erreur: too few arguments to function 
>>>> ?H5Gopen2?
>>>> libsrc/hdf_convenience.c: In function ?hdf_var_add?:
>>>> libsrc/hdf_convenience.c:185: erreur: too few arguments to function 
>>>>     
>>>>         
>>> I haven't seen this problem, but here is an idea.
>>>
>>> Which version of HDF5 have you installed? minc2 has been tested
>>> with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would suggest
>>> to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I recall,
>>> 5-1.8.X is not 100% compatible with previous versions.
>>>
>>> The problem may be different too, but making sure you are using
>>> a compatible version of HDF5 is the first step.
>>>
>>> Yours,
>>>
>>> Claude
>>>  
>>>   
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>   
>>>       
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>     
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>     

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: config.log
Url: http://www2.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20090405/43f70996/attachment-0001.txt 

From se at hst.aau.dk  Sun Apr  5 07:27:16 2009
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Sun, 5 Apr 2009 13:27:16 +0200 (CEST)
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <2040299049.400481238930658288.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <1269874905.400501238930836459.JavaMail.root@zimbra-store01.hst.aau.dk>

Hi Mohamed,
Try using double quotation marks instead of single:

./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local CFLAGS="${CFLAGS} -fpic" CPPFLAGS="${CPPFLAGS} -fpic" CXXFLAGS="${CXXFLAGS} -fpic"

As far as I remember bash does not expand into single quatation marks. If it does not help, try exporting the flags before configuring:

export CFLAGS="${CFLAGS} -fpic"
export CPPFLAGS="${CPPFLAGS} -fpic"
export CXXFLAGS="${CXXFLAGS} -fpic"
./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local

Simon

----- "mohamed Ali Bahri" <m.bahri at ulg.ac.be> wrote:

> Hi Claude,
> 
> I tried with your command line and it gave me the following error:
> 
> -----------------------------------------------------------------------------------------------------------
> [root at localhost hdf5-1.6.6]# ./configure --disable-shared 
> --prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} 
> -fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking shell variables initial values... done
> checking if basename works... yes
> checking if xargs works... yes
> checking for cached host... none
> checking for sizeof hsize_t and hssize_t... large
> checking for config x86_64-unknown-linux-gnu... no
> checking for config x86_64-unknown-linux-gnu... no
> checking for config unknown-linux-gnu... no
> checking for config unknown-linux-gnu... no
> checking for config x86_64-linux-gnu... no
> checking for config x86_64-linux-gnu... no
> checking for config x86_64-unknown... no
> checking for config linux-gnu... found
> compiler 'gcc' is GNU gcc-4.3.0
> checking for config
> ./config/site-specific/host-localhost.localdomain... no
> checking for config ./config/site-specific/host-localdomain... no
> checking for gcc... gcc
> checking for C compiler default output file name...
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
> ------------------------------------------------------------------------------------------------------
> As compiler I use gcc 4.3 (gcc (GCC) 4.3.0 20080428 (Red Hat
> 4.3.0-8).
> I also attached the config.log if this could give information about my
> 
> problem.
> 
> Thank you very much for your help
> 
> Best regards
> Mohamed
> 
> 
> 
> 
> 
> Claude LEPAGE a ?crit :
> > Hi,
> >
> >   
> >> Thank you for your answer. I tried to use HDF5-1.6.6 instead of 
> >> hdf5-1.8.2 but now I have errors with HDF5.
> >> I use the following command lines:
> >>
> >> 1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/ 
> >> --with-zlib=/usr/local/ --enable-fortran --enable-cxx
> >> 2) make
> >>     
> >
> > Here is how I compile HDF5-1.6.6 in 64 bits Linux:
> >
> > ./configure --disable-shared --prefix=/usr/local
> --with-build-path=/usr/local CFLAGS='${CFLAGS} -fpic'
> CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
> > make 
> > make install
> >
> > --disable-shared is optional
> > no need to fuss about fortran (not needed by minc2)
> >
> > By the way, which compiler are you using? It looks like your C++
> > compiler does not like the code. Strange...
> >
> > gcc --version
> >
> > minc2 may compile with gcc 4.2+, but not all MNI tools do (yet).
> >
> > Claude
> >
> >
> >   
> >> ===============================================
> >>
> >> g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE 
> >> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
> >> -I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o
> .libs/H5PropList.lo
> >> H5PropList.cpp: In member function 'std::string 
> >> H5::PropList::getClassName() const':
> >> H5PropList.cpp:428: error: 'free' was not declared in this scope
> >> make[3]: *** [H5PropList.lo] Erreur 1
> >> make[3]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++/src ?
> >> make[2]: *** [lib] Erreur 1
> >> make[2]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++ ?
> >> make[1]: *** [lib] Erreur 1
> >> make[1]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6 ?
> >> make: *** [all] Erreur 2
> >> =======================================================
> >>
> >> Thanks a lot,
> >> Mohamed
> >>
> >> Claude LEPAGE a ?crit :
> >>     
> >>> Hi,
> >>>
> >>>   
> >>>       
> >>>> I have a problem with minc-2.0.17 installation (make command
> fails). Any 
> >>>> one have an idea how I can solve that?
> >>>> I use linux (Fedora 9, 64-bit).
> >>>>
> >>>> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
> >>>> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
> >>>> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT
> libsrc/hdf_convenience.lo 
> >>>> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c
> libsrc/hdf_convenience.c 
> >>>> -o libsrc/hdf_convenience.o
> >>>> libsrc/hdf_convenience.c: In function ?hdf_id_add?:
> >>>> libsrc/hdf_convenience.c:83: erreur: too few arguments to
> function 
> >>>> ?H5Gopen2?
> >>>> libsrc/hdf_convenience.c: In function ?hdf_var_add?:
> >>>> libsrc/hdf_convenience.c:185: erreur: too few arguments to
> function 
> >>>>     
> >>>>         
> >>> I haven't seen this problem, but here is an idea.
> >>>
> >>> Which version of HDF5 have you installed? minc2 has been tested
> >>> with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would
> suggest
> >>> to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I
> recall,
> >>> 5-1.8.X is not 100% compatible with previous versions.
> >>>
> >>> The problem may be different too, but making sure you are using
> >>> a compatible version of HDF5 is the first step.
> >>>
> >>> Yours,
> >>>
> >>> Claude
> >>>  
> >>>   
> >>>
> ------------------------------------------------------------------------
> >>>
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>   
> >>>       
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >>     
> >>
> ------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>     
> 
> 
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
> 
> It was created by HDF5 configure 1.6.6, which was
> generated by GNU Autoconf 2.61.  Invocation command line was
> 
>   $ ./configure --disable-shared --prefix=/usr/local
> --with-build-path=/usr/local CFLAGS=${CFLAGS} -fpic
> CPPFLAGS=${CPPFLAGS} -fpic CXXFLAGS=${CXXFLAGS} -fpic
> 
> ## --------- ##
> ## Platform. ##
> ## --------- ##
> 
> hostname = localhost.localdomain
> uname -m = x86_64
> uname -r = 2.6.27.21-78.2.41.fc9.x86_64
> uname -s = Linux
> uname -v = #1 SMP Mon Mar 23 23:22:15 EDT 2009
> 
> /usr/bin/uname -p = unknown
> /bin/uname -X     = unknown
> 
> /bin/arch              = x86_64
> /usr/bin/arch -k       = unknown
> /usr/convex/getsysinfo = unknown
> /usr/bin/hostinfo      = unknown
> /bin/machine           = unknown
> /usr/bin/oslevel       = unknown
> /bin/universe          = unknown
> 
> PATH: /usr/kerberos/sbin
> PATH: /usr/
> PATH: /home/Mohamed/Bureau/Sources_Codes/camino/bin
> PATH: /usr/java/latest/bin
> PATH: /usr/
> PATH: /home/Mohamed/Bureau/Sources_Codes/camino/bin
> PATH: /usr/java/latest/bin
> PATH: /usr/lib64/qt-3.3/bin
> PATH: /usr/kerberos/bin
> PATH: /usr/lib64/ccache
> PATH: /usr/local/bin
> PATH: /usr/bin
> PATH: /bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin_lnx
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/pvelab-20080317/Canterbury
> PATH: /usr/local/caret/bin
> PATH: /usr/local/bin
> PATH: /home/Mohamed/bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin_lnx
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/pvelab-20081112/Canterbury
> PATH: /usr/local/caret/bin
> 
> 
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
> 
> configure:2034: checking build system type
> configure:2052: result: x86_64-unknown-linux-gnu
> configure:2074: checking host system type
> configure:2089: result: x86_64-unknown-linux-gnu
> configure:2119: checking shell variables initial values
> BASH=/bin/sh
> BASH_ARGC=([0]="6")
> BASH_ARGV=([0]="CXXFLAGS=\${CXXFLAGS} -fpic"
> [1]="CPPFLAGS=\${CPPFLAGS} -fpic" [2]="CFLAGS=\${CFLAGS} -fpic"
> [3]="--with-build-path=/usr/local" [4]="--prefix=/usr/local"
> [5]="--disable-shared")
> BASH_LINENO=([0]="0")
> BASH_SOURCE=([0]="./configure")
> BASH_VERSINFO=([0]="3" [1]="2" [2]="33" [3]="1" [4]="release"
> [5]="x86_64-redhat-linux-gnu")
> BASH_VERSION='3.2.33(1)-release'
> CCACHE_DIR=/var/cache/ccache
> CCACHE_UMASK=002
> CFLAGS='${CFLAGS} -fpic'
> COLORTERM=gnome-terminal
> CPPFLAGS='${CPPFLAGS} -fpic'
> CVS_RSH=ssh
> CXXFLAGS='${CXXFLAGS} -fpic'
> DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-qhDa2Oiw19,guid=4739190599a2a029607aa83c49d775c0
> DEFAULT_LIBS=
> DESKTOP_SESSION=kde
> DESKTOP_STARTUP_ID=
> DIRSTACK=()
> DISPLAY=:0.0
> DUALCASE=1
> ECHO=echo
> ECHO_C=
> ECHO_N=-n
> ECHO_T=
> EUID=0
> GDMSESSION=kde
> GDM_LANG=fr_FR.UTF-8
> GNOME_KEYRING_PID=2988
> GNOME_KEYRING_SOCKET=/tmp/keyring-CdaPEr/socket
> GPG_AGENT_INFO=/tmp/gpg-aiPs2p/S.gpg-agent:3059:1
> GROUPS=()
> GS_LIB=
> GTK2_RC_FILES=/etc/gtk-2.0/gtkrc:/home/Mohamed/.gtkrc-2.0::/home/Mohamed/.kde/share/config/gtkrc-2.0
> GTK_RC_FILES=/etc/gtk/gtkrc:/home/Mohamed/.gtkrc::/home/Mohamed/.kde/share/config/gtkrc
> G_BROKEN_FILENAMES=1
> HISTSIZE=1000
> HOME=/root
> HOSTNAME=localhost.localdomain
> HOSTTYPE=x86_64
> IFS=' 	
> '
> INPUTRC=/etc/inputrc
> KDEDIRS=/usr
> KDE_FULL_SESSION=true
> KDE_IS_PRELINKED=1
> KDE_MULTIHEAD=false
> KDE_SESSION_UID=500
> KDE_SESSION_VERSION=4
> LANG=C
> LANGUAGE=C
> LC_ADDRESS=C
> LC_ALL=C
> LC_COLLATE=C
> LC_CTYPE=C
> LC_IDENTIFICATION=C
> LC_MEASUREMENT=C
> LC_MESSAGES=C
> LC_MONETARY=C
> LC_NAME=C
> LC_NUMERIC=C
> LC_PAPER=C
> LC_TELEPHONE=C
> LC_TIME=C
> LESSOPEN='|/usr/bin/lesspipe.sh %s'
> LIBOBJS=
> LINENO=2119
> LOGNAME=Mohamed
> LS_COLORS='no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:do=00;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.svgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.lzma=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.dz=00;31:*.gz=00;31:*.bz2=00;31:*.tbz2=00;31:*.bz=00;31:*.tz=00;31:*.deb=00;31:*.rpm=00;31:*.jar=00;31:*.rar=00;31:*.ace=00;31:*.zoo=00;31:*.cpio=00;31:*.7z=00;31:*.rz=00;31:*.jpg=00;35:*.jpeg=00;35:*.gif=00;35:*.bmp=00;35:*.pbm=00;35:*.pgm=00;35:*.ppm=00;35:*.tga=00;35:*.xbm=00;35:*.xpm=00;35:*.tif=00;35:*.tiff=00;35:*.png=00;35:*.mng=00;35:*.pcx=00;35:*.mov=00;35:*.mpg=00;35:*.mpeg=00;35:*.m2v=00;35:*.mkv=00;35:*.ogm=00;35:*.mp4=00;35:*.m4v=00;35:*.mp4v=00;35:*.vob=00;35:*.qt=00;35:*.nuv=00;35:*.wmv=00;35:*.asf=00;35:*.rm=00;35:*.rmvb=00;35:*.flc=00;35:*.avi=00;35:*.fli=00;35:*.gl=00;35:*.dl=00;35:*.xcf=00;35:*.xwd=00;35:*.yuv=00;35:*.svg=00;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:'
> MACHTYPE=x86_64-redhat-linux-gnu
> MAKEFLAGS=
> MANPATH=/home/Mohamed/Bureau/Sources_Codes/camino/man:/home/Mohamed/Bureau/Sources_Codes/camino/man:
> MFLAGS=
> OPTERR=1
> OPTIND=1
> OSTYPE=linux-gnu
> PACKAGE_BUGREPORT=help at hdfgroup.org
> PACKAGE_NAME=HDF5
> PACKAGE_STRING='HDF5 1.6.6'
> PACKAGE_TARNAME=hdf5
> PACKAGE_VERSION=1.6.6
> PATH=/usr/kerberos/sbin:/usr/:/home/Mohamed/Bureau/Sources_Codes/camino/bin:/usr/java/latest/bin:/usr/:/home/Mohamed/Bureau/Sources_Codes/camino/bin:/usr/java/latest/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/home/Mohamed/Bureau/Sources_Codes/bin_lnx:/home/Mohamed/Bureau/Sources_Codes/bin:/home/Mohamed/Bureau/Sources_Codes/pvelab-20080317/Canterbury:/usr/local/caret/bin:/usr/local/bin:/home/Mohamed/bin:/home/Mohamed/Bureau/Sources_Codes/bin_lnx:/home/Mohamed/Bureau/Sources_Codes/bin:/home/Mohamed/Bureau/Sources_Codes/pvelab-20081112/Canterbury:/usr/local/caret/bin
> PATH_SEPARATOR=:
> PIPESTATUS=([0]="0")
> POSIXLY_CORRECT=y
> PPID=18841
> PS1='$ '
> PS2='> '
> PS4='+ '
> PWD=/usr/local/hdf5-1.6.6
> QTDIR=/usr/lib64/qt-3.3
> QTINC=/usr/lib64/qt-3.3/include
> QTLIB=/usr/lib64/qt-3.3/lib
> QT_PLUGIN_PATH=/home/Mohamed/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/:/home/Mohamed/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/:/root/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/
> SDL_AUDIODRIVER=esd
> SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/3102,unix/unix:/tmp/.ICE-unix/3102
> SHELL=/bin/sh
> SHELLOPTS=braceexpand:hashall:interactive-comments:posix
> SHLVL=5
> SSH_AGENT_PID=3004
> SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
> SSH_AUTH_SOCK=/tmp/ssh-HrNOIy2989/agent.2989
> TERM=xterm
> UID=0
> USER=Mohamed
> USERNAME=Mohamed
> WINDOWID=69352330
> XAUTHORITY=/root/.xauthKzN42J
> XCURSOR_THEME=default
> XDG_DATA_DIRS=/usr/share/kde-settings/kde-profile/default/share:/usr/local/share:/usr/share
> XDG_MENU_PREFIX=kde4-
> XDG_SESSION_COOKIE=3c9951686a5e8d532a63fd49483d59e3-1238857151.730932-316909989
> _='checking shell variables initial values... '
> ac_abs_confdir=/usr/local/hdf5-1.6.6
> ac_arg='CPPFLAGS=${CPPFLAGS} -fpic'
> ac_aux_dir=bin
> ac_build_alias=x86_64-unknown-linux-gnu
> ac_cache_corrupted=false
> ac_clean_files=
> ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
> ac_compiler_gnu=
> ac_confdir=.
> ac_config_commands=' default-1'
> ac_config_guess='/bin/sh bin/config.guess'
> ac_config_headers=' src/H5config.h'
> ac_config_libobj_dir=.
> ac_config_sub='/bin/sh bin/config.sub'
> ac_configure='/bin/sh bin/configure'
> ac_configure_args=' '\''--disable-shared'\''
> '\''--prefix=/usr/local'\'' '\''--with-build-path=/usr/local'\''
> '\''CFLAGS=${CFLAGS} -fpic'\'' '\''CPPFLAGS=${CPPFLAGS} -fpic'\''
> '\''CXXFLAGS=${CXXFLAGS} -fpic'\'''
> ac_cpp='$CPP $CPPFLAGS'
> ac_cv_build=x86_64-unknown-linux-gnu
> ac_cv_env_CC_set=
> ac_cv_env_CC_value=
> ac_cv_env_CFLAGS_set=set
> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
> ac_cv_env_CPPFLAGS_set=set
> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
> ac_cv_env_CPP_set=
> ac_cv_env_CPP_value=
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_value=
> ac_cv_env_LIBS_set=
> ac_cv_env_LIBS_value=
> ac_cv_env_build_alias_set=
> ac_cv_env_build_alias_value=
> ac_cv_env_host_alias_set=
> ac_cv_env_host_alias_value=
> ac_cv_env_target_alias_set=
> ac_cv_env_target_alias_value=
> ac_cv_host=x86_64-unknown-linux-gnu
> ac_dashdash=
> ac_default_prefix=/usr/local/hdf5-1.6.6/hdf5
> ac_dir=bin
> ac_env_CC_set=
> ac_env_CC_value=
> ac_env_CFLAGS_set=set
> ac_env_CFLAGS_value='${CFLAGS} -fpic'
> ac_env_CPPFLAGS_set=set
> ac_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
> ac_env_CPP_set=
> ac_env_CPP_value=
> ac_env_LDFLAGS_set=
> ac_env_LDFLAGS_value=
> ac_env_LIBS_set=
> ac_env_LIBS_value=
> ac_env_build_alias_set=
> ac_env_build_alias_value=
> ac_env_host_alias_set=
> ac_env_host_alias_value=
> ac_env_target_alias_set=
> ac_env_target_alias_value=
> ac_envvar=CXXFLAGS
> ac_ext=c
> ac_feature=shared
> ac_hostname=localhost.localdomain
> ac_includes_default='#include <stdio.h>
> #ifdef HAVE_SYS_TYPES_H
> # include <sys/types.h>
> #endif
> #ifdef HAVE_SYS_STAT_H
> # include <sys/stat.h>
> #endif
> #ifdef STDC_HEADERS
> # include <stdlib.h>
> # include <stddef.h>
> #else
> # ifdef HAVE_STDLIB_H
> #  include <stdlib.h>
> # endif
> #endif
> #ifdef HAVE_STRING_H
> # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
> #  include <memory.h>
> # endif
> # include <string.h>
> #endif
> #ifdef HAVE_STRINGS_H
> # include <strings.h>
> #endif
> #ifdef HAVE_INTTYPES_H
> # include <inttypes.h>
> #endif
> #ifdef HAVE_STDINT_H
> # include <stdint.h>
> #endif
> #ifdef HAVE_UNISTD_H
> # include <unistd.h>
> #endif'
> ac_init_help=
> ac_init_version=false
> ac_install_sh='bin/install-sh -c'
> ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS
> conftest.$ac_ext $LIBS >&5'
> ac_ls_di='2613555 .'
> ac_msg='sources are in ., but `cd .'\'' does not work'
> ac_must_keep_next=false
> ac_new_set=
> ac_new_val=
> ac_old_set=
> ac_old_val=
> ac_optarg='${CXXFLAGS} -fpic'
> ac_option='CXXFLAGS=${CXXFLAGS} -fpic'
> ac_package=build_path
> ac_pass=2
> ac_precious_vars='build_alias
> host_alias
> target_alias
> CC
> CFLAGS
> LDFLAGS
> LIBS
> CPPFLAGS
> CPP'
> ac_prev=
> ac_pwd=/usr/local/hdf5-1.6.6
> ac_pwd_ls_di='2613555 .'
> ac_save_IFS=' 	
> '
> ac_signal=0
> ac_site_file=/usr/local/etc/config.site
> ac_srcdir_defaulted=yes
> ac_subdirs_all='${config_dirs}'
> ac_subst_files='DEPEND
> COMMENCE
> CONCLUDE'
> ac_subst_vars='SHELL
> PATH_SEPARATOR
> PACKAGE_NAME
> PACKAGE_TARNAME
> PACKAGE_VERSION
> PACKAGE_STRING
> PACKAGE_BUGREPORT
> exec_prefix
> prefix
> program_transform_name
> bindir
> sbindir
> libexecdir
> datarootdir
> datadir
> sysconfdir
> sharedstatedir
> localstatedir
> includedir
> oldincludedir
> docdir
> infodir
> htmldir
> dvidir
> pdfdir
> psdir
> libdir
> localedir
> mandir
> DEFS
> ECHO_C
> ECHO_N
> ECHO_T
> LIBS
> build_alias
> host_alias
> target_alias
> build
> build_cpu
> build_vendor
> build_os
> host
> host_cpu
> host_vendor
> host_os
> CPPFLAGS
> H5_CPPFLAGS
> H5_CFLAGS
> DEFAULT_LIBS
> HSIZET
> CC
> CFLAGS
> LDFLAGS
> ac_ct_CC
> EXEEXT
> OBJEXT
> config_dirs
> subdirs
> LT_STATIC_EXEC
> PERL
> AR
> SET_MAKE
> INSTALL_PROGRAM
> INSTALL_SCRIPT
> INSTALL_DATA
> PARALLEL
> RUNSERIAL
> RUNPARALLEL
> TESTPARALLEL
> BUILD_PARALLEL_CONDITIONAL_TRUE
> BUILD_PARALLEL_CONDITIONAL_FALSE
> LN_S
> ECHO
> RANLIB
> STRIP
> CPP
> GREP
> EGREP
> LIBTOOL
> USE_FILTER_DEFLATE
> USE_FILTER_SZIP
> SSL
> GASS
> TESTGASS
> SRB
> TESTSRB
> PTHREAD
> DEBUG_PKG
> TRACE_API
> INSTRUMENT_LIBRARY
> CLEARFILEBUF
> MPE
> MPI_GET_SIZE
> FILTERS
> USE_FILTER_SHUFFLE
> USE_FILTER_FLETCHER32
> H5_VERSION
> CONFIG_DATE
> CONFIG_USER
> CONFIG_MODE
> BYTESEX
> STATIC_SHARED
> CC_VERSION
> ROOT
> DYNAMIC_DIRS
> HL
> SEARCH
> SETX
> LIBOBJS
> LTLIBOBJS'
> ac_tool_prefix=
> ac_unique_file=src/H5.c
> ac_val='${datarootdir}/man'
> ac_var=CPP
> as_basename=basename
> as_cr_LETTERS=ABCDEFGHIJKLMNOPQRSTUVWXYZ
> as_cr_Letters=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ
> as_cr_alnum=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
> as_cr_digits=0123456789
> as_cr_letters=abcdefghijklmnopqrstuvwxyz
> as_dir=/usr/local/caret/bin
> as_dirname=dirname
> as_executable_p='test -x'
> as_expr=expr
> as_have_required=yes
> as_lineno_1=426
> as_lineno_2=427
> as_ln_s='ln -s'
> as_me=configure
> as_mkdir_p=:
> as_myself=./configure
> as_nl='
> '
> as_save_IFS=' 	
> '
> as_test_x='test -x'
> as_tr_cpp='eval sed
> '\''y%*abcdefghijklmnopqrstuvwxyz%PABCDEFGHIJKLMNOPQRSTUVWXYZ%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
> as_tr_sh='eval sed
> '\''y%*+%pp%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
> as_unset=unset
> as_var=LC_TIME
> bindir='${exec_prefix}/bin'
> build=x86_64-unknown-linux-gnu
> build_cpu=x86_64
> build_os=linux-gnu
> build_vendor=unknown
> cache_file=/dev/null
> cmd='sed 50q "$0"'
> cross_compiling=no
> datadir='${datarootdir}'
> datarootdir='${prefix}/share'
> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
> dvidir='${docdir}'
> echo=echo
> echo_test_string='#! /bin/sh
> # From configure.in Id: configure.in 14063 2007-08-09 20:51:55Z
> mcgreevy .
> # Guess values for system-dependent variables and create Makefiles.
> # Generated by GNU Autoconf 2.61 for HDF5 1.6.6.
> #
> # Report bugs to <help at hdfgroup.org>.
> #
> # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
> # 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
> # This configure script is free software; the Free Software
> Foundation
> # gives unlimited permission to copy, distribute and modify it.
> ## --------------------- ##
> ## M4sh Initialization.  ##
> ## --------------------- ##
> 
> # Be more Bourne compatible
> DUALCASE=1; export DUALCASE # for MKS sh
> if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
>   emulate sh
>   NULLCMD=:
>   # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
>   # is contrary to our usage.  Disable this feature.
>   alias -g '\''${1+"$@"}'\''='\''"$@"'\''
>   setopt NO_GLOB_SUBST
> else
>   case `(set -o) 2>/dev/null` in
>   *posix*) set -o posix ;;
> esac
> 
> fi
> 
> 
> 
> 
> # PATH needs CR
> # Avoid depending upon Character Ranges.
> as_cr_letters='\''abcdefghijklmnopqrstuvwxyz'\''
> as_cr_LETTERS='\''ABCDEFGHIJKLMNOPQRSTUVWXYZ'\''
> as_cr_Letters=$as_cr_letters$as_cr_LETTERS
> as_cr_digits='\''0123456789'\''
> as_cr_alnum=$as_cr_Letters$as_cr_digits
> 
> # The user is always right.
> if test "${PATH_SEPARATOR+set}" != set; then
>   echo "#! /bin/sh" >conf$$.sh
>   echo  "exit 0"   >>conf$$.sh
>   chmod +x conf$$.sh
>   if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
>     PATH_SEPARATOR='\'';'\''
>   else'
> echo_testing_string='#! /bin/sh
> # From configure.in Id: configure.in 14063 2007-08-09 20:51:55Z
> mcgreevy .
> # Guess values for system-dependent variables and create Makefiles.
> # Generated by GNU Autoconf 2.61 for HDF5 1.6.6.
> #
> # Report bugs to <help at hdfgroup.org>.
> #
> # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
> # 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
> # This configure script is free software; the Free Software
> Foundation
> # gives unlimited permission to copy, distribute and modify it.
> ## --------------------- ##
> ## M4sh Initialization.  ##
> ## --------------------- ##
> 
> # Be more Bourne compatible
> DUALCASE=1; export DUALCASE # for MKS sh
> if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
>   emulate sh
>   NULLCMD=:
>   # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
>   # is contrary to our usage.  Disable this feature.
>   alias -g '\''${1+"$@"}'\''='\''"$@"'\''
>   setopt NO_GLOB_SUBST
> else
>   case `(set -o) 2>/dev/null` in
>   *posix*) set -o posix ;;
> esac
> 
> fi
> 
> 
> 
> 
> # PATH needs CR
> # Avoid depending upon Character Ranges.
> as_cr_letters='\''abcdefghijklmnopqrstuvwxyz'\''
> as_cr_LETTERS='\''ABCDEFGHIJKLMNOPQRSTUVWXYZ'\''
> as_cr_Letters=$as_cr_letters$as_cr_LETTERS
> as_cr_digits='\''0123456789'\''
> as_cr_alnum=$as_cr_Letters$as_cr_digits
> 
> # The user is always right.
> if test "${PATH_SEPARATOR+set}" != set; then
>   echo "#! /bin/sh" >conf$$.sh
>   echo  "exit 0"   >>conf$$.sh
>   chmod +x conf$$.sh
>   if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
>     PATH_SEPARATOR='\'';'\''
>   else'
> enable_shared=no
> exec_prefix=NONE
> host=x86_64-unknown-linux-gnu
> host_cpu=x86_64
> host_os=linux-gnu
> host_vendor=unknown
> htmldir='${docdir}'
> includedir='${prefix}/include'
> infodir='${datarootdir}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localedir='${datarootdir}/locale'
> localstatedir='${prefix}/var'
> mandir='${datarootdir}/man'
> no_create=
> no_recursion=
> oldincludedir=/usr/include
> pdfdir='${docdir}'
> prefix=/usr/local
> program_prefix=NONE
> program_suffix=NONE
> program_transform_name=s,x,x,
> psdir='${docdir}'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> silent=
> site=
> srcdir=.
> subdirs=
> sysconfdir='${prefix}/etc'
> target=
> verbose=
> with_build_path=/usr/local
> x_includes=NONE
> x_libraries=NONE
> configure:2122: result: done
> configure:2127: checking if basename works
> configure:2135: result: yes
> configure:2139: checking if xargs works
> configure:2147: result: yes
> configure:2151: checking for cached host
> configure:2158: result: none
> configure:2200: checking for sizeof hsize_t and hssize_t
> configure:2203: result: large
> configure:2224: checking for config x86_64-unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-unknown
> configure:2232: result: no
> configure:2224: checking for config linux-gnu
> configure:2228: result: found
> configure:2243: checking for config
> ./config/site-specific/host-localhost.localdomain
> configure:2251: result: no
> configure:2243: checking for config
> ./config/site-specific/host-localdomain
> configure:2251: result: no
> configure:2306: checking for gcc
> configure:2333: result: gcc
> configure:2571: checking for C compiler version
> configure:2578: gcc --version >&5
> gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8)
> Copyright (C) 2008 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There
> is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
> 
> configure:2581: $? = 0
> configure:2588: gcc -v >&5
> Using built-in specs.
> Target: x86_64-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info
> --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
> --enable-shared --enable-threads=posix --enable-checking=release
> --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions
> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
> --enable-java-awt=gtk --disable-dssi --enable-plugin
> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
> --enable-libgcj-multifile --enable-java-maintainer-mode
> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar
> --disable-libjava-multilib --with-cpu=generic
> --build=x86_64-redhat-linux
> Thread model: posix
> gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC) 
> configure:2591: $? = 0
> configure:2598: gcc -V >&5
> gcc: '-V' option must have argument
> configure:2601: $? = 1
> configure:2624: checking for C compiler default output file name
> configure:2651: gcc ${CFLAGS} -fpic  -ansi ${CPPFLAGS} -fpic 
> conftest.c  >&5
> gcc: ${CFLAGS}: No such file or directory
> gcc: ${CPPFLAGS}: No such file or directory
> configure:2654: $? = 1
> configure:2692: result: 
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "HDF5"
> | #define PACKAGE_TARNAME "hdf5"
> | #define PACKAGE_VERSION "1.6.6"
> | #define PACKAGE_STRING "HDF5 1.6.6"
> | #define PACKAGE_BUGREPORT "help at hdfgroup.org"
> | #define HAVE_LARGE_HSIZET 1
> | /* end confdefs.h.  */
> | 
> | int
> | main ()
> | {
> | 
> |   ;
> |   return 0;
> | }
> configure:2699: error: C compiler cannot create executables
> See `config.log' for more details.
> 
> ## ---------------- ##
> ## Cache variables. ##
> ## ---------------- ##
> 
> ac_cv_build=x86_64-unknown-linux-gnu
> ac_cv_env_CC_set=
> ac_cv_env_CC_value=
> ac_cv_env_CFLAGS_set=set
> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
> ac_cv_env_CPPFLAGS_set=set
> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
> ac_cv_env_CPP_set=
> ac_cv_env_CPP_value=
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_value=
> ac_cv_env_LIBS_set=
> ac_cv_env_LIBS_value=
> ac_cv_env_build_alias_set=
> ac_cv_env_build_alias_value=
> ac_cv_env_host_alias_set=
> ac_cv_env_host_alias_value=
> ac_cv_env_target_alias_set=
> ac_cv_env_target_alias_value=
> ac_cv_host=x86_64-unknown-linux-gnu
> ac_cv_prog_ac_ct_CC=gcc
> hdf5_cv_host=x86_64-unknown-linux-gnu
> 
> ## ----------------- ##
> ## Output variables. ##
> ## ----------------- ##
> 
> AR=''
> BUILD_PARALLEL_CONDITIONAL_FALSE=''
> BUILD_PARALLEL_CONDITIONAL_TRUE=''
> BYTESEX=''
> CC='gcc'
> CC_VERSION=''
> CFLAGS='${CFLAGS} -fpic  -ansi'
> CLEARFILEBUF=''
> CONFIG_DATE=''
> CONFIG_MODE=''
> CONFIG_USER=''
> CPP=''
> CPPFLAGS='${CPPFLAGS} -fpic'
> DEBUG_PKG=''
> DEFAULT_LIBS=''
> DEFS=''
> DYNAMIC_DIRS=''
> ECHO='echo'
> ECHO_C=''
> ECHO_N='-n'
> ECHO_T=''
> EGREP=''
> EXEEXT=''
> FILTERS=''
> GASS=''
> GREP=''
> H5_CFLAGS=''
> H5_CPPFLAGS=''
> H5_VERSION=''
> HL=''
> HSIZET='large'
> INSTALL_DATA=''
> INSTALL_PROGRAM=''
> INSTALL_SCRIPT=''
> INSTRUMENT_LIBRARY=''
> LDFLAGS=''
> LIBOBJS=''
> LIBS=''
> LIBTOOL=''
> LN_S=''
> LTLIBOBJS=''
> LT_STATIC_EXEC=''
> MPE=''
> MPI_GET_SIZE=''
> OBJEXT=''
> PACKAGE_BUGREPORT='help at hdfgroup.org'
> PACKAGE_NAME='HDF5'
> PACKAGE_STRING='HDF5 1.6.6'
> PACKAGE_TARNAME='hdf5'
> PACKAGE_VERSION='1.6.6'
> PARALLEL=''
> PATH_SEPARATOR=':'
> PERL=''
> PTHREAD=''
> RANLIB=''
> ROOT=''
> RUNPARALLEL=''
> RUNSERIAL=''
> SEARCH=''
> SETX=''
> SET_MAKE=''
> SHELL='/bin/sh'
> SRB=''
> SSL=''
> STATIC_SHARED=''
> STRIP=''
> TESTGASS=''
> TESTPARALLEL=''
> TESTSRB=''
> TRACE_API=''
> USE_FILTER_DEFLATE=''
> USE_FILTER_FLETCHER32=''
> USE_FILTER_SHUFFLE=''
> USE_FILTER_SZIP=''
> ac_ct_CC='gcc'
> bindir='${exec_prefix}/bin'
> build='x86_64-unknown-linux-gnu'
> build_alias=''
> build_cpu='x86_64'
> build_os='linux-gnu'
> build_vendor='unknown'
> config_dirs=''
> datadir='${datarootdir}'
> datarootdir='${prefix}/share'
> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
> dvidir='${docdir}'
> exec_prefix='NONE'
> host='x86_64-unknown-linux-gnu'
> host_alias=''
> host_cpu='x86_64'
> host_os='linux-gnu'
> host_vendor='unknown'
> htmldir='${docdir}'
> includedir='${prefix}/include'
> infodir='${datarootdir}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localedir='${datarootdir}/locale'
> localstatedir='${prefix}/var'
> mandir='${datarootdir}/man'
> oldincludedir='/usr/include'
> pdfdir='${docdir}'
> prefix='/usr/local'
> program_transform_name='s,x,x,'
> psdir='${docdir}'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> subdirs=''
> sysconfdir='${prefix}/etc'
> target_alias=''
> 
> ## ------------------- ##
> ## File substitutions. ##
> ## ------------------- ##
> 
> COMMENCE=''
> CONCLUDE=''
> DEPEND=''
> 
> ## ----------- ##
> ## confdefs.h. ##
> ## ----------- ##
> 
> #define PACKAGE_NAME "HDF5"
> #define PACKAGE_TARNAME "hdf5"
> #define PACKAGE_VERSION "1.6.6"
> #define PACKAGE_STRING "HDF5 1.6.6"
> #define PACKAGE_BUGREPORT "help at hdfgroup.org"
> #define HAVE_LARGE_HSIZET 1
> 
> configure: exit 77
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From m.bahri at ulg.ac.be  Sun Apr  5 08:02:05 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Sun, 05 Apr 2009 14:02:05 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <1269874905.400501238930836459.JavaMail.root@zimbra-store01.hst.aau.dk>
References: <1269874905.400501238930836459.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <49D89DBD.8060802@ulg.ac.be>

