From minc-users@bic.mni.mcgill.ca  Mon Mar  1 19:31:06 2004
From: minc-users@bic.mni.mcgill.ca (John G. Sled)
Date: Mon Mar  1 19:31:06 2004
Subject: [MINC-users] nu_estimate missing files
In-Reply-To: <1077490281.403932692c1b3@mail.umich.edu>
References: <1077490281.403932692c1b3@mail.umich.edu>
Message-ID: <20040226155232.GB1451@sickkids.ca>

Dear Maytham,

class_statistics and estimate are old programs that are no longer
needed by N3.  nu_estimate shouldn't ask for them unless it's given
some undocumented options.  Do you have the most recent version of N3?
The latest is N3-1.07, although I understand that 1.08 is due out shortly.

with regards,

John

On Sun, Feb 22, 2004 at 05:51:21PM -0500, haytham@umich.edu wrote:
> When I run nu_estimate in.mnc in_field.imp , i get the following error
> 
> nu_estimate_np_and_em: couldn't find program "class_statistics"
> nu_estimate_np_and_em: couldn't find program "estimate"
> 
> I dot have these files installed nor do I know where to find them. Any ideas?
> 
> Thanks,
> 
> Haytham
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> 

From minc-users@bic.mni.mcgill.ca  Mon Mar  1 19:31:35 2004
From: minc-users@bic.mni.mcgill.ca (Deepa H. Shroff)
Date: Mon Mar  1 19:31:35 2004
Subject: [MINC-users] Reading MINC Files in SPM
Message-ID: <D3F5348B-6B9C-11D8-9A90-000A95773952@pitt.edu>

Hello:

I am using MINC API in my C code to generate a 3D image file.

The data is of type 'double' and size of image data is 64*64*16.

When i try to read the .mnc file in SPM it gives me an error.

I dont know whether SPM cant read MINC files or there is something 
wrong with the way i have generated the MINC files.

I am attaching my code with this email. Any feedback will be very 
helpful.

Thanks a lot.

Deepa

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

C Code to generate MINC file.
-----------------------------------------

  /* create minc file */
                 sprintf(buffer, "./files/f_t%d.mnc",i);
                  int fileid;
                 fileid = nccreate(buffer, NC_CLOBBER);



                 /* create image dimensions */
                 int image_dims = 3;     // X, Y, Z
                 int XSIZE = valResolution;	//64
                 int YSIZE = valResolution;	//64
                 int ZSIZE = valSlices;		//16

                 /* create dimension variable */
                 int dim[MAX_VAR_DIMS];

                 dim[2] = ncdimdef(fileid, MIxspace, XSIZE);
                 dim[1] = ncdimdef(fileid, MIyspace, YSIZE);
                 dim[0] = ncdimdef(fileid, MIzspace, ZSIZE);

                 /* define image varibale */
                 int imgid;

                 imgid = ncvardef(fileid, MIimage, NC_DOUBLE, 
image_dims, dim);

                 /* define max and min for image */
                 int maxid;
                 int minid;

    		maxid = ncvardef(fileid, MIimagemax, NC_DOUBLE, 0, NULL);
                 minid = ncvardef(fileid, MIimagemin, NC_DOUBLE, 0, 
NULL);

                 /* end definition mode */
                 ncendef(fileid);

                 /* writing image max and min */
                 ncvarput1(fileid, maxid, NULL, &max);
                 ncvarput1(fileid, minid, NULL, &min);

                 long count[MAX_VAR_DIMS];
                 long start[MAX_VAR_DIMS];

                 /* last dimension varies fastest. in our data set, X 
changes fastest, followed by Y and then Z */
                 count[2] = XSIZE;	
                 count[1] = YSIZE;
                 count[0] = ZSIZE;

                 start[2] = 0;
                 start[1] = 0;
                 start[0] = 0;

		// vetcor funtionalSlicesArr has image data
                 vector<double> temp(length);
                 int bn = i * length;
                 int en = bn + length;
                 
temp.insert(temp.begin(),functionalSlicesArr.begin()+bn, 
functionalSlicesArr.begin() + en);

                 double imageArr[length];
                 for(int i=0; i < length; i++)
                         imageArr[i] = temp[i];

                 ncvarput(fileid, imgid, start, count, imageArr);

                 ncclose(fileid);


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



From minc-users@bic.mni.mcgill.ca  Tue Mar  2 00:16:05 2004
From: minc-users@bic.mni.mcgill.ca (Andrew Janke)
Date: Tue Mar  2 00:16:05 2004
Subject: [MINC-users] Reading MINC Files in SPM
In-Reply-To: <D3F5348B-6B9C-11D8-9A90-000A95773952@pitt.edu>
References: <D3F5348B-6B9C-11D8-9A90-000A95773952@pitt.edu>
Message-ID: <Pine.SGI.4.53.0403021513490.26117@twodogs.cmr.uq.edu.au>

On Mon, 1 Mar 2004, Deepa H. Shroff wrote:

> I am using MINC API in my C code to generate a 3D image file.
> The data is of type 'double' and size of image data is 64*64*16.
>
> When i try to read the .mnc file in SPM it gives me an error.
> I dont know whether SPM cant read MINC files or there is something
> wrong with the way i have generated the MINC files.

I'm afraid I can't help you much with SPM as the MINC support in it does not use
the MINC API.  However if you have a file you know that SPM works with we should
be able to make a file that closely approximates this.

> I am attaching my code with this email. Any feedback will be very
> helpful.

What do mincinfo and mincstats return from your newly created file?


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581

From minc-users@bic.mni.mcgill.ca  Tue Mar  2 05:38:05 2004
From: minc-users@bic.mni.mcgill.ca (Gibby Koldenhof)
Date: Tue Mar  2 05:38:05 2004
Subject: [MINC-users] minc1.0 and 1.2 available for windows (win32)
Message-ID: <0a5601c40041$c5c85010$0affc30a@quark>

Hi,

I've been porting the minc tool chain and additional programs (Display, register, etc) to win32 the last couple of
years. Although up until some time ago they could be downloaded from the MNI site they can now be found at:

http://sourceforge.net/projects/mni-minc-win32/

The minc 1.0 toolchains + programs is up to build 3.1 and stabelized, the minc 1.2 toolchain is fresh and avalable as
the first (1.0) build. All come in handy user friendly win32 installer packages.

If you are interested in older builds contact me.

Oh yeah, source is of course included.

Cheers,
Gibby Koldenhof


From minc-users@bic.mni.mcgill.ca  Wed Mar  3 16:00:05 2004
From: minc-users@bic.mni.mcgill.ca (Andre MATOS)
Date: Wed Mar  3 16:00:05 2004
Subject: [MINC-users] Register Problem with Mac OS X
Message-ID: <Pine.LNX.4.44.0403031551530.13680-100000@hydra.bic.mni.mcgill.ca>

Hi List,
  
I am running the latest minc package for the Mac OS X 10.3.2, so when I 
run register, if I don't click on the title bar while the register is 
loading the images, it freezes. It freezes also when after loaded the 
images and I want to load a different image.
  
Does anyone have the same problem? Is there any way to go around this?

Thanks.
  
Andre

-- 
Andre Matos
amatos@mrs.mni.mcgill.ca



From minc-users@bic.mni.mcgill.ca  Wed Mar  3 16:24:04 2004
From: minc-users@bic.mni.mcgill.ca (Reza ADALAT)
Date: Wed Mar  3 16:24:04 2004
Subject: [MINC-users] Register Problem with Mac OS X
In-Reply-To: <Pine.LNX.4.44.0403031551530.13680-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0403031613340.3360251-100000@shadow.bic.mni.mcgill.ca>

Hi Andre,
This is a known bug and the work_around is exactly what you do! Jason
is aware of it and here is his posting regarding the latest binary
distributions for OSX 10.3:

rz >>


>>> On Wednesday, January 28, 2004, at 01:34 PM, Jason Lerch wrote:
>>>
>>>> Greetings all and apologies for cross-posting,
>>>>
>>>> I've just uploaded a new release of the OS 10.3 binaries to our
>>>> web-site:
>>>>
>>>> http://www.bic.mni.mcgill.ca/software/distribution/osx.html
>>>>
>>>> The package should solve most outstanding issues, such as the
>>>> broken N3, the lack of support for gzipped files, etc. The Register
>>>> problem is still unresolved, though a workaround has been posted.
>>>>
>>>> The new package contains the following:
>>>>
>>>> This binary distribution contains the following packages:
>>>> NetCDF             3.5.0
>>>> MINC                       1.3 from CVS
>>>> BICPL                      1.4.0-1
>>>> Register           1.3.4
>>>> Display            1.3.8
>>>> Conglomerate       1.3 from CVS with some still uncommitted patches
>>>> mni_autoreg                0.98k
>>>> mni_perllib                0.07
>>>> Getopt-Tabular     0.3
>>>> mni_autoreg_model 1.03
>>>> ray_trace          1.0
>>>> EBTKS              from CVS with still uncommitted patches
>>>> classify           from CVS
>>>> N3                 1.0.6 with ugly compile time hacks
>>>> mincmorph          1.1
>>>> mincblob           1.1
>>>> cortical_surface   1.0 from CVS
>>>> ana2mnc            from CVS
>>>>
>>>> Please let me know of any issues that might arise. The ReadMe file
>>>> should contain all the instructions necessary for using this
>>>> distribution.
>>>>
>>>> Cheers,
>>>>
>>>> Jason


On Wed, 3 Mar 2004, Andre MATOS wrote:

> Hi List,
>
> I am running the latest minc package for the Mac OS X 10.3.2, so when I
> run register, if I don't click on the title bar while the register is
> loading the images, it freezes. It freezes also when after loaded the
> images and I want to load a different image.
>
> Does anyone have the same problem? Is there any way to go around this?
>
> Thanks.
>
> Andre
>
> --
> Andre Matos
> amatos@mrs.mni.mcgill.ca
>
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From minc-users@bic.mni.mcgill.ca  Sun Mar  7 18:00:04 2004
From: minc-users@bic.mni.mcgill.ca (Jeff ATKINSON)
Date: Sun Mar  7 18:00:04 2004
Subject: [MINC-users] emma on OS X
Message-ID: <Pine.SGI.4.44.0403071756160.3584560-100000@shadow.bic.mni.mcgill.ca>

I need some help compiling emma for MAC OS 10.3.2 with MATLAB 6.5.1.

Preliminary attempts have resulted in multiple errors in mexutils.c and
mexutils.h.

I can send the whole error output and my Makefile.macosx and Makefile.site
in that will help.

Jeff Atkinson


From tomas.kasparek@email.cz  Mon Mar  8 13:32:04 2004
From: tomas.kasparek@email.cz (tomas.kasparek@email.cz)
Date: Mon Mar  8 13:32:04 2004
Subject: [MINC-users] histogram and tissue classification
Message-ID: <404CBBF6.000001.29922@db1.email.atc>

Hi,
I`ve just started to use Display - is there any other way to get histogram of MRI to compute for segmentation tresholding than "recompute histogram" in SliceWiew? Or how to get data from that histogram to compute for excluding CSF?
Thank you
Tomas Kasparek

________________________________________________________________________________
OBCHODNÍ-DŮM.cz: domácí spotřebiče a elektronika za nízké ceny, s pohodlnou dopravou aľ do domu, klidně i večer. Objednávky i telefonicky.
www.OBCHODNI-DUM.cz



From minc-users@bic.mni.mcgill.ca  Mon Mar  8 14:19:04 2004
From: minc-users@bic.mni.mcgill.ca (Nugent, Allison C. (NIH/NIMH))
Date: Mon Mar  8 14:19:04 2004
Subject: [MINC-users] N3-1.07??
Message-ID: <5F9DE1C25708B04EAD634A1AE3D9113001E521A8@nihexchange20.nih.gov>

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_001_01C40541.CE0E8637
Content-Type: text/plain

Hi,

            I've been using N3 version 1.05.  Most links on the MNI webpage
point to 1.05 as the current release, but one page,
http://www.bic.mni.mcgill.ca/software/distribution/
<http://www.bic.mni.mcgill.ca/software/distribution/> , points to 1.07.  In
the tar file for 1.07, there wasn't a clear explanation of what was
different between 1.05 and 1.07.  What are the advantages of 1.07?  Is it
truly the current version?  Which should I use?

 

Thanks!

Allison

 

Allison Nugent, PhD

MRI Physicist

MADP; NIMH; NIH

(301)451-8863

 


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<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">


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<div class=Section1>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi,</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I've been using N3 version 1.05.&nbsp; Most
links on the MNI webpage point to 1.05 as the current release, but one page, <a
href="http://www.bic.mni.mcgill.ca/software/distribution/">http://www.bic.mni.mcgill.ca/software/distribution/</a>,
points to 1.07.&nbsp; In the tar file for 1.07, there wasn't a clear
explanation of what was different between 1.05 and 1.07.&nbsp; What are the
advantages of 1.07?&nbsp; Is it truly the current version?&nbsp; Which should I use?</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks!</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Allison</span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Allison Nugent, PhD</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>MRI Physicist</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>MADP; NIMH; NIH</span></font></p>

<p class=MsoAutoSig><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>(301)451-8863</span></font></p>

<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>&nbsp;</span></font></p>

</div>

</body>

</html>

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From minc-users@bic.mni.mcgill.ca  Mon Mar  8 15:15:04 2004
From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween)
Date: Mon Mar  8 15:15:04 2004
Subject: [MINC-users] histogram and tissue classification
In-Reply-To: <404CBBF6.000001.29922@db1.email.atc>
Message-ID: <8D2BC25D-713C-11D8-8386-000A958920AA@som.llu.edu>

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Great question. Also, is there a way to compute a histogram for an ROI 
only?

Jon


Jon Erik Ween, MD, MS
Assistant Professor
Cognitive and Cerebrovascular Neurology
Director, Stroke Program
Loma Linda University


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On Monday, March 8, 2004, at 10:31 AM, <tomas.kasparek@email.cz> wrote:

> Hi,
> I`ve just started to use Display - is there any other way to get =20
> histogram of MRI to compute for segmentation tresholding than =20
> "recompute histogram" in SliceWiew? Or how to get data from that =20
> histogram to compute for excluding CSF?
> Thank you
> Tomas Kasparek
>
> =
_______________________________________________________________________=20=

> _________
> OBCHODN=CD-D=D9M.cz: dom=E1c=ED spot=F8ebi=E8e a elektronika za n=EDzk=E9=
 ceny, s =20
> pohodlnou dopravou a=BE do domu, klidn=EC i ve=E8er. Objedn=E1vky i =20=

> telefonicky.
> www.OBCHODNI-DUM.cz
>
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>


--Apple-Mail-15--462342622--


From minc-users@bic.mni.mcgill.ca  Mon Mar  8 15:28:05 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Mon Mar  8 15:28:05 2004
Subject: [MINC-users] histogram and tissue classification
In-Reply-To: <8D2BC25D-713C-11D8-8386-000A958920AA@som.llu.edu>
References: <8D2BC25D-713C-11D8-8386-000A958920AA@som.llu.edu>
Message-ID: <0B833DE4-713F-11D8-ABB0-000A95DBBFD8@bic.mni.mcgill.ca>

Yup. Open Display, paint the area you are interested in. Go to "slice  
view" (S from top menu). Select H or "Histogram of Label" and the  
histogram will be shown next to the colour bar.

Cheers,

Jason


On Mar 8, 2004, at 3:09 PM, Jon Erik Ween wrote:

> Great question. Also, is there a way to compute a histogram for an ROI  
> only?
>
> Jon
>
>
> Jon Erik Ween, MD, MS
> Assistant Professor
> Cognitive and Cerebrovascular Neurology
> Director, Stroke Program
> Loma Linda University
>
> <ADIlogoFinalSmall.jpg>
>
> On Monday, March 8, 2004, at 10:31 AM, <tomas.kasparek@email.cz> wrote:
>
>> Hi,
>> I`ve just started to use Display - is there any other way to get  
>> histogram of MRI to compute for segmentation tresholding than  
>> "recompute histogram" in SliceWiew? Or how to get data from that  
>> histogram to compute for excluding CSF?
>> Thank you
>> Tomas Kasparek
>>
>> ______________________________________________________________________ 
>> __________
>> OBCHODNÍ-DŮM.cz: domácí spotřebiče a elektronika za nízké ceny, s  
>> pohodlnou dopravou až do domu, klidně i večer. Objednávky i  
>> telefonicky.
>> www.OBCHODNI-DUM.cz
>>
>>
>> _______________________________________________
>> MINC-users@bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
>



From minc-users@bic.mni.mcgill.ca  Mon Mar  8 15:46:04 2004
From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween)
Date: Mon Mar  8 15:46:04 2004
Subject: [MINC-users] histogram and tissue classification
In-Reply-To: <0B833DE4-713F-11D8-ABB0-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <D4F9849C-7140-11D8-8386-000A958920AA@som.llu.edu>

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Great! Now, will it press my shirts?

Jon

On Monday, March 8, 2004, at 12:27 PM, Jason Lerch wrote:

>
> Yup. Open Display, paint the area you are interested in. Go to "slice =20=

> view" (S from top menu). Select H or "Histogram of Label" and the =20
> histogram will be shown next to the colour bar.
>
> Cheers,
>
> Jason
>
>
> On Mar 8, 2004, at 3:09 PM, Jon Erik Ween wrote:
>
>> Great question. Also, is there a way to compute a histogram for an =20=

>> ROI only?
>>
>> Jon
>>
>>
>> Jon Erik Ween, MD, MS
>> Assistant Professor
>> Cognitive and Cerebrovascular Neurology
>> Director, Stroke Program
>> Loma Linda University
>>
>> <ADIlogoFinalSmall.jpg>
>>
>> On Monday, March 8, 2004, at 10:31 AM, <tomas.kasparek@email.cz> =20
>> wrote:
>>
>>> Hi,
>>> I`ve just started to use Display - is there any other way to get =20
>>> histogram of MRI to compute for segmentation tresholding than =20
>>> "recompute histogram" in SliceWiew? Or how to get data from that =20
>>> histogram to compute for excluding CSF?
>>> Thank you
>>> Tomas Kasparek
>>>
>>> =
_____________________________________________________________________=20
>>> ___________
>>> OBCHODN=CD-D=D9M.cz: dom=E1c=ED spot=F8ebi=E8e a elektronika za =
n=EDzk=E9 ceny, s =20
>>> pohodlnou dopravou a=BE do domu, klidn=EC i ve=E8er. Objedn=E1vky i =20=

>>> telefonicky.
>>> www.OBCHODNI-DUM.cz
>>>
>>>
>>> _______________________________________________
>>> MINC-users@bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>>
>>
>
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
Jon Erik Ween, MD, MS
Assistant Professor
Cognitive and Cerebrovascular Neurology
Director, Stroke Program
Loma Linda University


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From minc-users@bic.mni.mcgill.ca  Mon Mar  8 15:54:05 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Mon Mar  8 15:54:05 2004
Subject: [MINC-users] histogram and tissue classification
In-Reply-To: <D4F9849C-7140-11D8-8386-000A958920AA@som.llu.edu>
References: <D4F9849C-7140-11D8-8386-000A958920AA@som.llu.edu>
Message-ID: <9FFE990A-7142-11D8-ABB0-000A95DBBFD8@bic.mni.mcgill.ca>

That's a still untested function to be released in version 1.5. Sorry  
for the delay.