Hi Simon,

Thank you very much for your suggestions, configure passes now without 
error but make check gave the following error:
Is it important that make check passes all tests?
Which version of netcdf should I install? and should I use the same 
options for configuration?

Thanks a lot,

make check errors
---------------------------------------------------------------------------------------------------------
Testing random sw long double -> float conversions                    
*FAILED*
HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 0.  Back 
trace follows.
  #000: H5T.c line 2435 in H5Tconvert(): unable to convert between src 
and dst data types
    major(13): Datatype interface
    minor(29): Unable to initialize object
  #001: H5T.c line 3984 in H5T_path_find(): no appropriate function for 
conversion path
    major(13): Datatype interface
    minor(29): Unable to initialize object
Testing random sw long double -> double conversions                   
*FAILED*
HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 0.  Back 
trace follows.
  #000: H5T.c line 2435 in H5Tconvert(): unable to convert between src 
and dst data types
    major(13): Datatype interface
    minor(29): Unable to initialize object
  #001: H5T.c line 3984 in H5T_path_find(): no appropriate function for 
conversion path
    major(13): Datatype interface
    minor(29): Unable to initialize object
***** 164 FAILURES! *****
1.55user 0.10system 0:01.66elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+1088outputs (0major+20505minor)pagefaults 0swaps
make[2]: *** [_check-s] Erreur 1
make[2]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/test ?
make[1]: *** [check] Erreur 2
make[1]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/test ?
make: *** [check] Erreur 1
------------------------------------------------------------------------------------------------------------------