Jason


On Mar 8, 2004, at 3:40 PM, Jon Erik Ween wrote:

> Great! Now, will it press my shirts?
>
> Jon
>
> On Monday, March 8, 2004, at 12:27 PM, Jason Lerch wrote:
>
>>
>> Yup. Open Display, paint the area you are interested in. Go to "slice  
>> view" (S from top menu). Select H or "Histogram of Label" and the  
>> histogram will be shown next to the colour bar.
>>
>> Cheers,
>>
>> Jason
>>
>>
>> On Mar 8, 2004, at 3:09 PM, Jon Erik Ween wrote:
>>
>>> Great question. Also, is there a way to compute a histogram for an  
>>> ROI only?
>>>
>>> Jon
>>>
>>>
>>> Jon Erik Ween, MD, MS
>>> Assistant Professor
>>> Cognitive and Cerebrovascular Neurology
>>> Director, Stroke Program
>>> Loma Linda University
>>>
>>> <ADIlogoFinalSmall.jpg>
>>>
>>> On Monday, March 8, 2004, at 10:31 AM, <tomas.kasparek@email.cz>  
>>> wrote:
>>>
>>>> Hi,
>>>> I`ve just started to use Display - is there any other way to get  
>>>> histogram of MRI to compute for segmentation tresholding than  
>>>> "recompute histogram" in SliceWiew? Or how to get data from that  
>>>> histogram to compute for excluding CSF?
>>>> Thank you
>>>> Tomas Kasparek
>>>>
>>>> ____________________________________________________________________ 
>>>> ____________
>>>> OBCHODNÍ-DŮM.cz: domácí spotřebiče a elektronika za nízké ceny, s  
>>>> pohodlnou dopravou až do domu, klidně i večer. Objednávky i  
>>>> telefonicky.
>>>> www.OBCHODNI-DUM.cz
>>>>
>>>>
>>>> _______________________________________________
>>>> MINC-users@bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> MINC-users@bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
> Jon Erik Ween, MD, MS
> Assistant Professor
> Cognitive and Cerebrovascular Neurology
> Director, Stroke Program
> Loma Linda University
>
> <ADIlogoFinalSmall.jpg>



From minc-users@bic.mni.mcgill.ca  Mon Mar  8 18:55:04 2004
From: minc-users@bic.mni.mcgill.ca (Andrew Janke)
Date: Mon Mar  8 18:55:04 2004
Subject: [MINC-users] histogram and tissue classification
In-Reply-To: <0B833DE4-713F-11D8-ABB0-000A95DBBFD8@bic.mni.mcgill.ca>
References: <8D2BC25D-713C-11D8-8386-000A958920AA@som.llu.edu>
 <0B833DE4-713F-11D8-ABB0-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.53.0403090953070.160302@twodogs.cmr.uq.edu.au>

On Mon, 8 Mar 2004, Jason Lerch wrote:

> Yup. Open Display, paint the area you are interested in. Go to "slice
> view" (S from top menu). Select H or "Histogram of Label" and the
> histogram will be shown next to the colour bar.

And if you wish a more permanent record of your histogram, use mincstats
ie:

   $ mincstats -histogram file.hist -histogram_bins 2000 infile.mnc

You can also add an optional -mask <mask.mnc>


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581

From minc-users@bic.mni.mcgill.ca  Tue Mar  9 00:46:04 2004
From: minc-users@bic.mni.mcgill.ca (Steve ROBBINS)
Date: Tue Mar  9 00:46:04 2004
Subject: [MINC-users] N3-1.07??
In-Reply-To: <5F9DE1C25708B04EAD634A1AE3D9113001E521A8@nihexchange20.nih.gov>; from nugenta@intra.nimh.nih.gov on Mon, Mar 08, 2004 at 02:18:27PM -0500
References: <5F9DE1C25708B04EAD634A1AE3D9113001E521A8@nihexchange20.nih.gov>
Message-ID: <20040309004555.A3637271@shadow.bic.mni.mcgill.ca>

On Mon, Mar 08, 2004 at 02:18:27PM -0500, Nugent, Allison C. (NIH/NIMH) wrote:
> Hi,
> 
>             I've been using N3 version 1.05.  Most links on the MNI webpage
> point to 1.05 as the current release, but one page,
> http://www.bic.mni.mcgill.ca/software/distribution/
> <http://www.bic.mni.mcgill.ca/software/distribution/> , points to 1.07.  In
> the tar file for 1.07, there wasn't a clear explanation of what was
> different between 1.05 and 1.07.

The file called NEWS is intended to be the clear explanation of what is
different.  It should have appeared in the tar file.

>  What are the advantages of 1.07?  Is it
> truly the current version?  Which should I use?

The newer version features an automated build procedure and code
updates to better conform to modern C++ compilers.
There should be no user-visible changes between 1.05 and 1.07.

-Steve
 

From minc-users@bic.mni.mcgill.ca  Tue Mar  9 10:58:04 2004
From: minc-users@bic.mni.mcgill.ca (Robert VINCENT)
Date: Tue Mar  9 10:58:04 2004
Subject: [MINC-users] N3 1.08 and EBTKS 1.2
Message-ID: <Pine.SGI.4.44.0403091052200.3705395-100000@shadow.bic.mni.mcgill.ca>

Hi everyone,

I've just placed new source distributions of both N3 and EBTKS in
http://www.bic.mni.mcgill.ca/software/distribution/packages

These releases fix two major issues with N3.  To benefit from these
changes you should build and install the new EBTKS and then build N3.
Please see the NEWS and ChangeLog files in each distribution for more
details.

In addition, the N3 test suite is now included in the N3 distribution.
That is why it is much larger than previous releases.

	-bert



From minc-users@bic.mni.mcgill.ca  Tue Mar  9 11:07:04 2004
From: minc-users@bic.mni.mcgill.ca (Nugent, Allison C. (NIH/NIMH))
Date: Tue Mar  9 11:07:04 2004
Subject: [MINC-users] N3-1.07??
Message-ID: <5F9DE1C25708B04EAD634A1AE3D9113001E521BF@nihexchange20.nih.gov>

That's interesting, because I still haven't been able to successfully build
1.07 on solaris!  The additional fortran libraries now required have been
the problem.  

Allison Nugent, PhD
MRI Physicist
MADP; NIMH; NIH
(301)451-8863


-----Original Message-----
From: Steve ROBBINS [mailto:stever@bic.mni.mcgill.ca] 
Sent: Tuesday, March 09, 2004 12:46 AM
To: minc-users@bic.mni.mcgill.ca
Subject: Re: [MINC-users] N3-1.07??

On Mon, Mar 08, 2004 at 02:18:27PM -0500, Nugent, Allison C. (NIH/NIMH)
wrote:
> Hi,
> 
>             I've been using N3 version 1.05.  Most links on the MNI
webpage
> point to 1.05 as the current release, but one page,
> http://www.bic.mni.mcgill.ca/software/distribution/
> <http://www.bic.mni.mcgill.ca/software/distribution/> , points to 1.07.
In
> the tar file for 1.07, there wasn't a clear explanation of what was
> different between 1.05 and 1.07.

The file called NEWS is intended to be the clear explanation of what is
different.  It should have appeared in the tar file.

>  What are the advantages of 1.07?  Is it
> truly the current version?  Which should I use?

The newer version features an automated build procedure and code
updates to better conform to modern C++ compilers.
There should be no user-visible changes between 1.05 and 1.07.

-Steve
 
_______________________________________________
MINC-users@bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From minc-users@bic.mni.mcgill.ca  Tue Mar  9 17:03:05 2004
From: minc-users@bic.mni.mcgill.ca (Jeff ATKINSON)
Date: Tue Mar  9 17:03:05 2004
Subject: [MINC-users] emma
Message-ID: <Pine.SGI.4.44.0403091656550.3758366-100000@shadow.bic.mni.mcgill.ca>

Is anyone maintaining emma right now.

I am still having trouble getting it to compile on OS X with Matlab 6.5.1.
The header files mex.h, matrix.h are somewhat different in the latest
version.

I also wondered whether the old code was completely gcc 3.3 compliant as I
get different errors when I use gcc3 vs gcc3.3, however I have no trouble
compling emma on SHADOW with gcc 3.3.

I have managed to get the c files (miwriteimages etc) to compile by
stealing the old headers from matlab 6.1 on the IRIX system but I still can't get the mex files to
compile at all.

If anyone is maintaining emma, or if anyone has had any success compiling
it with 6.5.1 on OS X -- I would appreciate the help.

Thanks

Jeff Atkinson


From minc-users@bic.mni.mcgill.ca  Tue Mar  9 19:24:05 2004
From: minc-users@bic.mni.mcgill.ca (=?iso-8859-1?Q?S=F8ren_Christensen?=)
Date: Tue Mar  9 19:24:05 2004
Subject: [MINC-users] using EMMA to write variables / 3d rendering export format
Message-ID: <FB47ED393635794CB4523F0C52A3D1C2229729@urd.svf.au.dk>

 
Hi,
 Does anyone know if it is possible to use EMMA to write custom variables to a mincfile (either existing or in the creation process).
Also, has anyone tried to export rendered files from Display into eg. 3D max or Maya?  I wonder if it should be possible?
Thanks in advance!
Soren 


From minc-users@bic.mni.mcgill.ca  Tue Mar  9 19:25:04 2004
From: minc-users@bic.mni.mcgill.ca (John G. Sled)
Date: Tue Mar  9 19:25:04 2004
Subject: [MINC-users] N3-1.07??
In-Reply-To: <5F9DE1C25708B04EAD634A1AE3D9113001E521A8@nihexchange20.nih.gov>
References: <5F9DE1C25708B04EAD634A1AE3D9113001E521A8@nihexchange20.nih.gov>
Message-ID: <20040308225342.GD10353@sickkids.ca>


Yes, N3 1.07 is the latest release of N3 and substantially more 
portable / easy to build than previous releases.  Unfortunately,
I haven't gotten around to updating the N3 web pages.  The new
version builds with the usual

./configure
make
make install

steps that are used with the other tools.  Unlike older versions of N3
it depends on the EBTKS library being installed separately.  I understand
that a bug has just been found in EBTKS that affects some versions of
gcc and that a patched version of EBTKS will be released shortly.


John 


On Mon, Mar 08, 2004 at 02:18:27PM -0500, Nugent, Allison C. (NIH/NIMH) wrote:
> Hi,
> 
>             I've been using N3 version 1.05.  Most links on the MNI webpage
> point to 1.05 as the current release, but one page,
> http://www.bic.mni.mcgill.ca/software/distribution/
> <http://www.bic.mni.mcgill.ca/software/distribution/> , points to 1.07.  In
> the tar file for 1.07, there wasn't a clear explanation of what was
> different between 1.05 and 1.07.  What are the advantages of 1.07?  Is it
> truly the current version?  Which should I use?
> 
>  
> 
> Thanks!
> 
> Allison
> 
>  
> 
> Allison Nugent, PhD
> 
> MRI Physicist
> 
> MADP; NIMH; NIH
> 
> (301)451-8863
> 
>  
> 

From minc-users@bic.mni.mcgill.ca  Tue Mar  9 19:25:08 2004
From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween)
Date: Tue Mar  9 19:25:08 2004
Subject: [MINC-users] histogram and tissue classification
In-Reply-To: <Pine.SGI.4.53.0403090953070.160302@twodogs.cmr.uq.edu.au>
Message-ID: <F9A3F5E8-7191-11D8-8386-000A958920AA@gte.net>

--Apple-Mail-34--425653418
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Thanks!