Mohamed


Simon Fristed Eskildsen a ?crit :
> Hi Mohamed,
> Try using double quotation marks instead of single:
>
> ./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local CFLAGS="${CFLAGS} -fpic" CPPFLAGS="${CPPFLAGS} -fpic" CXXFLAGS="${CXXFLAGS} -fpic"
>
> As far as I remember bash does not expand into single quatation marks. If it does not help, try exporting the flags before configuring:
>
> export CFLAGS="${CFLAGS} -fpic"
> export CPPFLAGS="${CPPFLAGS} -fpic"
> export CXXFLAGS="${CXXFLAGS} -fpic"
> ./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local
>
> Simon
>
> ----- "mohamed Ali Bahri" <m.bahri at ulg.ac.be> wrote:
>
>   
>> Hi Claude,
>>
>> I tried with your command line and it gave me the following error:
>>
>> -----------------------------------------------------------------------------------------------------------
>> [root at localhost hdf5-1.6.6]# ./configure --disable-shared 
>> --prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} 
>> -fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking shell variables initial values... done
>> checking if basename works... yes
>> checking if xargs works... yes
>> checking for cached host... none
>> checking for sizeof hsize_t and hssize_t... large
>> checking for config x86_64-unknown-linux-gnu... no
>> checking for config x86_64-unknown-linux-gnu... no
>> checking for config unknown-linux-gnu... no
>> checking for config unknown-linux-gnu... no
>> checking for config x86_64-linux-gnu... no
>> checking for config x86_64-linux-gnu... no
>> checking for config x86_64-unknown... no
>> checking for config linux-gnu... found
>> compiler 'gcc' is GNU gcc-4.3.0
>> checking for config
>> ./config/site-specific/host-localhost.localdomain... no
>> checking for config ./config/site-specific/host-localdomain... no
>> checking for gcc... gcc
>> checking for C compiler default output file name...
>> configure: error: C compiler cannot create executables
>> See `config.log' for more details.
>> ------------------------------------------------------------------------------------------------------
>> As compiler I use gcc 4.3 (gcc (GCC) 4.3.0 20080428 (Red Hat
>> 4.3.0-8).
>> I also attached the config.log if this could give information about my
>>
>> problem.
>>
>> Thank you very much for your help
>>
>> Best regards
>> Mohamed
>>
>>
>>
>>
>>
>> Claude LEPAGE a ?crit :
>>     
>>> Hi,
>>>
>>>   
>>>       
>>>> Thank you for your answer. I tried to use HDF5-1.6.6 instead of 
>>>> hdf5-1.8.2 but now I have errors with HDF5.
>>>> I use the following command lines:
>>>>
>>>> 1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/ 
>>>> --with-zlib=/usr/local/ --enable-fortran --enable-cxx
>>>> 2) make
>>>>     
>>>>         
>>> Here is how I compile HDF5-1.6.6 in 64 bits Linux:
>>>
>>> ./configure --disable-shared --prefix=/usr/local
>>>       
>> --with-build-path=/usr/local CFLAGS='${CFLAGS} -fpic'
>> CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
>>     
>>> make 
>>> make install
>>>
>>> --disable-shared is optional
>>> no need to fuss about fortran (not needed by minc2)
>>>
>>> By the way, which compiler are you using? It looks like your C++
>>> compiler does not like the code. Strange...
>>>
>>> gcc --version
>>>
>>> minc2 may compile with gcc 4.2+, but not all MNI tools do (yet).
>>>
>>> Claude
>>>
>>>
>>>   
>>>       
>>>> ===============================================
>>>>
>>>> g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE 
>>>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
>>>> -I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o
>>>>         
>> .libs/H5PropList.lo
>>     
>>>> H5PropList.cpp: In member function 'std::string 
>>>> H5::PropList::getClassName() const':
>>>> H5PropList.cpp:428: error: 'free' was not declared in this scope
>>>> make[3]: *** [H5PropList.lo] Erreur 1
>>>> make[3]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++/src ?
>>>> make[2]: *** [lib] Erreur 1
>>>> make[2]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6/c++ ?
>>>> make[1]: *** [lib] Erreur 1
>>>> make[1]: quittant le r?pertoire ? /usr/local/hdf5-1.6.6 ?
>>>> make: *** [all] Erreur 2
>>>> =======================================================
>>>>
>>>> Thanks a lot,
>>>> Mohamed
>>>>
>>>> Claude LEPAGE a ?crit :
>>>>     
>>>>         
>>>>> Hi,
>>>>>
>>>>>   
>>>>>       
>>>>>           
>>>>>> I have a problem with minc-2.0.17 installation (make command
>>>>>>             
>> fails). Any 
>>     
>>>>>> one have an idea how I can solve that?
>>>>>> I use linux (Fedora 9, 64-bit).
>>>>>>
>>>>>> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
>>>>>> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
>>>>>> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT
>>>>>>             
>> libsrc/hdf_convenience.lo 
>>     
>>>>>> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c
>>>>>>             
>> libsrc/hdf_convenience.c 
>>     
>>>>>> -o libsrc/hdf_convenience.o
>>>>>> libsrc/hdf_convenience.c: In function ?hdf_id_add?:
>>>>>> libsrc/hdf_convenience.c:83: erreur: too few arguments to
>>>>>>             
>> function 
>>     
>>>>>> ?H5Gopen2?
>>>>>> libsrc/hdf_convenience.c: In function ?hdf_var_add?:
>>>>>> libsrc/hdf_convenience.c:185: erreur: too few arguments to
>>>>>>             
>> function 
>>     
>>>>>>     
>>>>>>         
>>>>>>             
>>>>> I haven't seen this problem, but here is an idea.
>>>>>
>>>>> Which version of HDF5 have you installed? minc2 has been tested
>>>>> with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would
>>>>>           
>> suggest
>>     
>>>>> to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I
>>>>>           
>> recall,
>>     
>>>>> 5-1.8.X is not 100% compatible with previous versions.
>>>>>
>>>>> The problem may be different too, but making sure you are using
>>>>> a compatible version of HDF5 is the first step.
>>>>>
>>>>> Yours,
>>>>>
>>>>> Claude
>>>>>  
>>>>>   
>>>>>
>>>>>           
>> ------------------------------------------------------------------------
>>     
>>>>> _______________________________________________
>>>>> MINC-users at bic.mni.mcgill.ca
>>>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>>   
>>>>>       
>>>>>           
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>>     
>>>>
>>>>         
>> ------------------------------------------------------------------------
>>     
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>     
>>>>         
>> This file contains any messages produced by compilers while
>> running configure, to aid debugging if configure makes a mistake.
>>
>> It was created by HDF5 configure 1.6.6, which was
>> generated by GNU Autoconf 2.61.  Invocation command line was
>>
>>   $ ./configure --disable-shared --prefix=/usr/local
>> --with-build-path=/usr/local CFLAGS=${CFLAGS} -fpic
>> CPPFLAGS=${CPPFLAGS} -fpic CXXFLAGS=${CXXFLAGS} -fpic
>>
>> ## --------- ##
>> ## Platform. ##
>> ## --------- ##
>>
>> hostname = localhost.localdomain
>> uname -m = x86_64
>> uname -r = 2.6.27.21-78.2.41.fc9.x86_64
>> uname -s = Linux
>> uname -v = #1 SMP Mon Mar 23 23:22:15 EDT 2009
>>
>> /usr/bin/uname -p = unknown
>> /bin/uname -X     = unknown
>>
>> /bin/arch              = x86_64
>> /usr/bin/arch -k       = unknown
>> /usr/convex/getsysinfo = unknown
>> /usr/bin/hostinfo      = unknown
>> /bin/machine           = unknown
>> /usr/bin/oslevel       = unknown
>> /bin/universe          = unknown
>>
>> PATH: /usr/kerberos/sbin
>> PATH: /usr/
>> PATH: /home/Mohamed/Bureau/Sources_Codes/camino/bin
>> PATH: /usr/java/latest/bin
>> PATH: /usr/
>> PATH: /home/Mohamed/Bureau/Sources_Codes/camino/bin
>> PATH: /usr/java/latest/bin
>> PATH: /usr/lib64/qt-3.3/bin
>> PATH: /usr/kerberos/bin
>> PATH: /usr/lib64/ccache
>> PATH: /usr/local/bin
>> PATH: /usr/bin
>> PATH: /bin
>> PATH: /home/Mohamed/Bureau/Sources_Codes/bin_lnx
>> PATH: /home/Mohamed/Bureau/Sources_Codes/bin
>> PATH: /home/Mohamed/Bureau/Sources_Codes/pvelab-20080317/Canterbury
>> PATH: /usr/local/caret/bin
>> PATH: /usr/local/bin
>> PATH: /home/Mohamed/bin
>> PATH: /home/Mohamed/Bureau/Sources_Codes/bin_lnx
>> PATH: /home/Mohamed/Bureau/Sources_Codes/bin
>> PATH: /home/Mohamed/Bureau/Sources_Codes/pvelab-20081112/Canterbury
>> PATH: /usr/local/caret/bin
>>
>>
>> ## ----------- ##
>> ## Core tests. ##
>> ## ----------- ##
>>
>> configure:2034: checking build system type
>> configure:2052: result: x86_64-unknown-linux-gnu
>> configure:2074: checking host system type
>> configure:2089: result: x86_64-unknown-linux-gnu
>> configure:2119: checking shell variables initial values
>> BASH=/bin/sh
>> BASH_ARGC=([0]="6")
>> BASH_ARGV=([0]="CXXFLAGS=\${CXXFLAGS} -fpic"
>> [1]="CPPFLAGS=\${CPPFLAGS} -fpic" [2]="CFLAGS=\${CFLAGS} -fpic"
>> [3]="--with-build-path=/usr/local" [4]="--prefix=/usr/local"
>> [5]="--disable-shared")
>> BASH_LINENO=([0]="0")
>> BASH_SOURCE=([0]="./configure")
>> BASH_VERSINFO=([0]="3" [1]="2" [2]="33" [3]="1" [4]="release"
>> [5]="x86_64-redhat-linux-gnu")
>> BASH_VERSION='3.2.33(1)-release'
>> CCACHE_DIR=/var/cache/ccache
>> CCACHE_UMASK=002
>> CFLAGS='${CFLAGS} -fpic'
>> COLORTERM=gnome-terminal
>> CPPFLAGS='${CPPFLAGS} -fpic'
>> CVS_RSH=ssh
>> CXXFLAGS='${CXXFLAGS} -fpic'
>> DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-qhDa2Oiw19,guid=4739190599a2a029607aa83c49d775c0
>> DEFAULT_LIBS=
>> DESKTOP_SESSION=kde
>> DESKTOP_STARTUP_ID=
>> DIRSTACK=()
>> DISPLAY=:0.0
>> DUALCASE=1
>> ECHO=echo
>> ECHO_C=
>> ECHO_N=-n
>> ECHO_T=
>> EUID=0
>> GDMSESSION=kde
>> GDM_LANG=fr_FR.UTF-8
>> GNOME_KEYRING_PID=2988
>> GNOME_KEYRING_SOCKET=/tmp/keyring-CdaPEr/socket
>> GPG_AGENT_INFO=/tmp/gpg-aiPs2p/S.gpg-agent:3059:1
>> GROUPS=()
>> GS_LIB=
>> GTK2_RC_FILES=/etc/gtk-2.0/gtkrc:/home/Mohamed/.gtkrc-2.0::/home/Mohamed/.kde/share/config/gtkrc-2.0
>> GTK_RC_FILES=/etc/gtk/gtkrc:/home/Mohamed/.gtkrc::/home/Mohamed/.kde/share/config/gtkrc
>> G_BROKEN_FILENAMES=1
>> HISTSIZE=1000
>> HOME=/root
>> HOSTNAME=localhost.localdomain
>> HOSTTYPE=x86_64
>> IFS=' 	
>> '
>> INPUTRC=/etc/inputrc
>> KDEDIRS=/usr
>> KDE_FULL_SESSION=true
>> KDE_IS_PRELINKED=1
>> KDE_MULTIHEAD=false
>> KDE_SESSION_UID=500
>> KDE_SESSION_VERSION=4
>> LANG=C
>> LANGUAGE=C
>> LC_ADDRESS=C
>> LC_ALL=C
>> LC_COLLATE=C
>> LC_CTYPE=C
>> LC_IDENTIFICATION=C
>> LC_MEASUREMENT=C
>> LC_MESSAGES=C
>> LC_MONETARY=C
>> LC_NAME=C
>> LC_NUMERIC=C
>> LC_PAPER=C
>> LC_TELEPHONE=C
>> LC_TIME=C
>> LESSOPEN='|/usr/bin/lesspipe.sh %s'
>> LIBOBJS=
>> LINENO=2119
>> LOGNAME=Mohamed
>> LS_COLORS='no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:do=00;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.svgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.lzma=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.dz=00;31:*.gz=00;31:*.bz2=00;31:*.tbz2=00;31:*.bz=00;31:*.tz=00;31:*.deb=00;31:*.rpm=00;31:*.jar=00;31:*.rar=00;31:*.ace=00;31:*.zoo=00;31:*.cpio=00;31:*.7z=00;31:*.rz=00;31:*.jpg=00;35:*.jpeg=00;35:*.gif=00;35:*.bmp=00;35:*.pbm=00;35:*.pgm=00;35:*.ppm=00;35:*.tga=00;35:*.xbm=00;35:*.xpm=00;35:*.tif=00;35:*.tiff=00;35:*.png=00;35:*.mng=00;35:*.pcx=00;35:*.mov=00;35:*.mpg=00;35:*.mpeg=00;35:*.m2v=00;35:*.mkv=00;35:*.ogm=00;35:*.mp4=00;35:*.m4v=00;35:*.mp4v=00;35:*.vob=00;35:*.qt=00;35:*.nuv=00;35:*.wmv=00;35:*.asf=00;35:*.rm=00;35:*.rmvb=00;35:*.flc=00;35:*.avi=00;35:*.fli=00;35:*.gl=00;35:*.dl=00;35:*.xcf=00;35:*.xwd=00;35:*.yuv=00;35:*.svg=00;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:'
>> MACHTYPE=x86_64-redhat-linux-gnu
>> MAKEFLAGS=
>> MANPATH=/home/Mohamed/Bureau/Sources_Codes/camino/man:/home/Mohamed/Bureau/Sources_Codes/camino/man:
>> MFLAGS=
>> OPTERR=1
>> OPTIND=1
>> OSTYPE=linux-gnu
>> PACKAGE_BUGREPORT=help at hdfgroup.org
>> PACKAGE_NAME=HDF5
>> PACKAGE_STRING='HDF5 1.6.6'
>> PACKAGE_TARNAME=hdf5
>> PACKAGE_VERSION=1.6.6
>> PATH=/usr/kerberos/sbin:/usr/:/home/Mohamed/Bureau/Sources_Codes/camino/bin:/usr/java/latest/bin:/usr/:/home/Mohamed/Bureau/Sources_Codes/camino/bin:/usr/java/latest/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/home/Mohamed/Bureau/Sources_Codes/bin_lnx:/home/Mohamed/Bureau/Sources_Codes/bin:/home/Mohamed/Bureau/Sources_Codes/pvelab-20080317/Canterbury:/usr/local/caret/bin:/usr/local/bin:/home/Mohamed/bin:/home/Mohamed/Bureau/Sources_Codes/bin_lnx:/home/Mohamed/Bureau/Sources_Codes/bin:/home/Mohamed/Bureau/Sources_Codes/pvelab-20081112/Canterbury:/usr/local/caret/bin
>> PATH_SEPARATOR=:
>> PIPESTATUS=([0]="0")
>> POSIXLY_CORRECT=y
>> PPID=18841
>> PS1='$ '
>> PS2='> '
>> PS4='+ '
>> PWD=/usr/local/hdf5-1.6.6
>> QTDIR=/usr/lib64/qt-3.3
>> QTINC=/usr/lib64/qt-3.3/include
>> QTLIB=/usr/lib64/qt-3.3/lib
>> QT_PLUGIN_PATH=/home/Mohamed/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/:/home/Mohamed/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/:/root/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/
>> SDL_AUDIODRIVER=esd
>> SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/3102,unix/unix:/tmp/.ICE-unix/3102
>> SHELL=/bin/sh
>> SHELLOPTS=braceexpand:hashall:interactive-comments:posix
>> SHLVL=5
>> SSH_AGENT_PID=3004
>> SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
>> SSH_AUTH_SOCK=/tmp/ssh-HrNOIy2989/agent.2989
>> TERM=xterm
>> UID=0
>> USER=Mohamed
>> USERNAME=Mohamed
>> WINDOWID=69352330
>> XAUTHORITY=/root/.xauthKzN42J
>> XCURSOR_THEME=default
>> XDG_DATA_DIRS=/usr/share/kde-settings/kde-profile/default/share:/usr/local/share:/usr/share
>> XDG_MENU_PREFIX=kde4-
>> XDG_SESSION_COOKIE=3c9951686a5e8d532a63fd49483d59e3-1238857151.730932-316909989
>> _='checking shell variables initial values... '
>> ac_abs_confdir=/usr/local/hdf5-1.6.6
>> ac_arg='CPPFLAGS=${CPPFLAGS} -fpic'
>> ac_aux_dir=bin
>> ac_build_alias=x86_64-unknown-linux-gnu
>> ac_cache_corrupted=false
>> ac_clean_files=
>> ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
>> ac_compiler_gnu=
>> ac_confdir=.
>> ac_config_commands=' default-1'
>> ac_config_guess='/bin/sh bin/config.guess'
>> ac_config_headers=' src/H5config.h'
>> ac_config_libobj_dir=.
>> ac_config_sub='/bin/sh bin/config.sub'
>> ac_configure='/bin/sh bin/configure'
>> ac_configure_args=' '\''--disable-shared'\''
>> '\''--prefix=/usr/local'\'' '\''--with-build-path=/usr/local'\''
>> '\''CFLAGS=${CFLAGS} -fpic'\'' '\''CPPFLAGS=${CPPFLAGS} -fpic'\''
>> '\''CXXFLAGS=${CXXFLAGS} -fpic'\'''
>> ac_cpp='$CPP $CPPFLAGS'
>> ac_cv_build=x86_64-unknown-linux-gnu
>> ac_cv_env_CC_set=
>> ac_cv_env_CC_value=
>> ac_cv_env_CFLAGS_set=set
>> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
>> ac_cv_env_CPPFLAGS_set=set
>> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
>> ac_cv_env_CPP_set=
>> ac_cv_env_CPP_value=
>> ac_cv_env_LDFLAGS_set=
>> ac_cv_env_LDFLAGS_value=
>> ac_cv_env_LIBS_set=
>> ac_cv_env_LIBS_value=
>> ac_cv_env_build_alias_set=
>> ac_cv_env_build_alias_value=
>> ac_cv_env_host_alias_set=
>> ac_cv_env_host_alias_value=
>> ac_cv_env_target_alias_set=
>> ac_cv_env_target_alias_value=
>> ac_cv_host=x86_64-unknown-linux-gnu
>> ac_dashdash=
>> ac_default_prefix=/usr/local/hdf5-1.6.6/hdf5
>> ac_dir=bin
>> ac_env_CC_set=
>> ac_env_CC_value=
>> ac_env_CFLAGS_set=set
>> ac_env_CFLAGS_value='${CFLAGS} -fpic'
>> ac_env_CPPFLAGS_set=set
>> ac_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
>> ac_env_CPP_set=
>> ac_env_CPP_value=
>> ac_env_LDFLAGS_set=
>> ac_env_LDFLAGS_value=
>> ac_env_LIBS_set=
>> ac_env_LIBS_value=
>> ac_env_build_alias_set=
>> ac_env_build_alias_value=
>> ac_env_host_alias_set=
>> ac_env_host_alias_value=
>> ac_env_target_alias_set=
>> ac_env_target_alias_value=
>> ac_envvar=CXXFLAGS
>> ac_ext=c
>> ac_feature=shared
>> ac_hostname=localhost.localdomain
>> ac_includes_default='#include <stdio.h>
>> #ifdef HAVE_SYS_TYPES_H
>> # include <sys/types.h>
>> #endif
>> #ifdef HAVE_SYS_STAT_H
>> # include <sys/stat.h>
>> #endif
>> #ifdef STDC_HEADERS
>> # include <stdlib.h>
>> # include <stddef.h>
>> #else
>> # ifdef HAVE_STDLIB_H
>> #  include <stdlib.h>
>> # endif
>> #endif
>> #ifdef HAVE_STRING_H
>> # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
>> #  include <memory.h>
>> # endif
>> # include <string.h>
>> #endif
>> #ifdef HAVE_STRINGS_H
>> # include <strings.h>
>> #endif
>> #ifdef HAVE_INTTYPES_H
>> # include <inttypes.h>
>> #endif
>> #ifdef HAVE_STDINT_H
>> # include <stdint.h>
>> #endif
>> #ifdef HAVE_UNISTD_H
>> # include <unistd.h>
>> #endif'
>> ac_init_help=
>> ac_init_version=false
>> ac_install_sh='bin/install-sh -c'
>> ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS
>> conftest.$ac_ext $LIBS >&5'
>> ac_ls_di='2613555 .'
>> ac_msg='sources are in ., but `cd .'\'' does not work'
>> ac_must_keep_next=false
>> ac_new_set=
>> ac_new_val=
>> ac_old_set=
>> ac_old_val=
>> ac_optarg='${CXXFLAGS} -fpic'
>> ac_option='CXXFLAGS=${CXXFLAGS} -fpic'
>> ac_package=build_path
>> ac_pass=2
>> ac_precious_vars='build_alias
>> host_alias
>> target_alias
>> CC
>> CFLAGS
>> LDFLAGS
>> LIBS
>> CPPFLAGS
>> CPP'
>> ac_prev=
>> ac_pwd=/usr/local/hdf5-1.6.6
>> ac_pwd_ls_di='2613555 .'
>> ac_save_IFS=' 	
>> '
>> ac_signal=0
>> ac_site_file=/usr/local/etc/config.site
>> ac_srcdir_defaulted=yes
>> ac_subdirs_all='${config_dirs}'
>> ac_subst_files='DEPEND
>> COMMENCE
>> CONCLUDE'
>> ac_subst_vars='SHELL
>> PATH_SEPARATOR
>> PACKAGE_NAME
>> PACKAGE_TARNAME
>> PACKAGE_VERSION
>> PACKAGE_STRING
>> PACKAGE_BUGREPORT
>> exec_prefix
>> prefix
>> program_transform_name
>> bindir
>> sbindir
>> libexecdir
>> datarootdir
>> datadir
>> sysconfdir
>> sharedstatedir
>> localstatedir
>> includedir
>> oldincludedir
>> docdir
>> infodir
>> htmldir
>> dvidir
>> pdfdir
>> psdir
>> libdir
>> localedir
>> mandir
>> DEFS
>> ECHO_C
>> ECHO_N
>> ECHO_T
>> LIBS
>> build_alias
>> host_alias
>> target_alias
>> build
>> build_cpu
>> build_vendor
>> build_os
>> host
>> host_cpu
>> host_vendor
>> host_os
>> CPPFLAGS
>> H5_CPPFLAGS
>> H5_CFLAGS
>> DEFAULT_LIBS
>> HSIZET
>> CC
>> CFLAGS
>> LDFLAGS
>> ac_ct_CC
>> EXEEXT
>> OBJEXT
>> config_dirs
>> subdirs
>> LT_STATIC_EXEC
>> PERL
>> AR
>> SET_MAKE
>> INSTALL_PROGRAM
>> INSTALL_SCRIPT
>> INSTALL_DATA
>> PARALLEL
>> RUNSERIAL
>> RUNPARALLEL
>> TESTPARALLEL
>> BUILD_PARALLEL_CONDITIONAL_TRUE
>> BUILD_PARALLEL_CONDITIONAL_FALSE
>> LN_S
>> ECHO
>> RANLIB
>> STRIP
>> CPP
>> GREP
>> EGREP
>> LIBTOOL
>> USE_FILTER_DEFLATE
>> USE_FILTER_SZIP
>> SSL
>> GASS
>> TESTGASS
>> SRB
>> TESTSRB
>> PTHREAD
>> DEBUG_PKG
>> TRACE_API
>> INSTRUMENT_LIBRARY
>> CLEARFILEBUF
>> MPE
>> MPI_GET_SIZE
>> FILTERS
>> USE_FILTER_SHUFFLE
>> USE_FILTER_FLETCHER32
>> H5_VERSION
>> CONFIG_DATE
>> CONFIG_USER
>> CONFIG_MODE
>> BYTESEX
>> STATIC_SHARED
>> CC_VERSION
>> ROOT
>> DYNAMIC_DIRS
>> HL
>> SEARCH
>> SETX
>> LIBOBJS
>> LTLIBOBJS'
>> ac_tool_prefix=
>> ac_unique_file=src/H5.c
>> ac_val='${datarootdir}/man'
>> ac_var=CPP
>> as_basename=basename
>> as_cr_LETTERS=ABCDEFGHIJKLMNOPQRSTUVWXYZ
>> as_cr_Letters=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ
>> as_cr_alnum=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
>> as_cr_digits=0123456789
>> as_cr_letters=abcdefghijklmnopqrstuvwxyz
>> as_dir=/usr/local/caret/bin
>> as_dirname=dirname
>> as_executable_p='test -x'
>> as_expr=expr
>> as_have_required=yes
>> as_lineno_1=426
>> as_lineno_2=427
>> as_ln_s='ln -s'
>> as_me=configure
>> as_mkdir_p=:
>> as_myself=./configure
>> as_nl='
>> '
>> as_save_IFS=' 	
>> '
>> as_test_x='test -x'
>> as_tr_cpp='eval sed
>> '\''y%*abcdefghijklmnopqrstuvwxyz%PABCDEFGHIJKLMNOPQRSTUVWXYZ%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
>> as_tr_sh='eval sed
>> '\''y%*+%pp%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
>> as_unset=unset
>> as_var=LC_TIME
>> bindir='${exec_prefix}/bin'
>> build=x86_64-unknown-linux-gnu
>> build_cpu=x86_64
>> build_os=linux-gnu
>> build_vendor=unknown
>> cache_file=/dev/null
>> cmd='sed 50q "$0"'
>> cross_compiling=no
>> datadir='${datarootdir}'
>> datarootdir='${prefix}/share'
>> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
>> dvidir='${docdir}'
>> echo=echo
>> echo_test_string='#! /bin/sh
>> # From configure.in Id: configure.in 14063 2007-08-09 20:51:55Z
>> mcgreevy .
>> # Guess values for system-dependent variables and create Makefiles.
>> # Generated by GNU Autoconf 2.61 for HDF5 1.6.6.
>> #
>> # Report bugs to <help at hdfgroup.org>.
>> #
>> # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
>> # 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
>> # This configure script is free software; the Free Software
>> Foundation
>> # gives unlimited permission to copy, distribute and modify it.
>> ## --------------------- ##
>> ## M4sh Initialization.  ##
>> ## --------------------- ##
>>
>> # Be more Bourne compatible
>> DUALCASE=1; export DUALCASE # for MKS sh
>> if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
>>   emulate sh
>>   NULLCMD=:
>>   # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
>>   # is contrary to our usage.  Disable this feature.
>>   alias -g '\''${1+"$@"}'\''='\''"$@"'\''
>>   setopt NO_GLOB_SUBST
>> else
>>   case `(set -o) 2>/dev/null` in
>>   *posix*) set -o posix ;;
>> esac
>>
>> fi
>>
>>
>>
>>
>> # PATH needs CR
>> # Avoid depending upon Character Ranges.
>> as_cr_letters='\''abcdefghijklmnopqrstuvwxyz'\''
>> as_cr_LETTERS='\''ABCDEFGHIJKLMNOPQRSTUVWXYZ'\''
>> as_cr_Letters=$as_cr_letters$as_cr_LETTERS
>> as_cr_digits='\''0123456789'\''
>> as_cr_alnum=$as_cr_Letters$as_cr_digits
>>
>> # The user is always right.
>> if test "${PATH_SEPARATOR+set}" != set; then
>>   echo "#! /bin/sh" >conf$$.sh
>>   echo  "exit 0"   >>conf$$.sh
>>   chmod +x conf$$.sh
>>   if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
>>     PATH_SEPARATOR='\'';'\''
>>   else'
>> echo_testing_string='#! /bin/sh
>> # From configure.in Id: configure.in 14063 2007-08-09 20:51:55Z
>> mcgreevy .
>> # Guess values for system-dependent variables and create Makefiles.
>> # Generated by GNU Autoconf 2.61 for HDF5 1.6.6.
>> #
>> # Report bugs to <help at hdfgroup.org>.
>> #
>> # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
>> # 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
>> # This configure script is free software; the Free Software
>> Foundation
>> # gives unlimited permission to copy, distribute and modify it.
>> ## --------------------- ##
>> ## M4sh Initialization.  ##
>> ## --------------------- ##
>>
>> # Be more Bourne compatible
>> DUALCASE=1; export DUALCASE # for MKS sh
>> if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
>>   emulate sh
>>   NULLCMD=:
>>   # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
>>   # is contrary to our usage.  Disable this feature.
>>   alias -g '\''${1+"$@"}'\''='\''"$@"'\''
>>   setopt NO_GLOB_SUBST
>> else
>>   case `(set -o) 2>/dev/null` in
>>   *posix*) set -o posix ;;
>> esac
>>
>> fi
>>
>>
>>
>>
>> # PATH needs CR
>> # Avoid depending upon Character Ranges.
>> as_cr_letters='\''abcdefghijklmnopqrstuvwxyz'\''
>> as_cr_LETTERS='\''ABCDEFGHIJKLMNOPQRSTUVWXYZ'\''
>> as_cr_Letters=$as_cr_letters$as_cr_LETTERS
>> as_cr_digits='\''0123456789'\''
>> as_cr_alnum=$as_cr_Letters$as_cr_digits
>>
>> # The user is always right.
>> if test "${PATH_SEPARATOR+set}" != set; then
>>   echo "#! /bin/sh" >conf$$.sh
>>   echo  "exit 0"   >>conf$$.sh
>>   chmod +x conf$$.sh
>>   if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
>>     PATH_SEPARATOR='\'';'\''
>>   else'
>> enable_shared=no
>> exec_prefix=NONE
>> host=x86_64-unknown-linux-gnu
>> host_cpu=x86_64
>> host_os=linux-gnu
>> host_vendor=unknown
>> htmldir='${docdir}'
>> includedir='${prefix}/include'
>> infodir='${datarootdir}/info'
>> libdir='${exec_prefix}/lib'
>> libexecdir='${exec_prefix}/libexec'
>> localedir='${datarootdir}/locale'
>> localstatedir='${prefix}/var'
>> mandir='${datarootdir}/man'
>> no_create=
>> no_recursion=
>> oldincludedir=/usr/include
>> pdfdir='${docdir}'
>> prefix=/usr/local
>> program_prefix=NONE
>> program_suffix=NONE
>> program_transform_name=s,x,x,
>> psdir='${docdir}'
>> sbindir='${exec_prefix}/sbin'
>> sharedstatedir='${prefix}/com'
>> silent=
>> site=
>> srcdir=.
>> subdirs=
>> sysconfdir='${prefix}/etc'
>> target=
>> verbose=
>> with_build_path=/usr/local
>> x_includes=NONE
>> x_libraries=NONE
>> configure:2122: result: done
>> configure:2127: checking if basename works
>> configure:2135: result: yes
>> configure:2139: checking if xargs works
>> configure:2147: result: yes
>> configure:2151: checking for cached host
>> configure:2158: result: none
>> configure:2200: checking for sizeof hsize_t and hssize_t
>> configure:2203: result: large
>> configure:2224: checking for config x86_64-unknown-linux-gnu
>> configure:2232: result: no
>> configure:2224: checking for config x86_64-unknown-linux-gnu
>> configure:2232: result: no
>> configure:2224: checking for config unknown-linux-gnu
>> configure:2232: result: no
>> configure:2224: checking for config unknown-linux-gnu
>> configure:2232: result: no
>> configure:2224: checking for config x86_64-linux-gnu
>> configure:2232: result: no
>> configure:2224: checking for config x86_64-linux-gnu
>> configure:2232: result: no
>> configure:2224: checking for config x86_64-unknown
>> configure:2232: result: no
>> configure:2224: checking for config linux-gnu
>> configure:2228: result: found
>> configure:2243: checking for config
>> ./config/site-specific/host-localhost.localdomain
>> configure:2251: result: no
>> configure:2243: checking for config
>> ./config/site-specific/host-localdomain
>> configure:2251: result: no
>> configure:2306: checking for gcc
>> configure:2333: result: gcc
>> configure:2571: checking for C compiler version
>> configure:2578: gcc --version >&5
>> gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8)
>> Copyright (C) 2008 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There
>> is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>>
>> configure:2581: $? = 0
>> configure:2588: gcc -v >&5
>> Using built-in specs.
>> Target: x86_64-redhat-linux
>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
>> --infodir=/usr/share/info
>> --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
>> --enable-shared --enable-threads=posix --enable-checking=release
>> --with-system-zlib --enable-__cxa_atexit
>> --disable-libunwind-exceptions
>> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
>> --enable-java-awt=gtk --disable-dssi --enable-plugin
>> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
>> --enable-libgcj-multifile --enable-java-maintainer-mode
>> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar
>> --disable-libjava-multilib --with-cpu=generic
>> --build=x86_64-redhat-linux
>> Thread model: posix
>> gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC) 
>> configure:2591: $? = 0
>> configure:2598: gcc -V >&5
>> gcc: '-V' option must have argument
>> configure:2601: $? = 1
>> configure:2624: checking for C compiler default output file name
>> configure:2651: gcc ${CFLAGS} -fpic  -ansi ${CPPFLAGS} -fpic 
>> conftest.c  >&5
>> gcc: ${CFLAGS}: No such file or directory
>> gcc: ${CPPFLAGS}: No such file or directory
>> configure:2654: $? = 1
>> configure:2692: result: 
>> configure: failed program was:
>> | /* confdefs.h.  */
>> | #define PACKAGE_NAME "HDF5"
>> | #define PACKAGE_TARNAME "hdf5"
>> | #define PACKAGE_VERSION "1.6.6"
>> | #define PACKAGE_STRING "HDF5 1.6.6"
>> | #define PACKAGE_BUGREPORT "help at hdfgroup.org"
>> | #define HAVE_LARGE_HSIZET 1
>> | /* end confdefs.h.  */
>> | 
>> | int
>> | main ()
>> | {
>> | 
>> |   ;
>> |   return 0;
>> | }
>> configure:2699: error: C compiler cannot create executables
>> See `config.log' for more details.
>>
>> ## ---------------- ##
>> ## Cache variables. ##
>> ## ---------------- ##
>>
>> ac_cv_build=x86_64-unknown-linux-gnu
>> ac_cv_env_CC_set=
>> ac_cv_env_CC_value=
>> ac_cv_env_CFLAGS_set=set
>> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
>> ac_cv_env_CPPFLAGS_set=set
>> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
>> ac_cv_env_CPP_set=
>> ac_cv_env_CPP_value=
>> ac_cv_env_LDFLAGS_set=
>> ac_cv_env_LDFLAGS_value=
>> ac_cv_env_LIBS_set=
>> ac_cv_env_LIBS_value=
>> ac_cv_env_build_alias_set=
>> ac_cv_env_build_alias_value=
>> ac_cv_env_host_alias_set=
>> ac_cv_env_host_alias_value=
>> ac_cv_env_target_alias_set=
>> ac_cv_env_target_alias_value=
>> ac_cv_host=x86_64-unknown-linux-gnu
>> ac_cv_prog_ac_ct_CC=gcc
>> hdf5_cv_host=x86_64-unknown-linux-gnu
>>
>> ## ----------------- ##
>> ## Output variables. ##
>> ## ----------------- ##
>>
>> AR=''
>> BUILD_PARALLEL_CONDITIONAL_FALSE=''
>> BUILD_PARALLEL_CONDITIONAL_TRUE=''
>> BYTESEX=''
>> CC='gcc'
>> CC_VERSION=''
>> CFLAGS='${CFLAGS} -fpic  -ansi'
>> CLEARFILEBUF=''
>> CONFIG_DATE=''
>> CONFIG_MODE=''
>> CONFIG_USER=''
>> CPP=''
>> CPPFLAGS='${CPPFLAGS} -fpic'
>> DEBUG_PKG=''
>> DEFAULT_LIBS=''
>> DEFS=''
>> DYNAMIC_DIRS=''
>> ECHO='echo'
>> ECHO_C=''
>> ECHO_N='-n'
>> ECHO_T=''
>> EGREP=''
>> EXEEXT=''
>> FILTERS=''
>> GASS=''
>> GREP=''
>> H5_CFLAGS=''
>> H5_CPPFLAGS=''
>> H5_VERSION=''
>> HL=''
>> HSIZET='large'
>> INSTALL_DATA=''
>> INSTALL_PROGRAM=''
>> INSTALL_SCRIPT=''
>> INSTRUMENT_LIBRARY=''
>> LDFLAGS=''
>> LIBOBJS=''
>> LIBS=''
>> LIBTOOL=''
>> LN_S=''
>> LTLIBOBJS=''
>> LT_STATIC_EXEC=''
>> MPE=''
>> MPI_GET_SIZE=''
>> OBJEXT=''
>> PACKAGE_BUGREPORT='help at hdfgroup.org'
>> PACKAGE_NAME='HDF5'
>> PACKAGE_STRING='HDF5 1.6.6'
>> PACKAGE_TARNAME='hdf5'
>> PACKAGE_VERSION='1.6.6'
>> PARALLEL=''
>> PATH_SEPARATOR=':'
>> PERL=''
>> PTHREAD=''
>> RANLIB=''
>> ROOT=''
>> RUNPARALLEL=''
>> RUNSERIAL=''
>> SEARCH=''
>> SETX=''
>> SET_MAKE=''
>> SHELL='/bin/sh'
>> SRB=''
>> SSL=''
>> STATIC_SHARED=''
>> STRIP=''
>> TESTGASS=''
>> TESTPARALLEL=''
>> TESTSRB=''
>> TRACE_API=''
>> USE_FILTER_DEFLATE=''
>> USE_FILTER_FLETCHER32=''
>> USE_FILTER_SHUFFLE=''
>> USE_FILTER_SZIP=''
>> ac_ct_CC='gcc'
>> bindir='${exec_prefix}/bin'
>> build='x86_64-unknown-linux-gnu'
>> build_alias=''
>> build_cpu='x86_64'
>> build_os='linux-gnu'
>> build_vendor='unknown'
>> config_dirs=''
>> datadir='${datarootdir}'
>> datarootdir='${prefix}/share'
>> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
>> dvidir='${docdir}'
>> exec_prefix='NONE'
>> host='x86_64-unknown-linux-gnu'
>> host_alias=''
>> host_cpu='x86_64'
>> host_os='linux-gnu'
>> host_vendor='unknown'
>> htmldir='${docdir}'
>> includedir='${prefix}/include'
>> infodir='${datarootdir}/info'
>> libdir='${exec_prefix}/lib'
>> libexecdir='${exec_prefix}/libexec'
>> localedir='${datarootdir}/locale'
>> localstatedir='${prefix}/var'
>> mandir='${datarootdir}/man'
>> oldincludedir='/usr/include'
>> pdfdir='${docdir}'
>> prefix='/usr/local'
>> program_transform_name='s,x,x,'
>> psdir='${docdir}'
>> sbindir='${exec_prefix}/sbin'
>> sharedstatedir='${prefix}/com'
>> subdirs=''
>> sysconfdir='${prefix}/etc'
>> target_alias=''
>>
>> ## ------------------- ##
>> ## File substitutions. ##
>> ## ------------------- ##
>>
>> COMMENCE=''
>> CONCLUDE=''
>> DEPEND=''
>>
>> ## ----------- ##
>> ## confdefs.h. ##
>> ## ----------- ##
>>
>> #define PACKAGE_NAME "HDF5"
>> #define PACKAGE_TARNAME "hdf5"
>> #define PACKAGE_VERSION "1.6.6"
>> #define PACKAGE_STRING "HDF5 1.6.6"
>> #define PACKAGE_BUGREPORT "help at hdfgroup.org"
>> #define HAVE_LARGE_HSIZET 1
>>
>> configure: exit 77
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>     
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   