Jon

On Monday, March 8, 2004, at 03:54 PM, Andrew Janke wrote:

> On Mon, 8 Mar 2004, Jason Lerch wrote:
>
>> Yup. Open Display, paint the area you are interested in. Go to "slice
>> view" (S from top menu). Select H or "Histogram of Label" and the
>> histogram will be shown next to the colour bar.
>
> And if you wish a more permanent record of your histogram, use 
> mincstats
> ie:
>
>    $ mincstats -histogram file.hist -histogram_bins 2000 infile.mnc
>
> You can also add an optional -mask <mask.mnc>
>
>
> --
> Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
> Australia->University of Queensland->Centre for Magnetic Resonance
> W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
Jon Erik Ween, MD, MS
Assistant Professor
Cognitive and Cerebrovascular Neurology
Director, Stroke Program
Loma Linda University


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From tomas.kasparek@email.cz  Wed Mar 10 05:36:04 2004
From: tomas.kasparek@email.cz (tomas.kasparek@email.cz)
Date: Wed Mar 10 05:36:04 2004
Subject: [MINC-users] histogram and tissue classification
Message-ID: <404EEF70.000001.28562@db1.email.atc>

Thank you! Tomas


--- Původní zpráva ---
Od: Andrew Janke <rotor@cmr.uq.edu.au>
Datum: 09.03.2004 01:02:38

On Mon, 8 Mar 2004, Jason Lerch wrote:

> Yup. Open Display, paint the area you are interested in. Go to "slice
> view" (S from top menu). Select H or "Histogram of Label" and the
> histogram will be shown next to the colour bar.

And if you wish a more permanent record of your histogram, use mincstats
ie:

   $ mincstats -histogram file.hist -histogram_bins 2000 infile.mnc

You can also add an optional -mask <mask.mnc>


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581
_______________________________________________
MINC-users@bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


________________________________________________________________________________
OBCHODNÍ-DŮM.cz: domácí spotřebiče a elektronika za nízké ceny, s pohodlnou dopravou aľ do domu, klidně i večer. Objednávky i telefonicky.
www.OBCHODNI-DUM.cz



From minc-users@bic.mni.mcgill.ca  Wed Mar 10 15:07:03 2004
From: minc-users@bic.mni.mcgill.ca (Jason Lerch)
Date: Wed Mar 10 15:07:03 2004
Subject: [MINC-users] emma
In-Reply-To: <Pine.SGI.4.44.0403091656550.3758366-100000@shadow.bic.mni.mcgill.ca>
References: <Pine.SGI.4.44.0403091656550.3758366-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <63C49666-72CE-11D8-B74B-000A95DBBFD8@bic.mni.mcgill.ca>

Greetings,

the deafening silence to your appeals would indicate that nobody is 
actively supporting EMMA at this point. In my opinion it should be 
taken behind the shed and shot, as it is one horrible bit of code 
designed for matlab 4, which was quite a limited language (if my 
knowledge of EMMA history is correct).

It looks like you are mostly on your own. If you are really stuck I can 
wander by at some point to see if I can come up with anything obvious, 
but I have never compiled EMMA under any platform and don't have matlab 
on my mac to try it here.

Sorry ...

Jason


On Mar 9, 2004, at 5:02 PM, Jeff ATKINSON wrote:

> Is anyone maintaining emma right now.
>
> I am still having trouble getting it to compile on OS X with Matlab 
> 6.5.1.
> The header files mex.h, matrix.h are somewhat different in the latest
> version.
>
> I also wondered whether the old code was completely gcc 3.3 compliant 
> as I
> get different errors when I use gcc3 vs gcc3.3, however I have no 
> trouble
> compling emma on SHADOW with gcc 3.3.
>
> I have managed to get the c files (miwriteimages etc) to compile by
> stealing the old headers from matlab 6.1 on the IRIX system but I 
> still can't get the mex files to
> compile at all.
>
> If anyone is maintaining emma, or if anyone has had any success 
> compiling
> it with 6.5.1 on OS X -- I would appreciate the help.
>
> Thanks
>
> Jeff Atkinson
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Wed Mar 10 16:39:03 2004
From: minc-users@bic.mni.mcgill.ca (Jeff ATKINSON)
Date: Wed Mar 10 16:39:03 2004
Subject: [MINC-users] emma
In-Reply-To: <63C49666-72CE-11D8-B74B-000A95DBBFD8@bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0403101635010.3756221-100000@shadow.bic.mni.mcgill.ca>

I agree about emma but at present it is the only interface between matlab
minc and hence Keith's fMRI toolbox.

There exists some other matlab - netcdf tools available from various
sources and I am seriously considering installing those and rewriting
Keith's stuff to use the new tools. This may prove much easier than
getting emma updated for matlab 6.5.

Robert Vincent has provided some ideas I will try first.

Jeff Atkinson

On Wed, 10 Mar 2004, Jason Lerch wrote:

> Greetings,
>
> the deafening silence to your appeals would indicate that nobody is
> actively supporting EMMA at this point. In my opinion it should be
> taken behind the shed and shot, as it is one horrible bit of code
> designed for matlab 4, which was quite a limited language (if my
> knowledge of EMMA history is correct).
>
> It looks like you are mostly on your own. If you are really stuck I can
> wander by at some point to see if I can come up with anything obvious,
> but I have never compiled EMMA under any platform and don't have matlab
> on my mac to try it here.
>
> Sorry ...
>
> Jason
>
>
> On Mar 9, 2004, at 5:02 PM, Jeff ATKINSON wrote:
>
> > Is anyone maintaining emma right now.
> >
> > I am still having trouble getting it to compile on OS X with Matlab
> > 6.5.1.
> > The header files mex.h, matrix.h are somewhat different in the latest
> > version.
> >
> > I also wondered whether the old code was completely gcc 3.3 compliant
> > as I
> > get different errors when I use gcc3 vs gcc3.3, however I have no
> > trouble
> > compling emma on SHADOW with gcc 3.3.
> >
> > I have managed to get the c files (miwriteimages etc) to compile by
> > stealing the old headers from matlab 6.1 on the IRIX system but I
> > still can't get the mex files to
> > compile at all.
> >
> > If anyone is maintaining emma, or if anyone has had any success
> > compiling
> > it with 6.5.1 on OS X -- I would appreciate the help.
> >
> > Thanks
> >
> > Jeff Atkinson
> >
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From minc-users@bic.mni.mcgill.ca  Thu Mar 11 18:50:07 2004
From: minc-users@bic.mni.mcgill.ca (Yasser Ad-Dab'bagh)
Date: Thu Mar 11 18:50:07 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
Message-ID: <1078961441.21092.7.camel@rosaline>

Should we be concerned?

Yasser

-----Forwarded Message-----
From: Organization for Human Brain Mapping <info@humanbrainmapping.org>
To: yasser.ad-dabbagh@MAIL.MCGILL.CA
Subject: OHBM Announcement 3/9/04
Date: 09 Mar 2004 15:43:11 -0700



Dear OHBM Colleagues:

We are writing on behalf of the Data Format Working Group (DFWG), a
committee set up under the Neuroimaging Informatics Technology
Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly
sponsored by NIMH and NINDS. We have been charged with arriving "at a
technical solution to the problem of multiple data formats in fMRI." We
have met several times and decided that one of our first priorities is
to describe and attempt to merge the variants of the ANALYZE(TM) 7.5
image header that are being used by the developers of the major fMRI
data analysis packages.

We have defined a compromise data format, dubbed NIfTI-1, that is based
on these variants and is "mostly compatible" with the ANALYZE(TM) 7.5
header, while using many of the "unused and lesser-used" fields for
fMRI-specific purposes. Developers of five of the major fMRI data
analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) have
agreed to use this compromise format in the future, and will support
both input and output of the NIfTI-1 format. A considerable effort was
required to reach agreement with all of these developers. Given the
extremely limited space in the 348 byte header, it is unlikely that any
substantial changes will be possible in the NIfTI-1 format if we are to
retain the support of all five packages.

We envisage NIfTI-1 replacing the current range of ANALYZE 7.5 variants
both for file interchange and data storage.  NIfTI-1, while still
limited, contains a considerably richer set of metadata than exists in
the ANALYZE-based formats.

As of this message, the NIfTI-1 format specification, demonstration
programs, and related documents are being released to the general
neuroimaging community on the DFWG website  
http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for
comments and discussion. The DFWG committee will next meet in early May
2004, and any comments you care to make and would like to have
considered at the next committee meeting should be received by April 15,
2004.

Please feel free to pass this message along to any other person you
think might be interested.  Comments and questions should be directed to
the NIfTI-1 interactive forum, and not to DFWG committee members via
e-mail.  The full list of DFWG committee members can be found at the
DFWG website.

Stephen Strother, PhD    
Chair, Data Format Working Group  
NIfTI, National Institutes of Health     
             and                           
Professor of Radiology                    
University of Minnesota                   
mailto:steve@neurovia.umn.edu   
         

Robert W. Cox, PhD
Director, Scientific and Statistical Computing Core
National Institute of Mental Health
National Institutes of Health
Department of Health and Human Service
Mailto: rwcox@nih.gov   http://nifti.nimh.nih.gov/dfwg/  




To be removed from this mailing list, please click here.

-- 
 -----------------------------------------------------------------------
 Yasser Ad-Dab'bagh, MD, DPM, FRCPC.
 Divisions of Child & Adolescent Psychiatry (Montreal Children's 
 Hospital), and of Neuroscience (Brain-Imaging Center of the  Montreal 
 Neurological Institute), McGill University.
 
 Tel:		(514) 412-4400 ext 22359 [MCH], (514) 398-8330 [BIC]
 Fax:		(514) 412-4337 [MCH]
 Pager:		(514) 580-4388
 E-mail:	yaddab@bic.mni.mcgill.ca
 		yasser.ad-dabbagh@mail.mcgill.ca
 		yasser@doctoraddabbagh.com
 Web:		http://www.doctoraddabbagh.com
 -----------------------------------------------------------------------


From minc-users@bic.mni.mcgill.ca  Thu Mar 11 19:20:04 2004
From: minc-users@bic.mni.mcgill.ca (Andrew Janke)
Date: Thu Mar 11 19:20:04 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
In-Reply-To: <1078961441.21092.7.camel@rosaline>
References: <1078961441.21092.7.camel@rosaline>
Message-ID: <Pine.SGI.4.53.0403121010010.291038@twodogs.cmr.uq.edu.au>

On Thu, 10 Mar 2004, Yasser Ad-Dab'bagh wrote:

> Should we be concerned?

"perhaps".

I have been in contact with a few of the DFWG members in the last few days with
respect to this.  What seems to have happened so far is this:

  * NIfTI-1 is the patch-up job for the various forms of analyze.
     - this is actually a big improvement over previous versions.

  * NIfTI-2 is to be the replacement for ANALYZE that will be all-singing
       and all-dancing.

However no decision or specs are available so far for NIfTI-2.  Apparently a
number of the members of the comittee are all for just using MINC 1.2/2.0.
however there are some who are opposed to even HDF5 or NetCDF.  I have asked for
feedback on the problems these people on the comittee have against MINC 2.0 in
order that we might be able to alleviate their concerns with MINC 2.0.

I haven't recieved anything yet though.  Apaprently the group will be meeting
again soon to discuss NIfTI-2 in more detail.

In the meantime if you want your voice to be heard, send an email to the group
voicing your opinion, the more people who indicate that they would like to see
MINC 2.0 replace NIfTI-2 the better. However remember that the NIfTI group is
only concerned with Data formats for fMRI data.  Whilst MINC can (and does)  do
fMRI data, there is still a bit of work needed on MATLAB interfaces to MINC.


   http://nifti.nimh.nih.gov/


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581



> -----Forwarded Message-----
> From: Organization for Human Brain Mapping <info@humanbrainmapping.org>
> To: yasser.ad-dabbagh@MAIL.MCGILL.CA
>
> We are writing on behalf of the Data Format Working Group (DFWG), a
> committee set up under the Neuroimaging Informatics Technology
> Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly
> sponsored by NIMH and NINDS. We have been charged with arriving "at a
> technical solution to the problem of multiple data formats in fMRI." We
> have met several times and decided that one of our first priorities is
> to describe and attempt to merge the variants of the ANALYZE(TM) 7.5
> image header that are being used by the developers of the major fMRI
> data analysis packages.
>
> We have defined a compromise data format, dubbed NIfTI-1, that is based
> on these variants and is "mostly compatible" with the ANALYZE(TM) 7.5
> header, while using many of the "unused and lesser-used" fields for
> fMRI-specific purposes. Developers of five of the major fMRI data
> analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) have
> agreed to use this compromise format in the future, and will support
> both input and output of the NIfTI-1 format. A considerable effort was
> required to reach agreement with all of these developers. Given the
> extremely limited space in the 348 byte header, it is unlikely that any
> substantial changes will be possible in the NIfTI-1 format if we are to
> retain the support of all five packages.
>
> We envisage NIfTI-1 replacing the current range of ANALYZE 7.5 variants
> both for file interchange and data storage.  NIfTI-1, while still
> limited, contains a considerably richer set of metadata than exists in
> the ANALYZE-based formats.
>
> As of this message, the NIfTI-1 format specification, demonstration
> programs, and related documents are being released to the general
> neuroimaging community on the DFWG website
> http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for
> comments and discussion. The DFWG committee will next meet in early May
> 2004, and any comments you care to make and would like to have
> considered at the next committee meeting should be received by April 15,
> 2004.
>


From minc-users@bic.mni.mcgill.ca  Thu Mar 11 19:25:03 2004
From: minc-users@bic.mni.mcgill.ca (John D. Van Horn)
Date: Thu Mar 11 19:25:03 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
In-Reply-To: <1078961441.21092.7.camel@rosaline>
Message-ID: <000701c407c8$51e285b0$6801a8c0@DG76FG41>

Dear Yasser and other Minc users,

As someone who has been peripherally involved with the Nifti effort for
a couple of years, the committee has been very impressed with the new
directions of Minc, in particular, Minc 2.0.  Though my role has been
limited, I think that the group is taking a very serious look at Minc
2.0.  The Nifti file format is an attempt to improve on Analyze,
bringing it into the 21st century, and make it more suitable for fMRI.
This will form the basis of a basic format.  Odds are Minc 2.0 may be
recommended as the more fully featured format that gets recommended by
the committee.  Time will surely tell.

Respectfully yours,

Jack Van Horn
Dartmouth College



-----Original Message-----
From: minc-users-admin@bic.mni.mcgill.ca
[mailto:minc-users-admin@bic.mni.mcgill.ca] On Behalf Of Yasser
Ad-Dab'bagh
Sent: Wednesday, March 10, 2004 5:31 PM
To: MINC-users@bic.mni.mcgill.ca
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]


Should we be concerned?

Yasser

-----Forwarded Message-----
From: Organization for Human Brain Mapping <info@humanbrainmapping.org>
To: yasser.ad-dabbagh@MAIL.MCGILL.CA
Subject: OHBM Announcement 3/9/04
Date: 09 Mar 2004 15:43:11 -0700



Dear OHBM Colleagues:

We are writing on behalf of the Data Format Working Group (DFWG), a
committee set up under the Neuroimaging Informatics Technology
Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly
sponsored by NIMH and NINDS. We have been charged with arriving "at a
technical solution to the problem of multiple data formats in fMRI." We
have met several times and decided that one of our first priorities is
to describe and attempt to merge the variants of the ANALYZE(TM) 7.5
image header that are being used by the developers of the major fMRI
data analysis packages.

We have defined a compromise data format, dubbed NIfTI-1, that is based
on these variants and is "mostly compatible" with the ANALYZE(TM) 7.5
header, while using many of the "unused and lesser-used" fields for
fMRI-specific purposes. Developers of five of the major fMRI data
analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) have
agreed to use this compromise format in the future, and will support
both input and output of the NIfTI-1 format. A considerable effort was
required to reach agreement with all of these developers. Given the
extremely limited space in the 348 byte header, it is unlikely that any
substantial changes will be possible in the NIfTI-1 format if we are to
retain the support of all five packages.

We envisage NIfTI-1 replacing the current range of ANALYZE 7.5 variants
both for file interchange and data storage.  NIfTI-1, while still
limited, contains a considerably richer set of metadata than exists in
the ANALYZE-based formats.

As of this message, the NIfTI-1 format specification, demonstration
programs, and related documents are being released to the general
neuroimaging community on the DFWG website  
http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for
comments and discussion. The DFWG committee will next meet in early May
2004, and any comments you care to make and would like to have
considered at the next committee meeting should be received by April 15,
2004.

Please feel free to pass this message along to any other person you
think might be interested.  Comments and questions should be directed to
the NIfTI-1 interactive forum, and not to DFWG committee members via
e-mail.  The full list of DFWG committee members can be found at the
DFWG website.

Stephen Strother, PhD    
Chair, Data Format Working Group  
NIfTI, National Institutes of Health     
             and                           
Professor of Radiology                    
University of Minnesota                   
mailto:steve@neurovia.umn.edu   
         

Robert W. Cox, PhD
Director, Scientific and Statistical Computing Core
National Institute of Mental Health
National Institutes of Health
Department of Health and Human Service
Mailto: rwcox@nih.gov   http://nifti.nimh.nih.gov/dfwg/  




To be removed from this mailing list, please click here.

-- 
 -----------------------------------------------------------------------
 Yasser Ad-Dab'bagh, MD, DPM, FRCPC.
 Divisions of Child & Adolescent Psychiatry (Montreal Children's 
 Hospital), and of Neuroscience (Brain-Imaging Center of the  Montreal 
 Neurological Institute), McGill University.
 
 Tel:		(514) 412-4400 ext 22359 [MCH], (514) 398-8330 [BIC]
 Fax:		(514) 412-4337 [MCH]
 Pager:		(514) 580-4388
 E-mail:	yaddab@bic.mni.mcgill.ca
 		yasser.ad-dabbagh@mail.mcgill.ca
 		yasser@doctoraddabbagh.com
 Web:		http://www.doctoraddabbagh.com
 -----------------------------------------------------------------------

_______________________________________________
MINC-users@bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From minc-users@bic.mni.mcgill.ca  Thu Mar 11 20:21:03 2004
From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween)
Date: Thu Mar 11 20:21:03 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
In-Reply-To: <1078961441.21092.7.camel@rosaline>
Message-ID: <B65CF6FE-73C2-11D8-87EE-000A958920AA@som.llu.edu>

--Apple-Mail-28--184818626
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I would be in favor of the Minc format as a rich, compact and elegant 
standard. I wonder, though, how significant the issue is as long as all 
formats are transparent, non-proprietary and translatable? Knowing the 
community, I can't imagine there will be 100% agreement any time soon 
no matter what happens with the Analyze format. I would only hope that 
the capable minc-group is actively included in the development of a 
more widely adopted, uniform standard. I notice they are not mentioned 
in the statement!