From claude at bic.mni.mcgill.ca  Sun Apr  5 08:50:15 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Sun, 5 Apr 2009 08:50:15 -0400
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D89DBD.8060802@ulg.ac.be>
Message-ID: <200904051250.n35CoFmu018769@grumio.bic.mni.mcgill.ca>

Hi,

> Thank you very much for your suggestions, configure passes now without 
> error but make check gave the following error:
> Is it important that make check passes all tests?

I would ignore it at the moment. I never run these tests. Let's
see if minc works.

> Which version of netcdf should I install? and should I use the same 
> options for configuration?

netcdf-3.6.1 will work for you. You should stay away from 4.X.
Same config will work.

I recently compiled minc (also hdf5 and netcdf) with gcc 4.3.2
on CYGWIN so this should work for you with gcc 4.3. However, 
bicpl fails, if ever you intend to install this library... until
I fix it.

bye

Claude


From a.janke at gmail.com  Sun Apr  5 08:58:25 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 5 Apr 2009 22:58:25 +1000
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <200904051250.n35CoFmu018769@grumio.bic.mni.mcgill.ca>
References: <49D89DBD.8060802@ulg.ac.be>
	<200904051250.n35CoFmu018769@grumio.bic.mni.mcgill.ca>
Message-ID: <d747ed50904050558q6f76a15drd7fbe25d266d0b5d@mail.gmail.com>

>> Thank you very much for your suggestions, configure passes now without
>> error but make check gave the following error:
>> Is it important that make check passes all tests?
>
> I would ignore it at the moment. I never run these tests. Let's
> see if minc works.

FWIW I have had make check fail with netcdf also. As Claude says
though, MINC will often still build and work fine.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From a.janke at gmail.com  Sun Apr  5 09:47:27 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 5 Apr 2009 23:47:27 +1000
Subject: [MINC-users] Classify
In-Reply-To: <5587D58B-3469-439C-AE69-C89E003305AB@klaru-baycrest.on.ca>
References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca> 
	<A01ACA50-D5BB-43D6-ADA6-1AAF961F09A2@bic.mni.mcgill.ca>
	<3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca> 
	<d747ed50904010445g49cc595bie0729947b06ec9fb@mail.gmail.com> 
	<5587D58B-3469-439C-AE69-C89E003305AB@klaru-baycrest.on.ca>
Message-ID: <d747ed50904050647x65a7c462sb7e012fab9489d7@mail.gmail.com>

Hi Jon,

> 1) How to optimize the classification so the grey matter is more
> representative of that seen visually on the 3DT1 (particularly the
> cortical ribbon)?

To get a better classification I think the first thing you are going
to have to do is to remove more of the inhomogeneity in the GM/WM
signal. classify expects the input data to have similar intensities
for all the WM and GM voxels. Have these images been run through N3?

> 3) Saving the tagfile in "Display" gives you a bit different format
> (which classify doesn't like) ?compared to the tagfile in ../mni/share/
> classify/ntags_1000_bg.tag
>
> Display "save labels .tag": ?-82 -109 108 1 1 1
> /mni/share/classify/ntags_1000_bg.tag: ?-82 -109 108 "1"
>
> Am I using the wrong function here?

No, I have always just mashed the files about to suit with a text
editor. The tags from display are more about saving a list of 3D
points rather than for use with classify.

> 4) Once I get a classified volume (and I have flair lesion and 3DT1
> lesion in separate masks) how do I calculate volumes? I can't seem to
> find the functions that do this, though suspect they are in minmath or
> minccalc somewhere.

Close.

   mincstats -count -mask_binvalue <x>

Is probably what you want.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


From m.bahri at ulg.ac.be  Sun Apr  5 10:03:43 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Sun, 05 Apr 2009 16:03:43 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <200904051250.n35CoFmu018769@grumio.bic.mni.mcgill.ca>
References: <200904051250.n35CoFmu018769@grumio.bic.mni.mcgill.ca>
Message-ID: <49D8BA3F.30306@ulg.ac.be>

Hi Claude,

with netcdf-3.6.1 configure passes without error but make generate errors.

1) ./configure --disable-shared --prefix=/usr/local 
--with-build-path=/usr/local CFLAGS="${CFLAGS} -fpic" 
CPPFLAGS="${CPPFLAGS} -fpic" CXXFLAGS="${CXXFLAGS} -fpic"

ok

2) make

make[2]: entrant dans le r?pertoire ? /usr/local/netcdf-3.6.1/src/cxx ?
c++ -c -fpic -I../libsrc -I. -I.. -fpic netcdf.cpp
c++ -c -fpic -I../libsrc -I. -I.. -fpic ncvalues.cpp
ncvalues.cpp: In member function ?virtual char* 
NcValues_ncbyte::as_string(long int) const?:
ncvalues.cpp:236: erreur: ?strncpy? was not declared in this scope
ncvalues.cpp: In member function ?virtual char* 
NcValues_char::as_string(long int) const?:
ncvalues.cpp:244: erreur: ?strncpy? was not declared in this scope
make[2]: *** [ncvalues.o] Erreur 1
make[2]: quittant le r?pertoire ? /usr/local/netcdf-3.6.1/src/cxx ?
make[1]: *** [subdir_target] Erreur 1
make[1]: quittant le r?pertoire ? /usr/local/netcdf-3.6.1/src ?
make: *** [cxx/all] Erreur 2

mohamed

Claude LEPAGE a ?crit :
> Hi,
>
>   
>> Thank you very much for your suggestions, configure passes now without 
>> error but make check gave the following error:
>> Is it important that make check passes all tests?
>>     
>
> I would ignore it at the moment. I never run these tests. Let's
> see if minc works.
>
>   
>> Which version of netcdf should I install? and should I use the same 
>> options for configuration?
>>     
>
> netcdf-3.6.1 will work for you. You should stay away from 4.X.
> Same config will work.
>
> I recently compiled minc (also hdf5 and netcdf) with gcc 4.3.2
> on CYGWIN so this should work for you with gcc 4.3. However, 
> bicpl fails, if ever you intend to install this library... until
> I fix it.
>
> bye
>
> Claude
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From claude at bic.mni.mcgill.ca  Sun Apr  5 10:36:45 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Sun, 5 Apr 2009 10:36:45 -0400
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D8BA3F.30306@ulg.ac.be>
Message-ID: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>

Hi,

> with netcdf-3.6.1 configure passes without error but make generate errors.
>
> 1) ./configure --disable-shared --prefix=/usr/local 
> --with-build-path=/usr/local CFLAGS="${CFLAGS} -fpic" 
> CPPFLAGS="${CPPFLAGS} -fpic" CXXFLAGS="${CXXFLAGS} -fpic"

Sorry, my mistake. I was too lazy to check my config line.

./configure --prefix=/usr/local --without-F90 ${CFG_COMP_FLAGS} F90=false FC=false CXX=false CC=gcc

replace CFG_COMP_FLAGS by the above string with CFLAGS, etc.

This build will be sufficient for minc.