Jon

Jon Erik Ween, MD, MS
Assistant Professor
Cognitive and Cerebrovascular Neurology
Director, Stroke Program
Loma Linda University


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On Wednesday, March 10, 2004, at 03:30 PM, Yasser Ad-Dab'bagh wrote:

>
> Should we be concerned?
>
> Yasser
>
> -----Forwarded Message-----
> From: Organization for Human Brain Mapping <info@humanbrainmapping.org>
> To: yasser.ad-dabbagh@MAIL.MCGILL.CA
> Subject: OHBM Announcement 3/9/04
> Date: 09 Mar 2004 15:43:11 -0700
>
>
>
> Dear OHBM Colleagues:
>
> We are writing on behalf of the Data Format Working Group (DFWG), a
> committee set up under the Neuroimaging Informatics Technology
> Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly
> sponsored by NIMH and NINDS. We have been charged with arriving "at a
> technical solution to the problem of multiple data formats in fMRI." We
> have met several times and decided that one of our first priorities is
> to describe and attempt to merge the variants of the ANALYZE(TM) 7.5
> image header that are being used by the developers of the major fMRI
> data analysis packages.
>
> We have defined a compromise data format, dubbed NIfTI-1, that is based
> on these variants and is "mostly compatible" with the ANALYZE(TM) 7.5
> header, while using many of the "unused and lesser-used" fields for
> fMRI-specific purposes. Developers of five of the major fMRI data
> analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) have
> agreed to use this compromise format in the future, and will support
> both input and output of the NIfTI-1 format. A considerable effort was
> required to reach agreement with all of these developers. Given the
> extremely limited space in the 348 byte header, it is unlikely that any
> substantial changes will be possible in the NIfTI-1 format if we are to
> retain the support of all five packages.
>
> We envisage NIfTI-1 replacing the current range of ANALYZE 7.5 variants
> both for file interchange and data storage.  NIfTI-1, while still
> limited, contains a considerably richer set of metadata than exists in
> the ANALYZE-based formats.
>
> As of this message, the NIfTI-1 format specification, demonstration
> programs, and related documents are being released to the general
> neuroimaging community on the DFWG website
> http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for
> comments and discussion. The DFWG committee will next meet in early May
> 2004, and any comments you care to make and would like to have
> considered at the next committee meeting should be received by April  
> 15,
> 2004.
>
> Please feel free to pass this message along to any other person you
> think might be interested.  Comments and questions should be directed  
> to
> the NIfTI-1 interactive forum, and not to DFWG committee members via
> e-mail.  The full list of DFWG committee members can be found at the
> DFWG website.
>
> Stephen Strother, PhD
> Chair, Data Format Working Group
> NIfTI, National Institutes of Health
>              and
> Professor of Radiology
> University of Minnesota
> mailto:steve@neurovia.umn.edu
>
>
> Robert W. Cox, PhD
> Director, Scientific and Statistical Computing Core
> National Institute of Mental Health
> National Institutes of Health
> Department of Health and Human Service
> Mailto: rwcox@nih.gov   http://nifti.nimh.nih.gov/dfwg/
>
>
>
>
> To be removed from this mailing list, please click here.
>
> --  
>   
> -----------------------------------------------------------------------
>  Yasser Ad-Dab'bagh, MD, DPM, FRCPC.
>  Divisions of Child & Adolescent Psychiatry (Montreal Children's
>  Hospital), and of Neuroscience (Brain-Imaging Center of the  Montreal
>  Neurological Institute), McGill University.
>
>  Tel:		(514) 412-4400 ext 22359 [MCH], (514) 398-8330 [BIC]
>  Fax:		(514) 412-4337 [MCH]
>  Pager:		(514) 580-4388
>  E-mail:	yaddab@bic.mni.mcgill.ca
>  		yasser.ad-dabbagh@mail.mcgill.ca
>  		yasser@doctoraddabbagh.com
>  Web:		http://www.doctoraddabbagh.com
>   
> -----------------------------------------------------------------------
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>


--Apple-Mail-28--184818626--


From minc-users@bic.mni.mcgill.ca  Thu Mar 11 20:38:03 2004
From: minc-users@bic.mni.mcgill.ca (Andrew Janke)
Date: Thu Mar 11 20:38:03 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
In-Reply-To: <B65CF6FE-73C2-11D8-87EE-000A958920AA@som.llu.edu>
References: <B65CF6FE-73C2-11D8-87EE-000A958920AA@som.llu.edu>
Message-ID: <Pine.SGI.4.53.0403121129220.291038@twodogs.cmr.uq.edu.au>

On Thu, 11 Mar 2004, Jon Erik Ween wrote:

> I would be in favor of the Minc format as a rich, compact and elegant
> standard. I wonder, though, how significant the issue is as long as all
> formats are transparent, non-proprietary and translatable?

You're right it shouldn't be a problem so long as no format is a sub-set of the
other.  For example MINC supports arbitrary length header data, analyze doesn't,
however I assume NIfTI-2 will. Then there is dimensionality and ordering, SPM
defines radio vs neuro as a flipping of the image data.  Thus a conversion has
to know the "type" of the input data. MINC on the other hand (and a few others)
allow any arbitrary ordering of data the user would like.

I (and others) could ramble on forever regarding the technical issues with data
conversion. But you have hit the nail on the head, the "translatable" part is
the most important (and the most problematic!).


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581

From minc-users@bic.mni.mcgill.ca  Thu Mar 11 23:35:03 2004
From: minc-users@bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Thu Mar 11 23:35:03 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
In-Reply-To: <Pine.SGI.4.53.0403121010010.291038@twodogs.cmr.uq.edu.au>
References: <1078961441.21092.7.camel@rosaline>
 <Pine.SGI.4.53.0403121010010.291038@twodogs.cmr.uq.edu.au>
Message-ID: <20040312043453.GA11800@bic.mni.mcgill.ca>

This is also what I have picked up through the grapevine - that MINC
2.x has a reasonably high likelihood of becoming NIfTI-2. But I agree
that there probably is more work to be done to make that happen. I
would hope the DFWG will come out with some requirements/specs for
NIfTI-2 such that we (well some of you :) can focus (y)our
efforts. ANALYZE is after all still just ANALYZE.

Is there a timeline for NIfTI-1 and NIfTI-2 (their web site is
currently down)? Not that it's any of my concern, but I have to admit
I don't really see the point of first unifying ANALYZE for NIfTI-1,
and then possibly (probably) switching to something entirely new for
NIfTI-2. Seems like make-work to me, and also - if ANALYZE is actually
improved - it will be harder to get people away from it down the
road. Why not bite the NIfTI-2 bullet right away, me wonders.

-- Alex

On Fri, Mar 12, 2004 at 10:19:19AM +1000, Andrew Janke wrote:
> On Thu, 10 Mar 2004, Yasser Ad-Dab'bagh wrote:
> 
> > Should we be concerned?
> 
> "perhaps".
> 
> I have been in contact with a few of the DFWG members in the last few days with
> respect to this.  What seems to have happened so far is this:
> 
>   * NIfTI-1 is the patch-up job for the various forms of analyze.
>      - this is actually a big improvement over previous versions.
> 
>   * NIfTI-2 is to be the replacement for ANALYZE that will be all-singing
>        and all-dancing.
> 
> However no decision or specs are available so far for NIfTI-2.  Apparently a
> number of the members of the comittee are all for just using MINC 1.2/2.0.
> however there are some who are opposed to even HDF5 or NetCDF.  I have asked for
> feedback on the problems these people on the comittee have against MINC 2.0 in
> order that we might be able to alleviate their concerns with MINC 2.0.
> 
> I haven't recieved anything yet though.  Apaprently the group will be meeting
> again soon to discuss NIfTI-2 in more detail.
> 
> In the meantime if you want your voice to be heard, send an email to the group
> voicing your opinion, the more people who indicate that they would like to see
> MINC 2.0 replace NIfTI-2 the better. However remember that the NIfTI group is
> only concerned with Data formats for fMRI data.  Whilst MINC can (and does)  do
> fMRI data, there is still a bit of work needed on MATLAB interfaces to MINC.
> 
> 
>    http://nifti.nimh.nih.gov/
> 
> 
> --
> Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
> Australia->University of Queensland->Centre for Magnetic Resonance
> W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581
> 
> 
> 
> > -----Forwarded Message-----
> > From: Organization for Human Brain Mapping <info@humanbrainmapping.org>
> > To: yasser.ad-dabbagh@MAIL.MCGILL.CA
> >
> > We are writing on behalf of the Data Format Working Group (DFWG), a
> > committee set up under the Neuroimaging Informatics Technology
> > Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly
> > sponsored by NIMH and NINDS. We have been charged with arriving "at a
> > technical solution to the problem of multiple data formats in fMRI." We
> > have met several times and decided that one of our first priorities is
> > to describe and attempt to merge the variants of the ANALYZE(TM) 7.5
> > image header that are being used by the developers of the major fMRI
> > data analysis packages.
> >
> > We have defined a compromise data format, dubbed NIfTI-1, that is based
> > on these variants and is "mostly compatible" with the ANALYZE(TM) 7.5
> > header, while using many of the "unused and lesser-used" fields for
> > fMRI-specific purposes. Developers of five of the major fMRI data
> > analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) have
> > agreed to use this compromise format in the future, and will support
> > both input and output of the NIfTI-1 format. A considerable effort was
> > required to reach agreement with all of these developers. Given the
> > extremely limited space in the 348 byte header, it is unlikely that any
> > substantial changes will be possible in the NIfTI-1 format if we are to
> > retain the support of all five packages.
> >
> > We envisage NIfTI-1 replacing the current range of ANALYZE 7.5 variants
> > both for file interchange and data storage.  NIfTI-1, while still
> > limited, contains a considerably richer set of metadata than exists in
> > the ANALYZE-based formats.
> >
> > As of this message, the NIfTI-1 format specification, demonstration
> > programs, and related documents are being released to the general
> > neuroimaging community on the DFWG website
> > http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for
> > comments and discussion. The DFWG committee will next meet in early May
> > 2004, and any comments you care to make and would like to have
> > considered at the next committee meeting should be received by April 15,
> > 2004.
> >
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From minc-users@bic.mni.mcgill.ca  Sun Mar 14 18:21:05 2004
From: minc-users@bic.mni.mcgill.ca (Jon Erik Ween)
Date: Sun Mar 14 18:21:05 2004
Subject: [MINC-users] [Fwd: OHBM Announcement 3/9/04]
In-Reply-To: <69.427e716d.2d83d904@aol.com>
Message-ID: <30BDFB87-7505-11D8-8473-000A958920AA@som.llu.edu>

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Great!