Claude

From jween at klaru-baycrest.on.ca  Sun Apr  5 13:29:51 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Sun,  5 Apr 2009 13:29:51 -0400
Subject: [MINC-users] Classify
In-Reply-To: <d747ed50904050647x65a7c462sb7e012fab9489d7@mail.gmail.com>
References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca>
	<A01ACA50-D5BB-43D6-ADA6-1AAF961F09A2@bic.mni.mcgill.ca>
	<3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca>
	<d747ed50904010445g49cc595bie0729947b06ec9fb@mail.gmail.com>
	<5587D58B-3469-439C-AE69-C89E003305AB@klaru-baycrest.on.ca>
	<d747ed50904050647x65a7c462sb7e012fab9489d7@mail.gmail.com>
Message-ID: <1238952591.49d8ea8f2980d@cortex.rotman-baycrest.on.ca>

Thanks Andrew see below:

Quoting Andrew Janke <a.janke at gmail.com>:

> > 1) How to optimize the classification so the grey matter is more
> > representative of that seen visually on the 3DT1 (particularly the
> > cortical ribbon)?
>
> To get a better classification I think the first thing you are going
> to have to do is to remove more of the inhomogeneity in the GM/WM
> signal. classify expects the input data to have similar intensities
> for all the WM and GM voxels. Have these images been run through N3?

The steps I used was:

1) nu_correct on the whole 3DT1 volume
2) mincbet -m to generate an initial brain mask
3) Re-run nu_correct on the masked native volume
4) Re-run mincbet -m for an optimized mask
5) subtract the masked subvolume (from 4) from the volume in step 3.

Just running minmask on the output from step 3 gave me a lot of white matter
holes for some reason.

> > 3) Saving the tagfile in "Display" gives you a bit different format
> > (which classify doesn't like) ?compared to the tagfile in ../mni/share/
> > classify/ntags_1000_bg.tag
> >
> > Display "save labels .tag": ?-82 -109 108 1 1 1
> > /mni/share/classify/ntags_1000_bg.tag: ?-82 -109 108 "1"
> >
> > Am I using the wrong function here?
>
> No, I have always just mashed the files about to suit with a text
> editor. The tags from display are more about saving a list of 3D
> points rather than for use with classify.

OK, thanks.

> > 4) Once I get a classified volume (and I have flair lesion and 3DT1
> > lesion in separate masks) how do I calculate volumes? I can't seem to
> > find the functions that do this, though suspect they are in minmath or
> > minccalc somewhere.
>
> Close.
>
>    mincstats -count -mask_binvalue <x>
>
> Is probably what you want.
>
Thanks. I'm supposing I can use this on the masks and the classified volumes
(mincbet mask for total brain volume, flair-mask for hyperintensities, T1 mask
for holes, classified volume for grey, whie and CSF)?

Cheers

Jon


From m.bahri at ulg.ac.be  Mon Apr  6 04:19:26 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Mon, 06 Apr 2009 10:19:26 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
Message-ID: <49D9BB0E.3040601@ulg.ac.be>

Hi Claude,

Thanks a lot for your help. Netcdf is now installed without any error. I 
installed minc-2.0.16 using the following command lines
./configure --prefix=/usr/local --with-build-path=/usr/local --enable-minc2
make & make install.
it install well without error only with make check I had the following 
errors which are probably caused by optimization
======================================
1 of 17 tests failed
Please report to a.janke at gmail.com
==================================
make[3]: *** [check-TESTS] Erreur 1
make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
make[2]: *** [check-am] Erreur 2
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
make[1]: *** [check-recursive] Erreur 1
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2 ?
make: *** [check-recursive] Erreur 1
========================================

After, I tried to install N3-1.10 package but unfortunately configure 
command did not fined minc library.
--------------------
checking for library minc... no
configure: error: cannot find required library minc
------------------------------------
The command line that I use for configuration is : 
./configure --prefix=/usr/local --with-build-path=/usr/local 
--with-minc2=/usr/local

Does the command line that I use for configure step is correct?

Mohamed




Claude LEPAGE a ?crit :
> Hi,
>
>   
>> with netcdf-3.6.1 configure passes without error but make generate errors.
>>
>> 1) ./configure --disable-shared --prefix=/usr/local 
>> --with-build-path=/usr/local CFLAGS="${CFLAGS} -fpic" 
>> CPPFLAGS="${CPPFLAGS} -fpic" CXXFLAGS="${CXXFLAGS} -fpic"
>>     
>
> Sorry, my mistake. I was too lazy to check my config line.
>
> ./configure --prefix=/usr/local --without-F90 ${CFG_COMP_FLAGS} F90=false FC=false CXX=false CC=gcc
>
> replace CFG_COMP_FLAGS by the above string with CFLAGS, etc.
>
> This build will be sufficient for minc.
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From a.janke at gmail.com  Mon Apr  6 04:46:28 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 6 Apr 2009 18:46:28 +1000
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D9BB0E.3040601@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca> 
	<49D9BB0E.3040601@ulg.ac.be>
Message-ID: <d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>

Hi Mohamed,

> it install well without error only with make check I had the following
> errors which are probably caused by optimization
> ======================================
> 1 of 17 tests failed
> Please report to a.janke at gmail.com
> ==================================
> make[3]: *** [check-TESTS] Erreur 1
> make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
> make[2]: *** [check-am] Erreur 2
> make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
> make[1]: *** [check-recursive] Erreur 1
> make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2 ?
> make: *** [check-recursive] Erreur 1
> ========================================

The above does not give enough information, what was the output above
the 1 of 17 tests failed line?

> After, I tried to install N3-1.10 package but unfortunately configure
> command did not fined minc library.
> --------------------
> checking for library minc... no
> configure: error: cannot find required library minc
> ------------------------------------
> The command line that I use for configuration is :
> ./configure --prefix=/usr/local --with-build-path=/usr/local
> --with-minc2=/usr/local

You will want:

   ./configure --prefix=/usr/local --with-build-path=/usr/local --with-minc2

I take it you did run "make install" after "make check"? Perhaps have
a look here:

   http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall

--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


From m.bahri at ulg.ac.be  Mon Apr  6 05:54:30 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Mon, 06 Apr 2009 11:54:30 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
Message-ID: <49D9D156.7020709@ulg.ac.be>


Hi Andrew,

Here are all what I obtain after make check.
--------------------------------------------------------------------------------------------------------------------------
[root at localhost minc-2.0.16]# make check
Making check in .
make[1]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16 ?
make[1]: Rien ? faire pour ? check-am ?.
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16 ?
Making check in volume_io
make[1]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/volume_io ?
Making check in Documentation
make[2]: entrant dans le r?pertoire ? 
/usr/local/minc-2.0.16/volume_io/Documentation ?
make[2]: Rien ? faire pour ? check ?.
make[2]: quittant le r?pertoire ? 
/usr/local/minc-2.0.16/volume_io/Documentation ?
Making check in Testing
make[2]: entrant dans le r?pertoire ? 
/usr/local/minc-2.0.16/volume_io/Testing ?
make  test-xfm
make[3]: entrant dans le r?pertoire ? 
/usr/local/minc-2.0.16/volume_io/Testing ?
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc -I../../volume_io/Include 
-I../../volume_io/Include -I../../progs/Proglib  -I/usr/local/include  
-g -O2 -MT test-xfm.o -MD -MP -MF .deps/test-xfm.Tpo -c -o test-xfm.o 
test-xfm.c
mv -f .deps/test-xfm.Tpo .deps/test-xfm.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc  -g -O2  
-L/usr/local/lib -o test-xfm test-xfm.o ../../libvolume_io2.la 
../../libminc2.la -lhdf5 -lz -lnetcdf -lm
gcc -g -O2 -o test-xfm test-xfm.o  -L/usr/local/lib 
../../.libs/libvolume_io2.a ../../.libs/libminc2.a 
/usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/volume_io/Testing ?
make  check-TESTS
make[3]: entrant dans le r?pertoire ? 
/usr/local/minc-2.0.16/volume_io/Testing ?
Setting tolerance to 0.900000.
PASS: check_xfm.sh
==================
All 1 tests passed
==================
make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/volume_io/Testing ?
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/volume_io/Testing ?
make[2]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/volume_io ?
make[2]: Rien ? faire pour ? check-am ?.
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/volume_io ?
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/volume_io ?
Making check in testdir
make[1]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/testdir ?
cd . && chmod +x run_tests.sh run_test2.sh xfmconcat_01.sh xfmconcat_02.sh
make  minc test_mconv minc_types icv icv_range icv_dim test_speed 
icv_dim1 icv_fillvalue test_xfm create_grid_xfm mincapi test_speed
make[2]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/testdir ?
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT minc.o -MD -MP 
-MF .deps/minc.Tpo -c -o minc.o minc.c
mv -f .deps/minc.Tpo .deps/minc.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o minc minc.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz -lnetcdf -lm
mkdir .libs
gcc -g -O2 -o minc minc.o  -L/usr/local/lib ../.libs/libvolume_io2.a 
../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT test_mconv.o 
-MD -MP -MF .deps/test_mconv.Tpo -c -o test_mconv.o test_mconv.c
mv -f .deps/test_mconv.Tpo .deps/test_mconv.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o test_mconv test_mconv.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o test_mconv test_mconv.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT minc_types.o 
-MD -MP -MF .deps/minc_types.Tpo -c -o minc_types.o minc_types.c
mv -f .deps/minc_types.Tpo .deps/minc_types.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o minc_types minc_types.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o minc_types minc_types.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT icv.o -MD -MP 
-MF .deps/icv.Tpo -c -o icv.o icv.c
mv -f .deps/icv.Tpo .deps/icv.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o icv icv.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz -lnetcdf -lm
gcc -g -O2 -o icv icv.o  -L/usr/local/lib ../.libs/libvolume_io2.a 
../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT icv_range.o -MD 
-MP -MF .deps/icv_range.Tpo -c -o icv_range.o icv_range.c
mv -f .deps/icv_range.Tpo .deps/icv_range.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o icv_range icv_range.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o icv_range icv_range.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT icv_dim.o -MD 
-MP -MF .deps/icv_dim.Tpo -c -o icv_dim.o icv_dim.c
mv -f .deps/icv_dim.Tpo .deps/icv_dim.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o icv_dim icv_dim.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o icv_dim icv_dim.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT test_speed.o 
-MD -MP -MF .deps/test_speed.Tpo -c -o test_speed.o test_speed.c
mv -f .deps/test_speed.Tpo .deps/test_speed.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o test_speed test_speed.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o test_speed test_speed.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT icv_dim1.o -MD 
-MP -MF .deps/icv_dim1.Tpo -c -o icv_dim1.o icv_dim1.c
mv -f .deps/icv_dim1.Tpo .deps/icv_dim1.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o icv_dim1 icv_dim1.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o icv_dim1 icv_dim1.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT icv_fillvalue.o 
-MD -MP -MF .deps/icv_fillvalue.Tpo -c -o icv_fillvalue.o icv_fillvalue.c
mv -f .deps/icv_fillvalue.Tpo .deps/icv_fillvalue.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o icv_fillvalue icv_fillvalue.o ../libvolume_io2.la ../libminc2.la 
-lhdf5 -lz -lnetcdf -lm
gcc -g -O2 -o icv_fillvalue icv_fillvalue.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT test_xfm.o -MD 
-MP -MF .deps/test_xfm.Tpo -c -o test_xfm.o test_xfm.c
mv -f .deps/test_xfm.Tpo .deps/test_xfm.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o test_xfm test_xfm.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o test_xfm test_xfm.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT 
create_grid_xfm.o -MD -MP -MF .deps/create_grid_xfm.Tpo -c -o 
create_grid_xfm.o create_grid_xfm.c
mv -f .deps/create_grid_xfm.Tpo .deps/create_grid_xfm.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o create_grid_xfm create_grid_xfm.o ../libvolume_io2.la ../libminc2.la 
-lhdf5 -lz -lnetcdf -lm
gcc -g -O2 -o create_grid_xfm create_grid_xfm.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -I../volume_io/Include 
-I../volume_io/Include  -I/usr/local/include  -g -O2 -MT mincapi.o -MD 
-MP -MF .deps/mincapi.Tpo -c -o mincapi.o mincapi.c
mv -f .deps/mincapi.Tpo .deps/mincapi.Po
/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib 
-o mincapi mincapi.o ../libvolume_io2.la ../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -g -O2 -o mincapi mincapi.o  -L/usr/local/lib 
../.libs/libvolume_io2.a ../.libs/libminc2.a /usr/local/lib/libhdf5.a 
-lz -lnetcdf -lm 
make[2]: ? test_speed ? est ? jour.
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/testdir ?
make  check-TESTS
make[2]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/testdir ?
Testing minc_types
Testing icv_range
Testing icv
Testing icv_dim
Testing icv_dim1
Testing icv_fillvalue
PASS: run_tests.sh
Testing minc_types
Testing icv_range
Testing icv
Testing icv_dim
Testing icv_dim1
Testing icv_fillvalue
PASS: run_test2.sh
PASS: xfmconcat_01.sh
PASS: xfmconcat_02.sh
**** Tests completed with no errors
PASS: mincapi
==================
All 5 tests passed
==================
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/testdir ?
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/testdir ?
Making check in doc
make[1]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/doc ?
make[1]: Rien ? faire pour ? check ?.
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/doc ?
Making check in libsrc2
make[1]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/libsrc2 ?
Making check in test
make[2]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
cd . && chmod +x testminctools.sh
make  create-test-images create-test-images-2 datatype-test 
dimension-test full-test grpattr-test hyper-test hyper-test-2 label-test 
record-test slice-test valid-test volprops-test multires-test 
convert-test vector_dimension-test
make[3]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT create-test-images.o -MD -MP -MF 
.deps/create-test-images.Tpo -c -o create-test-images.o create-test-images.c
mv -f .deps/create-test-images.Tpo .deps/create-test-images.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o create-test-images create-test-images.o 
../../libminc2.la -lhdf5 -lz -lnetcdf -lm
mkdir .libs
gcc -DAPPARENTORDER -g -O2 -o create-test-images create-test-images.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT create-test-images-2.o -MD -MP -MF 
.deps/create-test-images-2.Tpo -c -o create-test-images-2.o 
create-test-images-2.c
mv -f .deps/create-test-images-2.Tpo .deps/create-test-images-2.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o create-test-images-2 create-test-images-2.o 
../../libminc2.la -lhdf5 -lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o create-test-images-2 
create-test-images-2.o  -L/usr/local/lib ../../.libs/libminc2.a 
/usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT datatype-test.o -MD -MP -MF 
.deps/datatype-test.Tpo -c -o datatype-test.o datatype-test.c
mv -f .deps/datatype-test.Tpo .deps/datatype-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o datatype-test datatype-test.o ../../libminc2.la 
-lhdf5 -lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o datatype-test datatype-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT dimension-test.o -MD -MP -MF 
.deps/dimension-test.Tpo -c -o dimension-test.o dimension-test.c
mv -f .deps/dimension-test.Tpo .deps/dimension-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o dimension-test dimension-test.o ../../libminc2.la 
-lhdf5 -lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o dimension-test dimension-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT full-test.o -MD -MP -MF .deps/full-test.Tpo 
-c -o full-test.o full-test.c
mv -f .deps/full-test.Tpo .deps/full-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o full-test full-test.o ../../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o full-test full-test.o  -L/usr/local/lib 
../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT grpattr-test.o -MD -MP -MF 
.deps/grpattr-test.Tpo -c -o grpattr-test.o grpattr-test.c
mv -f .deps/grpattr-test.Tpo .deps/grpattr-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o grpattr-test grpattr-test.o ../../libminc2.la -lhdf5 
-lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o grpattr-test grpattr-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT hyper-test.o -MD -MP -MF .deps/hyper-test.Tpo 
-c -o hyper-test.o hyper-test.c
mv -f .deps/hyper-test.Tpo .deps/hyper-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o hyper-test hyper-test.o ../../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o hyper-test hyper-test.o  -L/usr/local/lib 
../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT hyper-test-2.o -MD -MP -MF 
.deps/hyper-test-2.Tpo -c -o hyper-test-2.o hyper-test-2.c
mv -f .deps/hyper-test-2.Tpo .deps/hyper-test-2.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o hyper-test-2 hyper-test-2.o ../../libminc2.la -lhdf5 
-lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o hyper-test-2 hyper-test-2.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT label-test.o -MD -MP -MF .deps/label-test.Tpo 
-c -o label-test.o label-test.c
mv -f .deps/label-test.Tpo .deps/label-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o label-test label-test.o ../../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o label-test label-test.o  -L/usr/local/lib 
../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT record-test.o -MD -MP -MF 
.deps/record-test.Tpo -c -o record-test.o record-test.c
mv -f .deps/record-test.Tpo .deps/record-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o record-test record-test.o ../../libminc2.la -lhdf5 
-lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o record-test record-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT slice-test.o -MD -MP -MF .deps/slice-test.Tpo 
-c -o slice-test.o slice-test.c
mv -f .deps/slice-test.Tpo .deps/slice-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o slice-test slice-test.o ../../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o slice-test slice-test.o  -L/usr/local/lib 
../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT valid-test.o -MD -MP -MF .deps/valid-test.Tpo 
-c -o valid-test.o valid-test.c
mv -f .deps/valid-test.Tpo .deps/valid-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o valid-test valid-test.o ../../libminc2.la -lhdf5 -lz 
-lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o valid-test valid-test.o  -L/usr/local/lib 
../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT volprops-test.o -MD -MP -MF 
.deps/volprops-test.Tpo -c -o volprops-test.o volprops-test.c
mv -f .deps/volprops-test.Tpo .deps/volprops-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o volprops-test volprops-test.o ../../libminc2.la 
-lhdf5 -lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o volprops-test volprops-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT multires-test.o -MD -MP -MF 
.deps/multires-test.Tpo -c -o multires-test.o multires-test.c
mv -f .deps/multires-test.Tpo .deps/multires-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o multires-test multires-test.o ../../libminc2.la 
-lhdf5 -lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o multires-test multires-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT convert-test.o -MD -MP -MF 
.deps/convert-test.Tpo -c -o convert-test.o convert-test.c
mv -f .deps/convert-test.Tpo .deps/convert-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o convert-test convert-test.o ../../libminc2.la -lhdf5 
-lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o convert-test convert-test.o  
-L/usr/local/lib ../../.libs/libminc2.a /usr/local/lib/libhdf5.a -lz 
-lnetcdf -lm 
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc2  -I/usr/local/include 
-DAPPARENTORDER -g -O2 -MT vector_dimension-test.o -MD -MP -MF 
.deps/vector_dimension-test.Tpo -c -o vector_dimension-test.o 
vector_dimension-test.c
mv -f .deps/vector_dimension-test.Tpo .deps/vector_dimension-test.Po
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DAPPARENTORDER -g -O2  
-L/usr/local/lib -o vector_dimension-test vector_dimension-test.o 
../../libminc2.la -lhdf5 -lz -lnetcdf -lm
gcc -DAPPARENTORDER -g -O2 -o vector_dimension-test 
vector_dimension-test.o  -L/usr/local/lib ../../.libs/libminc2.a 
/usr/local/lib/libhdf5.a -lz -lnetcdf -lm 
make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
make  check-TESTS
make[3]: entrant dans le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
Creating 2D image with IRREGULAR sample dimension!! (2D_image.mnc)
Creating 3D image with slice scaling!! (3D_image.mnc)
Creating 4D image with slice scaling!! (4D_image.mnc)

 No errors
PASS: create-test-images
Creating 3D image REAL stored as INT w/ slice scaling!! 
(real_as_int_image.mnc)
Creating 3D image REAL stored as FLOAT w/ slice scaling!! 
(real_as_float_image.mnc)

 No errors
PASS: create-test-images-2
PASS: datatype-test
No errors
PASS: dimension-test
No errors
PASS: full-test
 /test1/stuff objtype
 /test1/stuff objname
 /test2 maxvals
 /test3 objtype
*****************
/test1
/test1/otherstuff
/test1/stuff
/test1/stuff/helloleila
/test1/theotherstuff
/test1/theotherstuff/thisstuff
/test2
/test2/stuff2
/test3
/test4
No errors
PASS: grpattr-test
miget_real_value_hyperslab()
miget_voxel_value_hyperslab, default dimensions
miget_voxel_value_hyperslab(), swapped dimensions
miget_voxel_hyperslab, reversed Z axis
Read 3x2x2 matrices of voxel values:
miget_hyperslab_normalized()
read and write entire hyperslab:
Read and verify hyperslab in original dimension order:
No errors
PASS: hyper-test
Creating image with slice scaling!!
Opening hyperslab-test2.mnc!
Sizes: 210, 245, 142

Getting a real value hyperslab
Starting at 4, 3, 5
Extending to 120, 180, 110

Test arbitrary location 70, 100, 104
Test from hyperslab: 9.519348
Test from voxel scaled: 9.519348
Test voxel value itself: 634.000000

HMMMMMMMMMM! let's try something else

Test arbitrary location 104, 100, 70
Test from hyperslab: 6.105524
Test from voxel scaled: 6.105524
Test voxel value itself: 181.000000

 No errors
PASS: hyper-test-2
Creating label image !!
 0
 6
Number of defined labels 6
Print label file with file order x,y,z
       0   ffffff   808080   ff0000     ff00       ff 
       0   ffffff   808080   ff0000     ff00       ff 
       0   ffffff   808080   ff0000     ff00       ff 
       0   ffffff   808080   ff0000     ff00       ff 
Print label file with apparent order z,y,x
       0   808080     ff00   808080     ff00        0 
    ff00        0   808080        0   808080     ff00 
  ffffff   ff0000       ff   ff0000       ff   ffffff 
      ff   ffffff   ff0000   ffffff   ff0000       ff 
No errors
PASS: label-test
No errors
PASS: record-test
PASS: slice-test
PASS: valid-test
Multiresolution enabled: 1 depth: 2
Set compression type to 0
Got compression type 0
Set zlib level to 4
Got zlib level 4
No errors
PASS: volprops-test
Creating volume...
Writing data...
Selecting half-size image
Selecting quarter-size image
Return to full resolution.
Flush any remaining thumbnails.
No errors
PASS: multires-test
No errors
PASS: convert-test
 
Opening vector-dimension file!
 