Jon

On Friday, March 12, 2004, at 07:24 PM, Scskiwiz@aol.com wrote:

> Jon and Yasser:
> =A0
> The DFWG committee is very aware of the latest MINC developments =20
> through Colin Holmes' able and enthusiastic advocacy of MINC to the =20=

> committee. In addition, we have been provided with MINC 1.0 namespace =20=

> (7/5/2003) and MINC 2.0 file format (11/18/2003) documents by Robert =20=

> Vincent in Montreal. Most of the DFWG committee meet with Alan Evans, =20=

> John Sled, Robert Vincent and several others to discuss MINC and its =20=

> proposed developments at the last OHBM meeting in NewYork.
> =A0
> I will discuss lines of communication between the DFWG and MINC =20
> development community with Alan Evans and Colin Holmes. It=A0is my =20
> current impression that information is flowing freely, particularly =20=

> from the MINC community to the committee.
> =A0
> Stephen Strother
> =A0
> In a message dated 3/11/2004 7:20:23 PM Central Standard Time, =20
> jween@som.llu.edu writes:
>
> I would be in favor of the Minc format as a rich, compact and elegant
> standard. I wonder, though, how significant the issue is as long as =
all
> formats are transparent, non-proprietary and translatable? Knowing the
> community, I can't imagine there will be 100% agreement any time soon
> no matter what happens with the Analyze format. I would only hope that
> the capable minc-group is actively included in the development of a
> more widely adopted, uniform standard. I notice they are not mentioned
> in the statement!
>
> Jon
>
> Jon Erik Ween, MD, MS
> Assistant Professor
> Cognitive and Cerebrovascular Neurology
> Director, Stroke Program
> Loma Linda University
>
>
>
<image.tiff>
>
>
> On Wednesday, March 10, 2004, at 03:30 PM, Yasser Ad-Dab'bagh wrote:
>
> >
> > Should we be concerned?
> >
> > Yasser
> >
> > -----Forwarded Message-----
> > From: Organization for Human Brain Mapping =20
> <info@humanbrainmapping.org>
> > To: yasser.ad-dabbagh@MAIL.MCGILL.CA
> > Subject: OHBM Announcement 3/9/04
> > Date: 09 Mar 2004 15:43:11 -0700
> >
> >
> >
> > Dear OHBM Colleagues:
> >
> > We are writing on behalf of the Data Format Working Group (DFWG), a
> > committee set up under the Neuroimaging Informatics Technology
> > Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly
> > sponsored by NIMH and NINDS. We have been charged with arriving "at =
a
> > technical solution to the problem of multiple data formats in fMRI." =
=20
> We
> > have met several times and decided that one of our first priorities =20=

> is
> > to describe and attempt to merge the variants of the ANALYZE(TM) 7.5
> > image header that are being used by the developers of the major fMRI
> > data analysis packages.
> >
> > We have defined a compromise data format, dubbed NIfTI-1, that is =20=

> based
> > on these variants and is "mostly compatible" with the ANALYZE(TM) =
7.5
> > header, while using many of the "unused and lesser-used" fields for
> > fMRI-specific purposes. Developers of five of the major fMRI data
> > analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) =
have
> > agreed to use this compromise format in the future, and will support
> > both input and output of the NIfTI-1 format. A considerable effort =20=

> was
> > required to reach agreement with all of these developers. Given the
> > extremely limited space in the 348 byte header, it is unlikely that =20=

> any
> > substantial changes will be possible in the NIfTI-1 format if we are =
=20
> to
> > retain the support of all five packages.
> >
> > We envisage NIfTI-1 replacing the current range of ANALYZE 7.5 =20
> variants
> > both for file interchange and data storage.=A0 NIfTI-1, while still
> > limited, contains a considerably richer set of metadata than exists =20=

> in
> > the ANALYZE-based formats.
> >
> > As of this message, the NIfTI-1 format specification, demonstration
> > programs, and related documents are being released to the general
> > neuroimaging community on the DFWG website
> > http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for
> > comments and discussion. The DFWG committee will next meet in early =20=

> May
> > 2004, and any comments you care to make and would like to have
> > considered at the next committee meeting should be received by =
April=A0
> > 15,
> > 2004.
> >
> > Please feel free to pass this message along to any other person you
> > think might be interested.=A0 Comments and questions should be =20
> directed=A0
> > to
> > the NIfTI-1 interactive forum, and not to DFWG committee members via
> > e-mail.=A0 The full list of DFWG committee members can be found at =
the
> > DFWG website.
> >
> > Stephen Strother, PhD
> > Chair, Data Format Working Group
> > NIfTI, National Institutes of Health
> >=A0 =A0 =A0 =A0 =A0 =A0 =A0 and
> > Professor of Radiology
> > University of Minnesota
> > mailto:steve@neurovia.umn.edu
> >
> >
> > Robert W. Cox, PhD
> > Director, Scientific and Statistical Computing Core
> > National Institute of Mental Health
> > National Institutes of Health
> > Department of Health and Human Service
> > Mailto: rwcox@nih.gov=A0=A0 http://nifti.nimh.nih.gov/dfwg/
> >
> >
> >
> >
> > To be removed from this mailing list, please click here.
> >
> > --=A0
> >=A0=A0
> > =20
> =
-----------------------------------------------------------------------
> >=A0 Yasser Ad-Dab'bagh, MD, DPM, FRCPC.
> >=A0 Divisions of Child & Adolescent Psychiatry (Montreal Children's
> >=A0 Hospital), and of Neuroscience (Brain-Imaging Center of the=A0 =20=

> Montreal
> >=A0 Neurological Institute), McGill University.
> >
> >=A0 Tel:=A0 =A0 =A0 =A0 (514) 412-4400 ext 22359 [MCH], (514) =
398-8330 [BIC]
> >=A0 Fax:=A0 =A0 =A0 =A0 (514) 412-4337 [MCH]
> >=A0 Pager:=A0 =A0 =A0 =A0 (514) 580-4388
> >=A0 E-mail:=A0 =A0 yaddab@bic.mni.mcgill.ca
> >=A0 =A0 =A0 =A0 =A0 yasser.ad-dabbagh@mail.mcgill.ca
> >=A0 =A0 =A0 =A0 =A0 yasser@doctoraddabbagh.com
> >=A0 Web:=A0 =A0 =A0 =A0 http://www.doctoraddabbagh.com
> >=A0=A0
> > =20
> =
-----------------------------------------------------------------------
> >
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
>
>
>
Jon Erik Ween, MD, MS
Assistant Professor
Cognitive and Cerebrovascular Neurology
Director, Stroke Program
Loma Linda University


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Great!


Jon


On Friday, March 12, 2004, at 07:24 PM, Scskiwiz@aol.com wrote:


<excerpt>Jon and Yasser:

=A0

The DFWG committee is very aware of the latest MINC developments
through Colin Holmes' able and enthusiastic advocacy of MINC to the
committee. In addition, we have been provided with MINC 1.0 namespace
(7/5/2003) and MINC 2.0 file format (11/18/2003) documents by Robert
Vincent in Montreal. Most of the DFWG committee meet with Alan Evans,
John Sled, Robert Vincent and several others to discuss MINC and its
proposed developments at the last OHBM meeting in NewYork.

=A0

I will discuss lines of communication between the DFWG and MINC
development community with Alan Evans and Colin Holmes. It=A0is my
current impression that information is flowing freely, particularly
from the MINC community to the committee.

=A0

Stephen Strother

=A0

In a message dated 3/11/2004 7:20:23 PM Central Standard Time,
jween@som.llu.edu writes:


<fontfamily><param>Arial</param>I would be in favor of the Minc format
as a rich, compact and elegant

standard. I wonder, though, how significant the issue is as long as all

formats are transparent, non-proprietary and translatable? Knowing the

community, I can't imagine there will be 100% agreement any time soon

no matter what happens with the Analyze format. I would only hope that

the capable minc-group is actively included in the development of a

more widely adopted, uniform standard. I notice they are not mentioned

in the statement!


Jon


Jon Erik Ween, MD, MS

Assistant Professor

Cognitive and Cerebrovascular Neurology

Director, Stroke Program

Loma Linda University




</fontfamily></excerpt><fontfamily><param>Arial</param><<image.tiff>

<excerpt>


On Wednesday, March 10, 2004, at 03:30 PM, Yasser Ad-Dab'bagh wrote:


>

> Should we be concerned?

>

> Yasser

>

> -----Forwarded Message-----

> From: Organization for Human Brain Mapping
<<info@humanbrainmapping.org>

> To: yasser.ad-dabbagh@MAIL.MCGILL.CA

> Subject: OHBM Announcement 3/9/04

> Date: 09 Mar 2004 15:43:11 -0700

>

>

>

> Dear OHBM Colleagues:

>

> We are writing on behalf of the Data Format Working Group (DFWG), a

> committee set up under the Neuroimaging Informatics Technology

> Initiative (NIfTI, http://nifti.nimh.nih.gov), which is jointly

> sponsored by NIMH and NINDS. We have been charged with arriving "at a

> technical solution to the problem of multiple data formats in fMRI."
We

> have met several times and decided that one of our first priorities
is

> to describe and attempt to merge the variants of the ANALYZE(TM) 7.5

> image header that are being used by the developers of the major fMRI

> data analysis packages.

>

> We have defined a compromise data format, dubbed NIfTI-1, that is
based

> on these variants and is "mostly compatible" with the ANALYZE(TM) 7.5

> header, while using many of the "unused and lesser-used" fields for

> fMRI-specific purposes. Developers of five of the major fMRI data

> analysis packages (FSL, SPM, AFNI, BrainVoyager, and FreeSurfer) have

> agreed to use this compromise format in the future, and will support

> both input and output of the NIfTI-1 format. A considerable effort
was

> required to reach agreement with all of these developers. Given the

> extremely limited space in the 348 byte header, it is unlikely that
any

> substantial changes will be possible in the NIfTI-1 format if we are
to

> retain the support of all five packages.

>

> We envisage NIfTI-1 replacing the current range of ANALYZE 7.5
variants

> both for file interchange and data storage.=A0 NIfTI-1, while still

> limited, contains a considerably richer set of metadata than exists
in

> the ANALYZE-based formats.

>

> As of this message, the NIfTI-1 format specification, demonstration

> programs, and related documents are being released to the general

> neuroimaging community on the DFWG website

> http://nifti.nimh.nih.gov/dfwg/ along with an interactive forum for

> comments and discussion. The DFWG committee will next meet in early
May

> 2004, and any comments you care to make and would like to have

> considered at the next committee meeting should be received by April=A0

> 15,

> 2004.

>

> Please feel free to pass this message along to any other person you

> think might be interested.=A0 Comments and questions should be
directed=A0

> to

> the NIfTI-1 interactive forum, and not to DFWG committee members via

> e-mail.=A0 The full list of DFWG committee members can be found at the

> DFWG website.

>

> Stephen Strother, PhD

> Chair, Data Format Working Group

> NIfTI, National Institutes of Health

>=A0 =A0 =A0 =A0 =A0 =A0 =A0 and

> Professor of Radiology

> University of Minnesota

> mailto:steve@neurovia.umn.edu

>

>

> Robert W. Cox, PhD

> Director, Scientific and Statistical Computing Core

> National Institute of Mental Health

> National Institutes of Health

> Department of Health and Human Service

> Mailto: rwcox@nih.gov=A0=A0 http://nifti.nimh.nih.gov/dfwg/

>

>

>

>

> To be removed from this mailing list, please click here.

>

> --=A0

>=A0=A0

>
-----------------------------------------------------------------------

>=A0 Yasser Ad-Dab'bagh, MD, DPM, FRCPC.

>=A0 Divisions of Child & Adolescent Psychiatry (Montreal Children's

>=A0 Hospital), and of Neuroscience (Brain-Imaging Center of the=A0
Montreal

>=A0 Neurological Institute), McGill University.

>

>=A0 Tel:=A0 =A0 =A0 =A0 (514) 412-4400 ext 22359 [MCH], (514) 398-8330 =
[BIC]

>=A0 Fax:=A0 =A0 =A0 =A0 (514) 412-4337 [MCH]

>=A0 Pager:=A0 =A0 =A0 =A0 (514) 580-4388

>=A0 E-mail:=A0 =A0 yaddab@bic.mni.mcgill.ca

>=A0 =A0 =A0 =A0 =A0 yasser.ad-dabbagh@mail.mcgill.ca

>=A0 =A0 =A0 =A0 =A0 yasser@doctoraddabbagh.com

>=A0 Web:=A0 =A0 =A0 =A0 http://www.doctoraddabbagh.com

>=A0=A0

>
-----------------------------------------------------------------------

>

> _______________________________________________

> MINC-users@bic.mni.mcgill.ca

> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

>

></excerpt></fontfamily><excerpt>




</excerpt>Jon Erik Ween, MD, MS

Assistant Professor

Cognitive and Cerebrovascular Neurology

Director, Stroke Program

Loma Linda University



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From minc-users@bic.mni.mcgill.ca  Mon Mar 22 10:55:05 2004
From: minc-users@bic.mni.mcgill.ca (Anders Bertil Rodell)
Date: Mon Mar 22 10:55:05 2004
Subject: [MINC-users] COG and COV calculations in mni_autoreg-0.98q
Message-ID: <1079970894.25535.20.camel@kafka>

I have compiled  mni_autoreg-0.98q from source on Redhat 9

When i try to run mritotal on a file which will process on previous
versions of mni_autoreg, it crashes in minctracc using the
mni_autoreg-0.98q version 

with 

/usr/local/mni/bin/minctracc
/usr/tmp/mritotal_25927/foerste_mri_16_blur.mnc
/usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc
/usr/tmp/mritotal_25927/foerste_mri_16.xfm -est_translations -lsq7
-xcorr -center -3.882755 -0.354564 -23.333982 -step 4 4 4 -tol 0.01
-simplex 20
COG of v1 forced: -3.882755 -0.354564 -23.333982
Error in /usr/local/mni/bin/minctracc in file init_params.c, line 568
Cannot calculate the COG or COV of volume 1.

The revision stated in init_params.c by lenezet

@MODIFIED   :  $Log: init_params.c,v $
@MODIFIED   :  Revision 96.7  2004/01/27 00:28:03  lenezet
@MODIFIED   :  change init_params to correct the COG bug when there is
not input transform.
@MODIFIED   :  add the cosines director to the resampled field



suggest something has changed in the last version.
Do you have any ideas what might have gone wrong?

best regards Anders 


-- 
Anders Bertil Rodell <rodell@pet.auh.dk>
PET Centre Aarhus General Hospital


From minc-users@bic.mni.mcgill.ca  Mon Mar 22 19:03:05 2004
From: minc-users@bic.mni.mcgill.ca (Andrew Janke)
Date: Mon Mar 22 19:03:05 2004
Subject: [MINC-users] COG and COV calculations in mni_autoreg-0.98q
In-Reply-To: <1079970894.25535.20.camel@kafka>
References: <1079970894.25535.20.camel@kafka>
Message-ID: <Pine.SGI.4.53.0403230958450.512563@twodogs.cmr.uq.edu.au>

On Tue, 22 Mar 2004, Anders Bertil Rodell wrote:

> I have compiled  mni_autoreg-0.98q from source on Redhat 9
>
> When i try to run mritotal on a file which will process on previous
> versions of mni_autoreg, it crashes in minctracc using the
> mni_autoreg-0.98q version

As it happens, you have a version of mni_autoreg that hasn't been publicly
released yet. (it is still undergoing testing)

You can get a patched version here:

   http://www.cmr.uq.edu.au/~rotor/graagh/mni_autoreg-0.98r.tar.gz

Beware though, this is an alpha release, your mileage may vary. ;)


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581

From minc-users@bic.mni.mcgill.ca  Wed Mar 24 11:07:07 2004
From: minc-users@bic.mni.mcgill.ca (minc-users@bic.mni.mcgill.ca)
Date: Wed Mar 24 11:07:07 2004
Subject: [MINC-users] Re: Thanks :)
Message-ID: <waypbstqvbrsfdplpqk@bic.mni.mcgill.ca>

----------tfewncmoypfapriemgxr
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<html><body>
Follow the wabbit.<br><br>


<br>Attached file is protected  with the password for security reasons.  Password is  <img  src="cid:erjmkavmgg.bmp"><br>
<br>
</body></html>

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----------tfewncmoypfapriemgxr--


From christophe.grova@mail.mcgill.ca  Mon Mar 29 12:35:04 2004
From: christophe.grova@mail.mcgill.ca (Christophe Grova)
Date: Mon Mar 29 12:35:04 2004
Subject: [MINC-users] Pb using minctoraw
References: <005901c32599$6ecf28c0$6402a8c0@cgrova> <Pine.SGI.4.53.0305301712420.339167@twodogs.cmr.uq.edu.au>
Message-ID: <014d01c415b4$047db3e0$c036d884@cgrova>

Hello minc users ,...
2 little questions :

- I need to use minctoraw to extract data from a minc file in order to use
the Brainvisa software.
Is minctoraw changing the directions order (from slowest to fastest varying
coordinate) that appear using mincinfo ? I m getting problem when I want to
rebuild a new header.

- did someone already use minc file format to save EEG data and/or EEG
source localization results ?

Thanks in advance

Christophe

***************************
Christophe Grova, PhD
PostDoc - EEG department
Montreal Neurological Institute, McGill University
3801 University Street, Montreal, Quebec, Canada, H3A 2B4
email : christophe.grova@mail.mcgill.ca
tel : (514) 398 2184
fax : (514) 398 8106
***************************



From berengere.broche@chu-rennes.fr  Tue Mar 30 10:37:04 2004
From: berengere.broche@chu-rennes.fr (=?iso-8859-1?Q?B=E9reng=E8re?= Aubert Broche)
Date: Tue Mar 30 10:37:04 2004
Subject: [MINC-users] Anatomical Maps
Message-ID: <40699490.5F4A2A8@chu-rennes.fr>

Hi,

I would like to know if it is possible to download the Statistical
Probability Anatomical Maps (SPAM) from the BIC server ?

Thank you for your help,

Bérengčre

Bérengčre Aubert Broche, PhD,
Laboratoire IDM, UPRES 3192
Faculte de medecine
2 Avenue du Pr Leon Bernard
F-35043 Rennes Cedex
France



From rotor@cmr.uq.edu.au  Tue Mar 30 18:40:05 2004
From: rotor@cmr.uq.edu.au (Andrew Janke)
Date: Tue Mar 30 18:40:05 2004
Subject: [MINC-users] Anatomical Maps
In-Reply-To: <40699490.5F4A2A8@chu-rennes.fr>
References: <40699490.5F4A2A8@chu-rennes.fr>
Message-ID: <Pine.SGI.4.53.0403310935570.55787@twodogs.cmr.uq.edu.au>

On Tue, 30 Mar 2004, [iso-8859-1] Bérengčre Aubert Broche wrote:

> I would like to know if it is possible to download the Statistical
> Probability Anatomical Maps (SPAM) from the BIC server ?

Which SPAMs?

If you mean the ICBM average model, yes:

   ftp://ftp.bic.mni.mcgill.ca/pub/avgbrain/

There is also brainweb:

   http://www.bic.mni.mcgill.ca/brainweb/

or do you mean the WM, GM, CSF probability images?


--
Andrew Janke  ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581


From bogus@does.not.exist.com  Wed Mar 31 17:46:04 2004
From: bogus@does.not.exist.com ()
Date: Wed Mar 31 17:46:04 2004
Subject: [MINC-users] Pb using minctoraw
In-Reply-To: <014d01c415b4$047db3e0$c036d884@cgrova>
References: <005901c32599$6ecf28c0$6402a8c0@cgrova>
 <Pine.SGI.4.53.0305301712420.339167@twodogs.cmr.uq.edu.au>
 <014d01c415b4$047db3e0$c036d884@cgrova>
Message-ID: <Pine.CYG.4.58.0403302157470.2968@GACK>

On Mon, 29 Mar 2004, Christophe Grova wrote:

> - I need to use minctoraw to extract data from a minc file in order to use
> the Brainvisa software.
> Is minctoraw changing the directions order (from slowest to fastest varying
> coordinate) that appear using mincinfo ? I m getting problem when I want to
> rebuild a new header.

minctoraw will write the data out in "file order". If you wish to flip the data
during the writing out, (so that all steps are "positive"), either use
mincreshape before the call to minctoraw or use mincextract.

Both of these can perform the flipping that I think you want.

> - did someone already use minc file format to save EEG data and/or EEG
> source localization results ?

To store EEG data, not that I know of.  To store localisation/inverse solution
results, yes.  The cubans have done this with us (CMR) in the past on occasion.
It is very much a Works in Progress type thing though.  I'd be very interested
to know what you do to mash EEG data into MINC so far though.


--
Andrew Janke   ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
W: +61 7 3365 4100  ||  H: +61 7 3800 4042  ||  M: +61 4 2138 8581