Total number of dimensions : 4
Dimension Size in file order :  41  410  530  3 
Dim class RECORD present check dim name for *vector_dimension*
Let's get the first 10 data values of each vector component (file order)
 FILE ORDER --> zspace, yspace, xspace, vector_dimension
Vector Componenet 1
 0  3  6  9  12  15  18  21  24  27 
Vector Componenet 2
 1  4  7  10  13  16  19  22  25  28 
Vector Componenet 3
 2  5  8  11  14  17  20  23  26  29 
APPARENT ORDER --> vector_dimension, zspace, yspace, xspace
APPARENT ORDER SET
Vector Componenet 1
 0  3  6  9  12  15  18  21  24  27 
Vector Componenet 2
 1  4  7  10  13  16  19  22  25  28 
Vector Componenet 3
 2  5  8  11  14  17  20  23  26  29 
No errors
PASS: vector_dimension-test
Abort: Converting Version 1 (netCDF) to itself!!
FAIL: testminctools.sh
==================================
1 of 17 tests failed
Please report to a.janke at gmail.com
==================================
make[3]: *** [check-TESTS] Erreur 1
make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
make[2]: *** [check-am] Erreur 2
make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
make[1]: *** [check-recursive] Erreur 1
make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2 ?
make: *** [check-recursive] Erreur 1
[root at localhost minc-2.0.16]#
----------------------------------------------------------------------------------------------------------------------------------------------------

Even with these make check error I did make install and then tried to 
install N3-1.10 package but the configure of the N3 did not fined minc.

Here is the config.log of minc (attached file)

Thanks

Mohamed




Andrew Janke a ?crit :
> Hi Mohamed,
>
>   
>> it install well without error only with make check I had the following
>> errors which are probably caused by optimization
>> ======================================
>> 1 of 17 tests failed
>> Please report to a.janke at gmail.com
>> ==================================
>> make[3]: *** [check-TESTS] Erreur 1
>> make[3]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
>> make[2]: *** [check-am] Erreur 2
>> make[2]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2/test ?
>> make[1]: *** [check-recursive] Erreur 1
>> make[1]: quittant le r?pertoire ? /usr/local/minc-2.0.16/libsrc2 ?
>> make: *** [check-recursive] Erreur 1
>> ========================================
>>     
>
> The above does not give enough information, what was the output above
> the 1 of 17 tests failed line?
>
>   
>> After, I tried to install N3-1.10 package but unfortunately configure
>> command did not fined minc library.
>> --------------------
>> checking for library minc... no
>> configure: error: cannot find required library minc
>> ------------------------------------
>> The command line that I use for configuration is :
>> ./configure --prefix=/usr/local --with-build-path=/usr/local
>> --with-minc2=/usr/local
>>     
>
> You will want:
>
>    ./configure --prefix=/usr/local --with-build-path=/usr/local --with-minc2
>
> I take it you did run "make install" after "make check"? Perhaps have
> a look here:
>
>    http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From a.janke at gmail.com  Mon Apr  6 06:11:57 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 6 Apr 2009 20:11:57 +1000
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D9D156.7020709@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca> 
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com> 
	<49D9D156.7020709@ulg.ac.be>
Message-ID: <d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com>

2009/4/6 mohamed Ali Bahri <m.bahri at ulg.ac.be>:
> FAIL: testminctools.sh

Interesting, if you cd to the minc directory (where you built it) and run this:

   cd libsrc2/test
   ./testminctools.sh

What do you get?

> Here is the config.log of minc (attached file)

Sorry, the list doesn't allow attachments. Can you chop the pertinent
bit out of the config.log and post it?


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From m.bahri at ulg.ac.be  Mon Apr  6 08:36:01 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Mon, 06 Apr 2009 14:36:01 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be>
	<d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com>
Message-ID: <49D9F731.5000003@ulg.ac.be>

Andrew Janke a ?crit :
> Interesting, if you cd to the minc directory (where you built it) and run this:
>
>    cd libsrc2/test
>    ./testminctools.sh
>
> What do you get?
>   
[root at localhost test]# ./testminctools.sh
Abort: Converting Version 1 (netCDF) to itself!!
[root at localhost test]#
>> Here is the config.log of minc (attached file)
>>     
>
> Sorry, the list doesn't allow attachments. Can you chop the pertinent
> bit out of the config.log and post it?
>   
 $ ./configure --with-build-path=/usr/local --prefix=/usr/local 
--enable-minc2

## --------- ##
## Platform. ##
## --------- ##

hostname = localhost.localdomain
uname -m = x86_64
uname -r = 2.6.27.21-78.2.41.fc9.x86_64
uname -s = Linux
uname -v = #1 SMP Mon Mar 23 23:22:15 EDT 2009

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown
## ----------- ##
## Core tests. ##
## ----------- ##
.
.
.
configure:2002: checking for a BSD-compatible install
configure:2058: result: /usr/local/bin/install -c
configure:2069: checking whether build environment is sane
configure:2112: result: yes
configure:2140: checking for a thread-safe mkdir -p
configure:2179: result: /usr/local/bin/mkdir -p
configure:2192: checking for gawk
configure:2208: found /usr/bin/gawk
configure:2219: result: gawk
configure:2230: checking whether make sets $(MAKE)
configure:2251: result: yes
configure:2457: checking for a BSD-compatible install
configure:2513: result: /usr/local/bin/install -c
configure:2524: checking whether ln -s works
configure:2528: result: yes
configure:2535: checking whether make sets $(MAKE)
configure:2556: result: yes
configure:2578: checking for style of include used by make
configure:2606: result: GNU
configure:2676: checking for gcc
configure:2692: found /usr/lib64/ccache/gcc
configure:2703: result: gcc
configure:2941: checking for C compiler version
configure:2948: gcc --version >&5
gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8)
Copyright (C) 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
.
.
.
configure:7427: checking the maximum length of command line arguments
configure:7539: result: 1966080
configure:7551: checking command to parse /usr/bin/nm -B output from gcc 
object
configure:7656: g++ -c -g -O2  conftest.cpp >&5
configure:7659: $? = 0
configure:7663: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[     
]\([ABCDGIRSTW][ABCDGIRSTW]*\)[     ][     
]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:7666: $? = 0
configure:7718: g++ -o conftest -g -O2   conftest.cpp conftstm.o >&5
configure:7721: $? = 0
configure:7759: result: ok
configure:7763: checking for objdir
configure:7778: result: .libs
configure:7870: checking for ar
configure:7886: found /usr/bin/ar
configure:7897: result: ar
configure:7966: checking for ranlib
configure:7993: result: ranlib
configure:8062: checking for strip
configure:8078: found /usr/bin/strip
configure:8089: result: strip
configure:8687: checking if gcc supports -fno-rtti -fno-exceptions
configure:8705: gcc -c -g -O2  -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ 
but not for C
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ 
but not for C
configure:8709: $? = 0
configure:8722: result: no
configure:8737: checking for gcc option to produce PIC
configure:8969: result: -fPIC
configure:8977: checking if gcc PIC flag -fPIC works
configure:8995: gcc -c -g -O2  -fPIC -DPIC conftest.c >&5
configure:8999: $? = 0
configure:9012: result: yes
configure:9040: checking if gcc static flag -static works
configure:9068: result: yes
configure:9078: checking if gcc supports -c -o file.o
configure:9099: gcc -c -g -O2  -o out/conftest2.o conftest.c >&5
configure:9103: $? = 0
configure:9125: result: yes
configure:9151: checking whether the gcc linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:10132: result: yes
configure:10199: checking dynamic linker characteristics
configure:10813: result: GNU/Linux ld.so
configure:10837: checking how to hardcode library paths into programs
configure:10862: result: immediate
configure:10876: checking whether stripping libraries is possible
configure:10881: result: yes
configure:11683: checking if libtool supports shared libraries
configure:11685: result: yes
configure:11688: checking whether to build shared libraries
configure:11709: result: no
configure:11712: checking whether to build static libraries
configure:11716: result: yes
configure:11810: creating libtool
configure:12403: checking for ld used by g++
configure:12470: result: /usr/bin/ld -m elf_x86_64
configure:12479: checking if the linker (/usr/bin/ld -m elf_x86_64) is 
GNU ld
configure:12494: result: yes
configure:12545: checking whether the g++ linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:13491: result: yes
configure:13508: g++ -c -g -O2  conftest.cpp >&5
configure:13511: $? = 0
configure:13667: checking for g++ option to produce PIC
configure:13951: result: -fPIC
configure:13959: checking if g++ PIC flag -fPIC works
configure:13977: g++ -c -g -O2  -fPIC -DPIC conftest.cpp >&5
configure:13981: $? = 0
configure:13994: result: yes
configure:14022: checking if g++ static flag -static works
configure:14050: result: yes
configure:14060: checking if g++ supports -c -o file.o
configure:14081: g++ -c -g -O2  -o out/conftest2.o conftest.cpp >&5
configure:14085: $? = 0
configure:14107: result: yes
configure:14133: checking whether the g++ linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:14162: result: yes
configure:14229: checking dynamic linker characteristics
configure:14791: result: GNU/Linux ld.so
configure:14815: checking how to hardcode library paths into programs
configure:14840: result: immediate
configure:15379: checking if libtool supports shared libraries
configure:15381: result: yes
configure:15384: checking whether to build shared libraries
configure:15404: result: no
configure:15407: checking whether to build static libraries
configure:15411: result: yes
configure:15421: checking for gfortran option to produce PIC
configure:15653: result: -fPIC
configure:15661: checking if gfortran PIC flag -fPIC works
configure:15679: gfortran -c -g -O2 -fPIC conftest.f >&5
configure:15683: $? = 0
configure:15696: result: yes
configure:15724: checking if gfortran static flag -static works
configure:15752: result: yes
configure:15762: checking if gfortran supports -c -o file.o
configure:15783: gfortran -c -g -O2 -o out/conftest2.o conftest.f >&5
configure:15787: $? = 0
configure:15809: result: yes
configure:15835: checking whether the gfortran linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:16796: result: yes
configure:16863: checking dynamic linker characteristics
configure:17425: result: GNU/Linux ld.so
configure:17449: checking how to hardcode library paths into programs
configure:17474: result: immediate
configure:21107: checking for library m
configure:21131: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lm  >&5
configure:21137: $? = 0
configure:21153: result: yes
configure:21162: checking for library netcdf
configure:21186: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lnetcdf -lm  >&5
configure:21192: $? = 0
configure:21208: result: yes
configure:21240: checking for library z
configure:21264: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lz -lnetcdf -lm  >&5
configure:21270: $? = 0
configure:21286: result: yes
configure:21295: checking for library hdf5
configure:21319: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21325: $? = 0
configure:21341: result: yes
configure:21367: checking for strdup
configure:21423: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
conftest.c:58: warning: conflicting types for built-in function 'strdup'
configure:21429: $? = 0
configure:21447: result: yes
configure:21472: checking for mkstemp
configure:21528: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21534: $? = 0
configure:21552: result: yes
configure:21472: checking for tempnam
configure:21528: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
/tmp/ccSJJHHk.o: In function `main':
/usr/local/minc-2.0.16/conftest.c:71: warning: the use of `tempnam' is 
dangerous, better use `mkstemp'
configure:21534: $? = 0
configure:21552: result: yes
configure:21472: checking for tmpnam
configure:21528: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
/tmp/ccQfKCwo.o: In function `main':
/usr/local/minc-2.0.16/conftest.c:72: warning: the use of `tmpnam' is 
dangerous, better use `mkstemp'
configure:21534: $? = 0
configure:21552: result: yes
configure:21570: checking for getpwnam
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21570: checking for select
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21570: checking for strerror
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21570: checking for sysconf
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21662: checking for pid_t
configure:21692: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
configure:21698: $? = 0
configure:21713: result: yes
configure:21740: checking vfork.h usability
configure:21757: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
conftest.c:76:19: error: vfork.h: No such file or directory
configure:21763: $? = 1
configure: failed program was:


From a.janke at gmail.com  Mon Apr  6 08:48:54 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 6 Apr 2009 22:48:54 +1000
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D9F731.5000003@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca> 
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com> 
	<49D9D156.7020709@ulg.ac.be>
	<d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com> 
	<49D9F731.5000003@ulg.ac.be>
Message-ID: <d747ed50904060548m4a598c13m504346c34591445d@mail.gmail.com>

>> What do you get?
>>
> [root at localhost test]# ./testminctools.sh
> Abort: Converting Version 1 (netCDF) to itself!!

Ah, yes this is an error that is now fixed in CVS IIRC.

> ?$ ./configure --with-build-path=/usr/local --prefix=/usr/local
> --enable-minc2
>
> configure:21757: gcc -c -g -O2 ?-I/usr/local/include conftest.c >&5
> conftest.c:76:19: error: vfork.h: No such file or directory

Hrm, this bit doesn't seem right.  What system are you trying to build on?


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


From M.Bahri at ulg.ac.be  Mon Apr  6 09:03:45 2009
From: M.Bahri at ulg.ac.be (Bahri)
Date: Mon, 06 Apr 2009 15:03:45 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <d747ed50904060548m4a598c13m504346c34591445d@mail.gmail.com>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be>	<d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com>
	<49D9F731.5000003@ulg.ac.be>
	<d747ed50904060548m4a598c13m504346c34591445d@mail.gmail.com>
Message-ID: <49D9FDB1.20201@ulg.ac.be>

Andrew Janke a ?crit :
>>> What do you get?
>>>
>>>       
>> [root at localhost test]# ./testminctools.sh
>> Abort: Converting Version 1 (netCDF) to itself!!
>>     
>
> Ah, yes this is an error that is now fixed in CVS IIRC.
>   
I am not expert in informatics could you explain more please?
>   
>>  $ ./configure --with-build-path=/usr/local --prefix=/usr/local
>> --enable-minc2
>>
>> configure:21757: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
>> conftest.c:76:19: error: vfork.h: No such file or directory
>>     
>
> Hrm, this bit doesn't seem right.  What system are you trying to build on?
>   
Linux Fedora 9, 64bit
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From acveilleux at mrs.mni.mcgill.ca  Mon Apr  6 12:04:14 2009
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 6 Apr 2009 12:04:14 -0400
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D9FDB1.20201@ulg.ac.be>;
	from M.Bahri@ulg.ac.be on Mon, Apr 06, 2009 at 03:03:45PM +0200
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be>
	<d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com>
	<49D9F731.5000003@ulg.ac.be>
	<d747ed50904060548m4a598c13m504346c34591445d@mail.gmail.com>
	<49D9FDB1.20201@ulg.ac.be>
Message-ID: <20090406120414.D5031@mrs.mni.mcgill.ca>

	Why is it looking for vfork.h? On fedora (and indeed, most/all
Linux distro) vfork is in unistd.h.

	Incidentally, nowhere does Minc2 use vfork() so I'm not sure why
it's checked for. I guess AC_FUNC_FORK includes a check for it. Finally,
the only fork() call appears to be to work around a bug in NetCDF 2.3.2.

	Failure of a check for vfork.h should not cause a failure however,
from my own config.log:

configure:21101: checking vfork.h usability
configure:21118: gcc -c -O2 -arch x86_64 -m64  conftest.c >&5
conftest.c:75:19: error: vfork.h: No such file or directory
configure:21124: $? = 1

	Later in the same file:

configure:21408: checking for working vfork
configure:21546: result: yes

	So vfork() is unlikely to be related with any problems..

Alex

On Mon, Apr 06, 2009 at 03:03:45PM +0200, Bahri wrote:
> Date: Mon, 06 Apr 2009 15:03:45 +0200
> From: Bahri <M.Bahri at ulg.ac.be>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Minc-2 installation problems
> 
> Andrew Janke a ?crit :
> >>> What do you get?
> >>>
> >>>       
> >> [root at localhost test]# ./testminctools.sh
> >> Abort: Converting Version 1 (netCDF) to itself!!
> >>     
> >
> > Ah, yes this is an error that is now fixed in CVS IIRC.
> >   
> I am not expert in informatics could you explain more please?
> >   
> >>  $ ./configure --with-build-path=/usr/local --prefix=/usr/local
> >> --enable-minc2
> >>
> >> configure:21757: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
> >> conftest.c:76:19: error: vfork.h: No such file or directory
> >>     
> >
> > Hrm, this bit doesn't seem right.  What system are you trying to build on?
> >   
> Linux Fedora 9, 64bit
> >
> > --
> > Andrew Janke
> > (a.janke at gmail.com || http://a.janke.googlepages.com/)
> > Canberra->Australia    +61 (402) 700 883
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >   
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From a.janke at gmail.com  Tue Apr  7 08:40:41 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 7 Apr 2009 22:40:41 +1000
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <49D9FDB1.20201@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca> 
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com> 
	<49D9D156.7020709@ulg.ac.be>
	<d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com> 
	<49D9F731.5000003@ulg.ac.be>
	<d747ed50904060548m4a598c13m504346c34591445d@mail.gmail.com> 
	<49D9FDB1.20201@ulg.ac.be>
Message-ID: <d747ed50904070540t44426e75r4e312e0d49a095e@mail.gmail.com>

>> Ah, yes this is an error that is now fixed in CVS IIRC.
>>
> I am not expert in informatics could you explain more please?

Sorry, the test that has been failing is fixed for the next release.

>>> configure:21757: gcc -c -g -O2 ?-I/usr/local/include conftest.c >&5
>>> conftest.c:76:19: error: vfork.h: No such file or directory
>>
>> Hrm, this bit doesn't seem right. ?What system are you trying to build on?
>>
> Linux Fedora 9, 64bit

As Alexandre says, this is strange. What is in config.log after this line?


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


From m.bahri at ulg.ac.be  Tue Apr  7 12:28:25 2009
From: m.bahri at ulg.ac.be (mohamed Ali Bahri)
Date: Tue, 07 Apr 2009 18:28:25 +0200
Subject: [MINC-users] Minc-2 installation problems
In-Reply-To: <d747ed50904070540t44426e75r4e312e0d49a095e@mail.gmail.com>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be>	<d747ed50904060311l16bf2c4fh3775962a65fcbc22@mail.gmail.com>
	<49D9F731.5000003@ulg.ac.be>	<d747ed50904060548m4a598c13m504346c34591445d@mail.gmail.com>
	<49D9FDB1.20201@ulg.ac.be>
	<d747ed50904070540t44426e75r4e312e0d49a095e@mail.gmail.com>
Message-ID: <49DB7F29.5030103@ulg.ac.be>


>>>> configure:21757: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
>>>> conftest.c:76:19: error: vfork.h: No such file or directory
>>>>         
>>> Hrm, this bit doesn't seem right.  What system are you trying to build on?
>>>
>>>       
>> Linux Fedora 9, 64bit
>>     
>
> As Alexandre says, this is strange. What is in config.log after this line?
>   
Here are:

| #include <ac_nonexistent.h>
configure:7427: checking the maximum length of command line arguments
configure:7539: result: 1966080
configure:7551: checking command to parse /usr/bin/nm -B output from gcc 
object
configure:7656: g++ -c -g -O2  conftest.cpp >&5
configure:7659: $? = 0
configure:7663: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[     
]\([ABCDGIRSTW][ABCDGIRSTW]*\)[     ][     
]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:7666: $? = 0
configure:7718: g++ -o conftest -g -O2   conftest.cpp conftstm.o >&5
configure:7721: $? = 0
configure:7759: result: ok
configure:7763: checking for objdir
configure:7778: result: .libs
configure:7870: checking for ar
configure:7886: found /usr/bin/ar
configure:7897: result: ar
configure:7966: checking for ranlib
configure:7993: result: ranlib
configure:8062: checking for strip
configure:8078: found /usr/bin/strip
configure:8089: result: strip
configure:8687: checking if gcc supports -fno-rtti -fno-exceptions
configure:8705: gcc -c -g -O2  -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ 
but not for C
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ 
but not for C
configure:8709: $? = 0
configure:8722: result: no
configure:8737: checking for gcc option to produce PIC
configure:8969: result: -fPIC
configure:8977: checking if gcc PIC flag -fPIC works
configure:8995: gcc -c -g -O2  -fPIC -DPIC conftest.c >&5
configure:8999: $? = 0
configure:9012: result: yes
configure:9040: checking if gcc static flag -static works
configure:9068: result: yes
configure:9078: checking if gcc supports -c -o file.o
configure:9099: gcc -c -g -O2  -o out/conftest2.o conftest.c >&5
configure:9103: $? = 0
configure:9125: result: yes
configure:9151: checking whether the gcc linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:10132: result: yes
configure:10199: checking dynamic linker characteristics
configure:10813: result: GNU/Linux ld.so
configure:10837: checking how to hardcode library paths into programs
configure:10862: result: immediate
configure:10876: checking whether stripping libraries is possible
configure:10881: result: yes
configure:11683: checking if libtool supports shared libraries
configure:11685: result: yes
configure:11688: checking whether to build shared libraries
configure:11709: result: no
configure:11712: checking whether to build static libraries
configure:11716: result: yes
configure:11810: creating libtool
configure:12403: checking for ld used by g++
configure:12470: result: /usr/bin/ld -m elf_x86_64
configure:12479: checking if the linker (/usr/bin/ld -m elf_x86_64) is 
GNU ld
configure:12494: result: yes
configure:12545: checking whether the g++ linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:13491: result: yes
configure:13508: g++ -c -g -O2  conftest.cpp >&5
configure:13511: $? = 0
configure:13667: checking for g++ option to produce PIC
configure:13951: result: -fPIC
configure:13959: checking if g++ PIC flag -fPIC works
configure:13977: g++ -c -g -O2  -fPIC -DPIC conftest.cpp >&5
configure:13981: $? = 0
configure:13994: result: yes
configure:14022: checking if g++ static flag -static works
configure:14050: result: yes
configure:14060: checking if g++ supports -c -o file.o
configure:14081: g++ -c -g -O2  -o out/conftest2.o conftest.cpp >&5
configure:14085: $? = 0
configure:14107: result: yes
configure:14133: checking whether the g++ linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:14162: result: yes
configure:14229: checking dynamic linker characteristics
configure:14791: result: GNU/Linux ld.so
configure:14815: checking how to hardcode library paths into programs
configure:14840: result: immediate
configure:15379: checking if libtool supports shared libraries
configure:15381: result: yes
configure:15384: checking whether to build shared libraries
configure:15404: result: no
configure:15407: checking whether to build static libraries
configure:15411: result: yes
configure:15421: checking for gfortran option to produce PIC
configure:15653: result: -fPIC
configure:15661: checking if gfortran PIC flag -fPIC works
configure:15679: gfortran -c -g -O2 -fPIC conftest.f >&5
configure:15683: $? = 0
configure:15696: result: yes
configure:15724: checking if gfortran static flag -static works
configure:15752: result: yes
configure:15762: checking if gfortran supports -c -o file.o
configure:15783: gfortran -c -g -O2 -o out/conftest2.o conftest.f >&5
configure:15787: $? = 0
configure:15809: result: yes
configure:15835: checking whether the gfortran linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:16796: result: yes
configure:16863: checking dynamic linker characteristics
configure:17425: result: GNU/Linux ld.so
configure:17449: checking how to hardcode library paths into programs
configure:17474: result: immediate
configure:21107: checking for library m
configure:21131: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lm  >&5
configure:21137: $? = 0
configure:21153: result: yes
configure:21162: checking for library netcdf
configure:21186: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lnetcdf -lm  >&5
configure:21192: $? = 0
configure:21208: result: yes
configure:21240: checking for library z
configure:21264: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lz -lnetcdf -lm  >&5
configure:21270: $? = 0
configure:21286: result: yes
configure:21295: checking for library hdf5
configure:21319: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21325: $? = 0
configure:21341: result: yes
configure:21367: checking for strdup
configure:21423: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
conftest.c:58: warning: conflicting types for built-in function 'strdup'
configure:21429: $? = 0
configure:21447: result: yes
configure:21472: checking for mkstemp
configure:21528: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21534: $? = 0
configure:21552: result: yes
configure:21472: checking for tempnam
configure:21528: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
/tmp/ccSJJHHk.o: In function `main':
/usr/local/minc-2.0.16/conftest.c:71: warning: the use of `tempnam' is 
dangerous, better use `mkstemp'
configure:21534: $? = 0
configure:21552: result: yes
configure:21472: checking for tmpnam
configure:21528: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
/tmp/ccQfKCwo.o: In function `main':
/usr/local/minc-2.0.16/conftest.c:72: warning: the use of `tmpnam' is 
dangerous, better use `mkstemp'
configure:21534: $? = 0
configure:21552: result: yes
configure:21570: checking for getpwnam
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21570: checking for select
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21570: checking for strerror
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21570: checking for sysconf
configure:21626: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21632: $? = 0
configure:21650: result: yes
configure:21662: checking for pid_t
configure:21692: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
configure:21698: $? = 0
configure:21713: result: yes
configure:21740: checking vfork.h usability
configure:21757: gcc -c -g -O2  -I/usr/local/include conftest.c >&5
conftest.c:76:19: error: vfork.h: No such file or directory
configure:21763: $? = 1
configure: failed program was:
...

| #include <vfork.h>
configure:21816: result: no
configure:21849: checking for vfork.h
configure:21857: result: no
configure:21875: checking for fork
configure:21931: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
conftest.c:66: warning: conflicting types for built-in function 'fork'
configure:21937: $? = 0
configure:21955: result: yes
configure:21875: checking for vfork
configure:21931: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:21937: $? = 0
configure:21955: result: yes
configure:21966: checking for working fork
configure:21998: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:22001: $? = 0
configure:22007: ./conftest
configure:22010: $? = 0
configure:22026: result: yes
configure:22047: checking for working vfork
configure:22185: result: yes
configure:22221: checking for system
configure:22277: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:22283: $? = 0
configure:22301: result: yes
configure:22221: checking for popen
configure:22277: gcc -o conftest -g -O2  -I/usr/local/include  
-L/usr/local/lib conftest.c -lhdf5 -lz -lnetcdf -lm  >&5
configure:22283: $? = 0
configure:22301: result: yes
configure:22475: creating ./config.status



From mishkind at gmail.com  Wed Apr  8 14:55:41 2009
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Wed, 8 Apr 2009 14:55:41 -0400
Subject: [MINC-users] object file display problems
Message-ID: <9c5abb60904081155v32cdec6fkfb02d9f0f2e2d705@mail.gmail.com>

Hi,
I'm having some problems displaying a .obj file with a txt file of
values in brain-view.

Data and screenshot are here:
screenshot: http://www.bic.mni.mcgill.ca/users/mishkin/lines.png
obj: http://www.bic.mni.mcgill.ca/users/mishkin/lh.pial.obj.gz (unzip it first)
txt: http://www.bic.mni.mcgill.ca/users/mishkin/lh.output.txt

As you can see I have some unwanted lines in the middle. I'm pretty
sure this is a display problem as I set the value at these vertices to
0.

Claude you helped me once with a similar problem where the txt value
had an extra space at the end of every line, but this isn't the case
this time.

Any ideas?

mishkin

From mishkind at gmail.com  Wed Apr  8 15:11:38 2009
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Wed, 8 Apr 2009 15:11:38 -0400
Subject: [MINC-users] object file display problems
In-Reply-To: <9c5abb60904081155v32cdec6fkfb02d9f0f2e2d705@mail.gmail.com>
References: <9c5abb60904081155v32cdec6fkfb02d9f0f2e2d705@mail.gmail.com>
Message-ID: <9c5abb60904081211h72a0fd27leb888ee1c6870e2@mail.gmail.com>

Hi,
Sent off that email too soon. Seems my vertex indices were off by one.
sorry for the trouble,
mishkin


On Wed, Apr 8, 2009 at 2:55 PM, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Hi,
> I'm having some problems displaying a .obj file with a txt file of
> values in brain-view.
>
> Data and screenshot are here:
> screenshot: http://www.bic.mni.mcgill.ca/users/mishkin/lines.png
> obj: http://www.bic.mni.mcgill.ca/users/mishkin/lh.pial.obj.gz (unzip it first)
> txt: http://www.bic.mni.mcgill.ca/users/mishkin/lh.output.txt
>
> As you can see I have some unwanted lines in the middle. I'm pretty
> sure this is a display problem as I set the value at these vertices to
> 0.
>
> Claude you helped me once with a similar problem where the txt value
> had an extra space at the end of every line, but this isn't the case
> this time.
>
> Any ideas?
>
> mishkin
>

From giovanna_p at hotmail.com  Thu Apr  9 17:03:54 2009
From: giovanna_p at hotmail.com (Giovanna Pellecchia)
Date: Thu, 9 Apr 2009 21:03:54 +0000
Subject: [MINC-users] nii2mnc problems.
Message-ID: <SNT106-W7784986B16487C6E8D5DB9F7830@phx.gbl>


Howdy all,

if I try to use nii2mnc I get this interesting error message:

nii2mnc test_image_00001.hdr
** ERROR: nifti_convert_nhdr2nim: bad dim[0]
** ERROR (nifti_image_read): cannot create nifti image from header 'test_image_00001.hdr'
Segmentation fault
______________________
The same test image works fine on another computer:
nii2mnc test_image_00001.hdr
orient = 0
<nifti_image
  nifti_type = 'ANALYZE-7.5'
  header_filename = 'test_image_00001.hdr'
  image_filename = 'test_image_00001.img'
  image_offset = '0'
  ndim = '4'
  nx = '163'
  ny = '186'
  nz = '72'
  nt = '1'
  dx = '-1.06677'
  dy = '1.06677'
  dz = '1.87482'
  dt = '1'
  datatype = '16'
  datatype_name = 'FLOAT32'
  nvox = '2182896'
  nbyper = '4'
  byteorder = 'MSB_FIRST'
  cal_min = '0'
  cal_max = '1'
  descrip = 'MINC file'
  num_ext = '0'
/>
Unknown XYZ units 0
xspace start:  86.9418 step:  -1.0668 cosines:   1.0000   0.0000   0.0000
yspace start: -99.2096 step:   1.0668 cosines:   0.0000   1.0000   0.0000
zspace start: -67.4934 step:   1.8748 cosines:   0.0000   0.0000   1.0000
(where:
nii2mnc -v
program: 2.0.15
libminc: 2.0.15
netcdf : 3.5.0 of Aug  8 2003 13:03:52 $
HDF5   : 1.6.2 )
(installed from source on Debian Sarge)
____________________

My current version:
nii2mnc -v
program: 2.0.15
libminc: 2.0.15
netcdf : "3.6.2" of May 10 2008 09:14:53 $
HDF5   : 1.6.6
(installed using mincbundle on a recent Ubuntu Intrepid install with all the recommended upgrades).
(I also have an unusual situation, as it turns out that most of the binaries are located in /bin and the libraries in /usr/lib by default - no idea why!)

Hope somebody can point to a solution... 
Thanks!
Giovanna.


_________________________________________________________________
News, entertainment and everything you care about at Live.com. Get it now!
http://www.live.com/getstarted.aspx

From rcomeau at mac.com  Thu Apr  9 22:06:27 2009
From: rcomeau at mac.com (Roch M. Comeau)
Date: Thu, 09 Apr 2009 22:06:27 -0400
Subject: [MINC-users] nii2mnc problems.
In-Reply-To: <SNT106-W7784986B16487C6E8D5DB9F7830@phx.gbl>
References: <SNT106-W7784986B16487C6E8D5DB9F7830@phx.gbl>
Message-ID: <FD161774-F86B-4A8C-BD88-EBCAC36BCD7B@mac.com>

HI,

Maybe have a look at the value of dim[0]. I've seen images where  
dim[0] is incorrectly set to 0 instead of 3 or 4.

Roch Comeau
Rogue Research Inc.

On 9-Apr-09, at 5:03 PM, Giovanna Pellecchia wrote:

>
> Howdy all,
>
> if I try to use nii2mnc I get this interesting error message:
>
> nii2mnc test_image_00001.hdr
> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
> ** ERROR (nifti_image_read): cannot create nifti image from header  
> 'test_image_00001.hdr'
> Segmentation fault
> ______________________
> The same test image works fine on another computer:
> nii2mnc test_image_00001.hdr
> orient = 0
> <nifti_image
>  nifti_type = 'ANALYZE-7.5'
>  header_filename = 'test_image_00001.hdr'
>  image_filename = 'test_image_00001.img'
>  image_offset = '0'
>  ndim = '4'
>  nx = '163'
>  ny = '186'
>  nz = '72'
>  nt = '1'
>  dx = '-1.06677'
>  dy = '1.06677'
>  dz = '1.87482'
>  dt = '1'
>  datatype = '16'
>  datatype_name = 'FLOAT32'
>  nvox = '2182896'
>  nbyper = '4'
>  byteorder = 'MSB_FIRST'
>  cal_min = '0'
>  cal_max = '1'
>  descrip = 'MINC file'
>  num_ext = '0'
> />
> Unknown XYZ units 0
> xspace start:  86.9418 step:  -1.0668 cosines:   1.0000   0.0000    
> 0.0000
> yspace start: -99.2096 step:   1.0668 cosines:   0.0000   1.0000    
> 0.0000
> zspace start: -67.4934 step:   1.8748 cosines:   0.0000   0.0000    
> 1.0000
> (where:
> nii2mnc -v
> program: 2.0.15
> libminc: 2.0.15
> netcdf : 3.5.0 of Aug  8 2003 13:03:52 $
> HDF5   : 1.6.2 )
> (installed from source on Debian Sarge)
> ____________________
>
> My current version:
> nii2mnc -v
> program: 2.0.15
> libminc: 2.0.15
> netcdf : "3.6.2" of May 10 2008 09:14:53 $
> HDF5   : 1.6.6
> (installed using mincbundle on a recent Ubuntu Intrepid install with  
> all the recommended upgrades).
> (I also have an unusual situation, as it turns out that most of the  
> binaries are located in /bin and the libraries in /usr/lib by  
> default - no idea why!)
>
> Hope somebody can point to a solution...
> Thanks!
> Giovanna.
>
>
> _________________________________________________________________
> News, entertainment and everything you care about at Live.com. Get  
> it now!
> http://www.live.com/getstarted.aspx
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From vikingy at gmail.com  Sat Apr 11 07:29:44 2009
From: vikingy at gmail.com (vikingy)
Date: Sat, 11 Apr 2009 19:29:44 +0800
Subject: [MINC-users] Classify with the high resolution data
Message-ID: <200904111929425468400@gmail.com>

Dear all,

I have some high resolution data (such as 0.6x0.6x0.6) acquired from 7T scanner, and want to perform the segmentation with Classify in minc. It seems that Classify uses the 1x1x1 template. My question is that, would they have to be downsampled to 1x1x1 for use or not? Does the high resolution improve the performance of segmentation? 

Thanks in advance!

Bin Lv
2009-04-11 



The Key Lab of Complex Systems and Intelligence Science,
Institute of Automation,
Chinese Academy of Sciences. 

From raznahana at mail.nih.gov  Sat Apr 11 10:49:04 2009
From: raznahana at mail.nih.gov (Raznahan, Armin (NIH/NIMH) [V])
Date: Sat, 11 Apr 2009 10:49:04 -0400
Subject: [MINC-users] FW: CIVET Lobar Estimates of Surface Area,
	Thickness and Volume
References: <C5FA4642.B3C%raznahana@mail.nih.gov>
Message-ID: <BBF6CAD6146E924984CE6A2DD1B5F4FA21DB51@NIHCESMLBX15.nih.gov>




-----Original Message-----
From: Raznahan, Armin (NIH/NIMH) [V]
Sent: Thu 4/2/2009 10:38 AM
To: minc-users at bic.mni.mcgill.ca
Subject: CIVET Lobar Estimates of Surface Area, Thickness and Volume
 
Dear All

I am a CIVET newbie and have a quick question about the above that I hoped
the group may be able to help with.

How are lobar estimates of total surface area (SA), mean thickness (CT) and
total cortical volume (CV) generated? I have extracted these from the .dat
files in the segment sub-folder of the output.

I cannot find a reference for methodology and validation of automated
surface-based parcellation within CIVET. I am assuming lobar estimates are
derived from those of smaller sub-lobar regions. With regards to SA  - is
this SA of the white/gray surface of the gray/pial?

Many thanks in advance for any info you can provide about this

Best

Armin

---------------------------

Armin Raznahan
Visiting Fellow
Child Psychiatry Branch, NIMH
NIH, Bethesda, MD, USA 




From a.janke at gmail.com  Sat Apr 11 21:40:30 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 12 Apr 2009 11:40:30 +1000
Subject: [MINC-users] Classify with the high resolution data
In-Reply-To: <200904111929425468400@gmail.com>
References: <200904111929425468400@gmail.com>
Message-ID: <d747ed50904111840v34221e1cu57392fa6b9c2c857@mail.gmail.com>

2009/4/11 vikingy <vikingy at gmail.com>:
> I have some high resolution data (such as 0.6x0.6x0.6) acquired from 7T scanner, and want to perform the segmentation with Classify in minc. It seems that Classify uses the 1x1x1 template. My question is that, would they have to be downsampled to 1x1x1 for use or not? Does the high resolution improve the performance of segmentation?

Hi Bin,

No they will not have to be downsampled. The high res should make the
segmentation "better" but only because there will be less partial
voluming effects with smaller voxels. Classify uses an intensity based
approach so as far as classify is concerned the number of voxesl to
classify is irrelevant.


Andrew Janke


From vikingy at gmail.com  Sat Apr 11 22:43:21 2009
From: vikingy at gmail.com (vikingy)
Date: Sun, 12 Apr 2009 10:43:21 +0800
Subject: [MINC-users] Classify with the high resolution data
References: <200904111929425468400@gmail.com>
Message-ID: <200904121043182965997@gmail.com>

Thank you , Andrew,

In this way, if I input the high resolution data into the CIVET to measure cortical thickness, it will enhance the precision of results in theory? Am I right?

Bin Lv


2009-04-12 



The Key Lab of Complex Systems and Intelligence Science,
Institute of Automation,
Chinese Academy of Sciences. 



???? Andrew Janke 
????? 2009-04-12  09:42:56 
???? MINC users mailing list 
??? 
??? Re: [MINC-users] Classify with the high resolution data 
 
2009/4/11 vikingy <vikingy at gmail.com>:
> I have some high resolution data (such as 0.6x0.6x0.6) acquired from 7T scanner, and want to perform the segmentation with Classify in minc. It seems that Classify uses the 1x1x1 template. My question is that, would they have to be downsampled to 1x1x1 for use or not? Does the high resolution improve the performance of segmentation?
Hi Bin,
No they will not have to be downsampled. The high res should make the
segmentation "better" but only because there will be less partial
voluming effects with smaller voxels. Classify uses an intensity based
approach so as far as classify is concerned the number of voxesl to
classify is irrelevant.
Andrew Janke
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From a.janke at gmail.com  Sun Apr 12 21:29:18 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 13 Apr 2009 11:29:18 +1000
Subject: [MINC-users] Classify with the high resolution data
In-Reply-To: <200904121043182965997@gmail.com>
References: <200904111929425468400@gmail.com> <200904121043182965997@gmail.com>
Message-ID: <d747ed50904121829y6df34a9fj36ebbbcea1a12b0d@mail.gmail.com>

2009/4/12 vikingy <vikingy at gmail.com>:
> In this way, if I input the high resolution data into the CIVET to measure cortical thickness, it will enhance the precision of results in theory? Am I right?

Sure. Again the increase in precision will be due to the decrease in
partial volume effects that will allow a surface extraction technique
to work with greater precision.


a

From jween at klaru-baycrest.on.ca  Mon Apr 13 09:27:59 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Mon, 13 Apr 2009 09:27:59 -0400
Subject: [MINC-users] Classify
In-Reply-To: <d747ed50904050647x65a7c462sb7e012fab9489d7@mail.gmail.com>
References: <200903261410.n2QEATDP028660@grumio.bic.mni.mcgill.ca>
	<A01ACA50-D5BB-43D6-ADA6-1AAF961F09A2@bic.mni.mcgill.ca>
	<3B76FBAC-57FF-45EA-8A16-4507E2C42690@klaru-baycrest.on.ca>
	<d747ed50904010445g49cc595bie0729947b06ec9fb@mail.gmail.com>
	<5587D58B-3469-439C-AE69-C89E003305AB@klaru-baycrest.on.ca>
	<d747ed50904050647x65a7c462sb7e012fab9489d7@mail.gmail.com>
Message-ID: <BC23FCFD-63ED-4595-B992-B094B44BC4CA@klaru-baycrest.on.ca>

Andrew,

So I guess what I need to do is review the intensity histograms of my  
scans and review the results before and after nu_correct so that voxel  
intensities wind up in narrower bins (with a trimodal distribution)?  
I'm not seeing how one plots the histogram output from mincstats  
(maybe you use another program or that?) nor how to tweak nu-correct  
to optimize the normalization? My pipeline is as follows;

1) an initial run with nu-correct on whole head
2) an initial run with mincbet for a rough mask
3) a cleaner run with nu_correct using the mask from step#2, though I  
don't see any parameters to set to optimize this step.
4) a second mincbet step on the volume from step 3 for an optimal  
mask, subtract the non-masked areas from the original volume for step  
#5 (the brain from minbet leaves a lot o whitematter holes in  
infarcted brain, so mincmath -sub gives better results.)
5) A third nu_correct run on the skull-stripped brain from step #4

Thanks for any suggestions.

Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.



On 5-Apr-09, at 9:47 AM, Andrew Janke wrote:

> Hi Jon,
>
>> 1) How to optimize the classification so the grey matter is more
>> representative of that seen visually on the 3DT1 (particularly the
>> cortical ribbon)?
>
> To get a better classification I think the first thing you are going
> to have to do is to remove more of the inhomogeneity in the GM/WM
> signal. classify expects the input data to have similar intensities
> for all the WM and GM voxels. Have these images been run through N3?
>
>> 3) Saving the tagfile in "Display" gives you a bit different format
>> (which classify doesn't like)  compared to the tagfile in ../mni/ 
>> share/
>> classify/ntags_1000_bg.tag
>>
>> Display "save labels .tag":  -82 -109 108 1 1 1
>> /mni/share/classify/ntags_1000_bg.tag:  -82 -109 108 "1"
>>
>> Am I using the wrong function here?
>
> No, I have always just mashed the files about to suit with a text
> editor. The tags from display are more about saving a list of 3D
> points rather than for use with classify.
>
>> 4) Once I get a classified volume (and I have flair lesion and 3DT1
>> lesion in separate masks) how do I calculate volumes? I can't seem to
>> find the functions that do this, though suspect they are in minmath  
>> or
>> minccalc somewhere.
>
> Close.
>
>   mincstats -count -mask_binvalue <x>
>
> Is probably what you want.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From giovanna_p at hotmail.com  Tue Apr 14 16:38:02 2009
From: giovanna_p at hotmail.com (Giovanna Pellecchia)
Date: Tue, 14 Apr 2009 20:38:02 +0000
Subject: [MINC-users] nii2mnc problems.
In-Reply-To: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>
References: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>
Message-ID: <SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>


Thanks for your reply. I am new at this, so I am not sure how to check  the value of dim[0]. 
Why would that make a difference from one computer to another?

Giovanna Pellecchia
Research Analyst
Toronto Western Hospital
& Centre for Addiction and Mental Health

> Message: 2
> Date: Thu, 09 Apr 2009 22:06:27 -0400
> From: "Roch M. Comeau" <rcomeau at mac.com>
> Subject: Re: [MINC-users] nii2mnc problems.
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID: <FD161774-F86B-4A8C-BD88-EBCAC36BCD7B at mac.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> HI,
> 
> Maybe have a look at the value of dim[0]. I've seen images where  
> dim[0] is incorrectly set to 0 instead of 3 or 4.
> 
> Roch Comeau
> Rogue Research Inc.
> 
> On 9-Apr-09, at 5:03 PM, Giovanna Pellecchia wrote:
> 
> >
> > Howdy all,
> >
> > if I try to use nii2mnc I get this interesting error message:
> >
> > nii2mnc test_image_00001.hdr
> > ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
> > ** ERROR (nifti_image_read): cannot create nifti image from header  
> > 'test_image_00001.hdr'
> > Segmentation fault
> > ______________________
> > The same test image works fine on another computer:
> > nii2mnc test_image_00001.hdr
> > orient = 0
> > <nifti_image
> >  nifti_type = 'ANALYZE-7.5'
> >  header_filename = 'test_image_00001.hdr'
> >  image_filename = 'test_image_00001.img'
> >  image_offset = '0'
> >  ndim = '4'
> >  nx = '163'
> >  ny = '186'
> >  nz = '72'
> >  nt = '1'
> >  dx = '-1.06677'
> >  dy = '1.06677'
> >  dz = '1.87482'
> >  dt = '1'
> >  datatype = '16'
> >  datatype_name = 'FLOAT32'
> >  nvox = '2182896'
> >  nbyper = '4'
> >  byteorder = 'MSB_FIRST'
> >  cal_min = '0'
> >  cal_max = '1'
> >  descrip = 'MINC file'
> >  num_ext = '0'
> > />
> > Unknown XYZ units 0
> > xspace start:  86.9418 step:  -1.0668 cosines:   1.0000   0.0000    
> > 0.0000
> > yspace start: -99.2096 step:   1.0668 cosines:   0.0000   1.0000    
> > 0.0000
> > zspace start: -67.4934 step:   1.8748 cosines:   0.0000   0.0000    
> > 1.0000
> > (where:
> > nii2mnc -v
> > program: 2.0.15
> > libminc: 2.0.15
> > netcdf : 3.5.0 of Aug  8 2003 13:03:52 $
> > HDF5   : 1.6.2 )
> > (installed from source on Debian Sarge)
> > ____________________
> >
> > My current version:
> > nii2mnc -v
> > program: 2.0.15
> > libminc: 2.0.15
> > netcdf : "3.6.2" of May 10 2008 09:14:53 $
> > HDF5   : 1.6.6
> > (installed using mincbundle on a recent Ubuntu Intrepid install with  
> > all the recommended upgrades).
> > (I also have an unusual situation, as it turns out that most of the  
> > binaries are located in /bin and the libraries in /usr/lib by  
> > default - no idea why!)
> >
> > Hope somebody can point to a solution...
> > Thanks!
> > Giovanna.


_________________________________________________________________
Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy!
http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us

From mishkind at gmail.com  Tue Apr 14 16:59:56 2009
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Tue, 14 Apr 2009 16:59:56 -0400
Subject: [MINC-users] nii2mnc problems.
In-Reply-To: <SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>
References: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>
	<SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>
Message-ID: <9c5abb60904141359s1e138d9x9ef8f2dcbe842396@mail.gmail.com>

Hi Giocanna,
I'm no expert on nii2mnc, and this may be a long shot, but sometimes
if you email/store the .hdr file on a dos based machine it changes the
format. What are the details of the computer which failed, and the
computer which passed?

If you type:
file test_image_00001.hdr
on both computers it should read "ASCII text"

If it says something like "ASCII text, with CRLF line terminators"
then try this:
dos2unix test_image_00001.hdr

And then try nii2mnc again.

Like I said it is long shot, but it may be the problem.
mishkin




On Tue, Apr 14, 2009 at 4:38 PM, Giovanna Pellecchia
<giovanna_p at hotmail.com> wrote:
>
> Thanks for your reply. I am new at this, so I am not sure how to check ?the value of dim[0].
> Why would that make a difference from one computer to another?
>
> Giovanna Pellecchia
> Research Analyst
> Toronto Western Hospital
> & Centre for Addiction and Mental Health
>
>> Message: 2
>> Date: Thu, 09 Apr 2009 22:06:27 -0400
>> From: "Roch M. Comeau" <rcomeau at mac.com>
>> Subject: Re: [MINC-users] nii2mnc problems.
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Message-ID: <FD161774-F86B-4A8C-BD88-EBCAC36BCD7B at mac.com>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> HI,
>>
>> Maybe have a look at the value of dim[0]. I've seen images where
>> dim[0] is incorrectly set to 0 instead of 3 or 4.
>>
>> Roch Comeau
>> Rogue Research Inc.
>>
>> On 9-Apr-09, at 5:03 PM, Giovanna Pellecchia wrote:
>>
>> >
>> > Howdy all,
>> >
>> > if I try to use nii2mnc I get this interesting error message:
>> >
>> > nii2mnc test_image_00001.hdr
>> > ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> > ** ERROR (nifti_image_read): cannot create nifti image from header
>> > 'test_image_00001.hdr'
>> > Segmentation fault
>> > ______________________
>> > The same test image works fine on another computer:
>> > nii2mnc test_image_00001.hdr
>> > orient = 0
>> > <nifti_image
>> > ?nifti_type = 'ANALYZE-7.5'
>> > ?header_filename = 'test_image_00001.hdr'
>> > ?image_filename = 'test_image_00001.img'
>> > ?image_offset = '0'
>> > ?ndim = '4'
>> > ?nx = '163'
>> > ?ny = '186'
>> > ?nz = '72'
>> > ?nt = '1'
>> > ?dx = '-1.06677'
>> > ?dy = '1.06677'
>> > ?dz = '1.87482'
>> > ?dt = '1'
>> > ?datatype = '16'
>> > ?datatype_name = 'FLOAT32'
>> > ?nvox = '2182896'
>> > ?nbyper = '4'
>> > ?byteorder = 'MSB_FIRST'
>> > ?cal_min = '0'
>> > ?cal_max = '1'
>> > ?descrip = 'MINC file'
>> > ?num_ext = '0'
>> > />
>> > Unknown XYZ units 0
>> > xspace start: ?86.9418 step: ?-1.0668 cosines: ? 1.0000 ? 0.0000
>> > 0.0000
>> > yspace start: -99.2096 step: ? 1.0668 cosines: ? 0.0000 ? 1.0000
>> > 0.0000
>> > zspace start: -67.4934 step: ? 1.8748 cosines: ? 0.0000 ? 0.0000
>> > 1.0000
>> > (where:
>> > nii2mnc -v
>> > program: 2.0.15
>> > libminc: 2.0.15
>> > netcdf : 3.5.0 of Aug ?8 2003 13:03:52 $
>> > HDF5 ? : 1.6.2 )
>> > (installed from source on Debian Sarge)
>> > ____________________
>> >
>> > My current version:
>> > nii2mnc -v
>> > program: 2.0.15
>> > libminc: 2.0.15
>> > netcdf : "3.6.2" of May 10 2008 09:14:53 $
>> > HDF5 ? : 1.6.6
>> > (installed using mincbundle on a recent Ubuntu Intrepid install with
>> > all the recommended upgrades).
>> > (I also have an unusual situation, as it turns out that most of the
>> > binaries are located in /bin and the libraries in /usr/lib by
>> > default - no idea why!)
>> >
>> > Hope somebody can point to a solution...
>> > Thanks!
>> > Giovanna.
>
>
> _________________________________________________________________
> Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy!
> http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From jween at klaru-baycrest.on.ca  Wed Apr 15 19:24:17 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 15 Apr 2009 19:24:17 -0400
Subject: [MINC-users] mincbet
In-Reply-To: <9c5abb60904141359s1e138d9x9ef8f2dcbe842396@mail.gmail.com>
References: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>
	<SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>
	<9c5abb60904141359s1e138d9x9ef8f2dcbe842396@mail.gmail.com>
Message-ID: <CC92D297-DF92-47C9-BF2F-C64730C121F8@klaru-baycrest.on.ca>

Hi there

Would anybody know why volumes from the same scanner would yield  
vastly different mincbet results? On several scans, I wind up with  
only half the brain masked. I've tried with and without nu_correct  
first, though mincbet on the nu_corrected file often results in seg  
faults. Is there any way to compare the image files to see why and how  
they are different (I'm not sure what the critical parameters might  
be). Any suggestions would be appreciated.

Thanks

Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.

From vladimir.fonov at gmail.com  Wed Apr 15 20:07:52 2009
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Wed, 15 Apr 2009 20:07:52 -0400
Subject: [MINC-users] mincbet
In-Reply-To: <CC92D297-DF92-47C9-BF2F-C64730C121F8@klaru-baycrest.on.ca>
References: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>	<SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>	<9c5abb60904141359s1e138d9x9ef8f2dcbe842396@mail.gmail.com>
	<CC92D297-DF92-47C9-BF2F-C64730C121F8@klaru-baycrest.on.ca>
Message-ID: <49E676D8.1090404@gmail.com>

Hello,

Jon Erik Ween wrote:
> Would anybody know why volumes from the same scanner would yield  
> vastly different mincbet results? On several scans, I wind up with  
> only half the brain masked. I've tried with and without nu_correct  
> first, though mincbet on the nu_corrected file often results in seg  
> faults. Is there any way to compare the image files to see why and how  
> they are different (I'm not sure what the critical parameters might  
> be). Any suggestions would be appreciated.
This looks a lot like errors caused by irregular sampling , the easies 
way to check is to do
mincheader your_file.mnc |grep irregular
if you get something - the easies way to fix is just to replace it with 
regular sampling (for example if you happen to have irregular sampling 
in xspace):

minc_modify_header -sinsert 'xspace:spacing=regular__' your_file.mnc

-- 
Best regards,
  Vladimir S. Fonov ~ v.s.fonov <at> ilmarin.info

-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From jween at klaru-baycrest.on.ca  Wed Apr 15 20:39:20 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Wed, 15 Apr 2009 20:39:20 -0400
Subject: [MINC-users] mincbet
In-Reply-To: <49E676D8.1090404@gmail.com>
References: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>	<SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>	<9c5abb60904141359s1e138d9x9ef8f2dcbe842396@mail.gmail.com>
	<CC92D297-DF92-47C9-BF2F-C64730C121F8@klaru-baycrest.on.ca>
	<49E676D8.1090404@gmail.com>
Message-ID: <E6B2BF94-FAB5-4FE8-9747-75CC369BCD1F@klaru-baycrest.on.ca>

Thanks Vladimir

That was an issue, but has been corrected. I get the same problems  
with mincbet whether or not I change the header parameter and/or  
resample the volume with regular -dimsize. Actually, I seem to get  
better results by just changing the header and not reshaping the  
volume, but that's probably not the correct way to go about things. Is  
there another such parameter that might be off? I've tried comparing  
mincheader with a "good" scan, but there are so many differences that  
it's hard to know which are significant.

Thanks for your help.

Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.



On 15-Apr-09, at 8:07 PM, Vladimir S. Fonov wrote:

> Hello,
>
> Jon Erik Ween wrote:
>> Would anybody know why volumes from the same scanner would yield
>> vastly different mincbet results? On several scans, I wind up with
>> only half the brain masked. I've tried with and without nu_correct
>> first, though mincbet on the nu_corrected file often results in seg
>> faults. Is there any way to compare the image files to see why and  
>> how
>> they are different (I'm not sure what the critical parameters might
>> be). Any suggestions would be appreciated.
> This looks a lot like errors caused by irregular sampling , the easies
> way to check is to do
> mincheader your_file.mnc |grep irregular
> if you get something - the easies way to fix is just to replace it  
> with
> regular sampling (for example if you happen to have irregular sampling
> in xspace):
>
> minc_modify_header -sinsert 'xspace:spacing=regular__' your_file.mnc
>
> -- 
> Best regards,
>  Vladimir S. Fonov ~ v.s.fonov <at> ilmarin.info
>
> -- 
> Best regards,
>  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From vladimir.fonov at gmail.com  Wed Apr 15 21:04:51 2009
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Wed, 15 Apr 2009 21:04:51 -0400
Subject: [MINC-users] mincbet
In-Reply-To: <E6B2BF94-FAB5-4FE8-9747-75CC369BCD1F@klaru-baycrest.on.ca>
References: <mailman.5.1239379202.12741.minc-users@bic.mni.mcgill.ca>	<SNT106-W753E020A1D401346A4E5C8F77C0@phx.gbl>	<9c5abb60904141359s1e138d9x9ef8f2dcbe842396@mail.gmail.com>	<CC92D297-DF92-47C9-BF2F-C64730C121F8@klaru-baycrest.on.ca>	<49E676D8.1090404@gmail.com>
	<E6B2BF94-FAB5-4FE8-9747-75CC369BCD1F@klaru-baycrest.on.ca>
Message-ID: <49E68433.9050009@gmail.com>

Hello,

Jon Erik Ween wrote:
> That was an issue, but has been corrected. I get the same problems  
> with mincbet whether or not I change the header parameter and/or  
> resample the volume with regular -dimsize. Actually, I seem to get  
> better results by just changing the header and not reshaping the  
> volume, but that's probably not the correct way to go about things. Is  
> there another such parameter that might be off? I've tried comparing  
> mincheader with a "good" scan, but there are so many differences that  
> it's hard to know which are significant.

You can also try to normalize the whole intensity range after nu_correct 
to something standard, like 0-100. For example you can calculate 99.8th 
percentile with mincstats -pctT 99.8 your_file.mnc and then use it to 
normalize intensities.
-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From claude at bic.mni.mcgill.ca  Thu Apr 16 16:39:01 2009
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Thu, 16 Apr 2009 16:39:01 -0400
Subject: [MINC-users] mincbet
In-Reply-To: <49E68433.9050009@gmail.com>
Message-ID: <200904162039.n3GKd1QN011126@grumio.bic.mni.mcgill.ca>

Hi Jon,

To answer some of your questions in your recent messages...

> I'm not seeing how one plots the histogram output from mincstats 
> (maybe you use another program or that?) nor how to tweak nu-correct 
> to optimize the normalization? 

mincstats -histo t1.txt -bins 1024 t1.mnc
gnuplot
gnuplot> plot "t1.txt" u 1:2 w li
gnuplot> set grid
gnuplot> set xrange [0:400]        (choose suitable upper limit)
gnuplot> replot

You may want to cut off the first line of t1.txt which is a very
high voxel count for background.

> If mincbet fails to converge, does it not generate a mask if you have asked it to?

It will write out the last available mask, which may not be accurate at all.

> Would anybody know why volumes from the same scanner would yield 
> vastly different mincbet results? On several scans, I wind up with 
> only half the brain masked. I've tried with and without nu_correct 
> first, though mincbet on the nu_corrected file often results in seg 
> faults. Is there any way to compare the image files to see why and how 
> they are different (I'm not sure what the critical parameters might 
> be). Any suggestions would be appreciated.

In general, the masks should be similar. I have to admit though that
mincbet is quite sensitive to data at 3 Tesla. Moreover, to obtain
good non-uniformity correction, a good mask is needed. So there is no
easy solution. I have been trying to improve mincbet to remove noise
in the selection of the thresholds. It would be very useful if you 
could provide a pair of scans - one that works and one that fails -
for testing. I could give you a better answer of the problem and
solution. One thing you may want to try is to crop the image to 
remove the neck, something like:
  mincreshape -start 0,0,0 -count 160,180,240  in.mnc out.mnc
This will ensure that mincbet starts with a good centre of mass, which
does not seem to be that easy at 3 Tesla.

Claude



From jween at klaru-baycrest.on.ca  Fri Apr 17 08:47:25 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Fri, 17 Apr 2009 08:47:25 -0400
Subject: [MINC-users] mincbet
In-Reply-To: <200904162039.n3GKd1QN011126@grumio.bic.mni.mcgill.ca>
References: <200904162039.n3GKd1QN011126@grumio.bic.mni.mcgill.ca>
Message-ID: <1239972445.49e87a5dcf3c4@cortex.rotman-baycrest.on.ca>

Thanks Claude

You can find some test scans at:

ftp.rotman-baycrest.on.ca/pub/Jon/testscans.cpgz

subject 14017 skull stripos nicely, 14018 does not. Both are 3T GE acquisitions.
I can't see anything particularly different about their scans. I'll try cropping
out the neck though.

Cheers

Jon

Quoting Claude LEPAGE <claude at bic.mni.mcgill.ca>:

> Hi Jon,
>
> To answer some of your questions in your recent messages...
>
> > I'm not seeing how one plots the histogram output from mincstats
> > (maybe you use another program or that?) nor how to tweak nu-correct
> > to optimize the normalization?
>
> mincstats -histo t1.txt -bins 1024 t1.mnc
> gnuplot
> gnuplot> plot "t1.txt" u 1:2 w li
> gnuplot> set grid
> gnuplot> set xrange [0:400]        (choose suitable upper limit)
> gnuplot> replot
>
> You may want to cut off the first line of t1.txt which is a very
> high voxel count for background.
>
> > If mincbet fails to converge, does it not generate a mask if you have asked
> it to?
>
> It will write out the last available mask, which may not be accurate at all.
>
> > Would anybody know why volumes from the same scanner would yield
> > vastly different mincbet results? On several scans, I wind up with
> > only half the brain masked. I've tried with and without nu_correct
> > first, though mincbet on the nu_corrected file often results in seg
> > faults. Is there any way to compare the image files to see why and how
> > they are different (I'm not sure what the critical parameters might
> > be). Any suggestions would be appreciated.
>
> In general, the masks should be similar. I have to admit though that
> mincbet is quite sensitive to data at 3 Tesla. Moreover, to obtain
> good non-uniformity correction, a good mask is needed. So there is no
> easy solution. I have been trying to improve mincbet to remove noise
> in the selection of the thresholds. It would be very useful if you
> could provide a pair of scans - one that works and one that fails -
> for testing. I could give you a better answer of the problem and
> solution. One thing you may want to try is to crop the image to
> remove the neck, something like:
>   mincreshape -start 0,0,0 -count 160,180,240  in.mnc out.mnc
> This will ensure that mincbet starts with a good centre of mass, which
> does not seem to be that easy at 3 Tesla.
>
> Claude
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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From baghdadi at phenogenomics.ca  Fri Apr 17 14:22:56 2009
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Fri, 17 Apr 2009 14:22:56 -0400
Subject: [MINC-users] [MINC-development] using milist_grp_next
In-Reply-To: <d6e2d6550904170520t21fbee5dvfaeca354c1b3da9d@mail.gmail.com>
References: <d6e2d6550904140542j721c50b1x2dc87418f51d1e@mail.gmail.com>
Message-ID: <1239992577.7085.3.camel@mouse30.phenogenomics.ca>

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From a.janke at gmail.com  Fri Apr 24 02:48:10 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 24 Apr 2009 16:48:10 +1000
Subject: [MINC-users] For the Ubuntu Jaunty crash test dummies.
Message-ID: <d747ed50904232348q8c24012w319c23953ecd53d5@mail.gmail.com>

Hi all,

Here are some packages I just built and am uploading now.

   http://packages.bic.mni.mcgill.ca/ubuntu-jaunty/

Somewhat crash-test dummy stuff but should work fine.  let me know if
they break anything.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From a.janke at gmail.com  Thu Apr 30 00:15:57 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 30 Apr 2009 14:15:57 +1000
Subject: [MINC-users] MINC 2.0.18
Message-ID: <d747ed50904292115g54c8e737vb8809b8011bd51b4@mail.gmail.com>

Is available here:

   http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.18.tar.gz

This is mainly a bug-fix release (stack smashing in mincinfo) and some
work on optimising chunking by Claude LePage. The stack smash was a
show stopper bug for mincinfo on later versions in which stack
smashing is automatically detected. (Ubunty Jaunty for example).

Jaunty packages based upon this will follow soon.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883