From a.janke at gmail.com  Sun Jul  1 07:10:38 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 1 Jul 2007 21:10:38 +1000
Subject: [MINC-users] MINC Images - Center of Mass and/or Gravity
In-Reply-To: <eb9fb4b10706301034q4de0aba8gd6dcfbca94f3678e@mail.gmail.com>
References: <Pine.SGI.4.58.0706291819260.29771282@yorick.bic.mni.mcgill.ca>
	<eb9fb4b10706301034q4de0aba8gd6dcfbca94f3678e@mail.gmail.com>
Message-ID: <d747ed50707010410h74d4d136u84c0acfb6fd94698@mail.gmail.com>

> Taking a look at the mincstats code, it looks like CoM calculates the voxel
> and world coordinates for the centre by summing each image voxel's
> coordinates weighted by its image intensity. This is, I think, just the
> geometric centre if the input was binary. The results also depends on
> whether you have applied a mask or not to the input image.

Correct.

> This might be what minctracc does, but I'm not familiar enough with the code
> to comment.

One and the same.


a

From davids at bic.mni.mcgill.ca  Tue Jul  3 14:57:50 2007
From: davids at bic.mni.mcgill.ca (David SEMINOWICZ)
Date: Tue, 3 Jul 2007 14:57:50 -0400
Subject: [MINC-users] change orientation
Message-ID: <Pine.SGI.4.58.0707031441180.42539663@yorick.bic.mni.mcgill.ca>

I'm trying to change the orientation of my images (rat brains).

I've played with mincresample/xfm2param and mincreshape but I can't really figure out what
I'm doing.  I'd really appreciate a step-by-step style explanation if
possible.

dave

From Jean-Francois.Malouin at bic.mni.mcgill.ca  Tue Jul  3 16:01:39 2007
From: Jean-Francois.Malouin at bic.mni.mcgill.ca (Jean-Francois Malouin)
Date: Tue, 3 Jul 2007 16:01:39 -0400
Subject: [MINC-users] (forw) Citing MNI tools
Message-ID: <20070703200139.GB42906598@yorick.bic.mni.mcgill.ca>

Anyone cares to answer?
jf

----- Forwarded message from Mubeena Mirza <mmirza at loni.ucla.edu> -----

From: "Mubeena Mirza" <mmirza at loni.ucla.edu>
To: trinity at bic.mni.mcgill.ca
Subject: Citing MNI tools
Date: Thu, 28 Jun 2007 11:12:19 -0700
Message-ID: <a8d102bd0706281112n7e99c149lcf58ef5747408eec at mail.gmail.com>

Hi,
I am working on citing various MNI tools (listed below) in the LONI
pipeline. Could you possibly direct me to publications linked to these
tools?

Thank you,
Mubeena

Ana2Mnc
MincBlur
MINC Mask
Mincresample
Minctracc
Minc Math
Minc2Ana
N3 correction
N3 estimate
N3 evaluate
Print All Labels
Raw to MINC
XFM Concatenate
XFM Invert

----- End forwarded message -----

-- 
<? ><

From a.janke at gmail.com  Tue Jul  3 20:35:57 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 4 Jul 2007 10:35:57 +1000
Subject: [MINC-users] change orientation
In-Reply-To: <Pine.SGI.4.58.0707031441180.42539663@yorick.bic.mni.mcgill.ca>
References: <Pine.SGI.4.58.0707031441180.42539663@yorick.bic.mni.mcgill.ca>
Message-ID: <d747ed50707031735o536bb3eal65480308a27606d@mail.gmail.com>

Hi David,

if you mean you need to "rotate" the data as the conversion was not
all that good then I suggest you use the little script below.

Note that if your files are not "square" then things may rotate out of
view.  The other option is to use dirty tricks with minc_modify_header
and swap dimension names.

   http://packages.bic.mni.mcgill.ca/scripts/volrot

If you use the -verbose flag you can see the commands that are used to do it.


a

On 7/4/07, David SEMINOWICZ <davids at bic.mni.mcgill.ca> wrote:
> I'm trying to change the orientation of my images (rat brains).
>
> I've played with mincresample/xfm2param and mincreshape but I can't really figure out what
> I'm doing.  I'd really appreciate a step-by-step style explanation if
> possible.
>
> dave
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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

From oliver.gress at medizin.uni-leipzig.de  Wed Jul  4 04:39:36 2007
From: oliver.gress at medizin.uni-leipzig.de (oliver.gress@medizin.uni-leipzig.de)
Date: Wed, 4 Jul 2007 10:39:36 +0200
Subject: [MINC-users] averaging displacement -> black slices
Message-ID: <200707041039.36237.oliver.gress@medizin.uni-leipzig.de>

Hello,

I'm registering histological slices (minc volumes with z-depth=1) with 
hierarchical non-linear fitting using minctracc. I register each slice 
to its predecessor and successor. I get two minc files for the 
displacement volumes, which I average by mincaverage.

My problem now is that after applying the averaged displacement to the slices 
by mincresample, almost every second slice just contains 'zero'-values, so 
they appear black. The problem seem to be the averaged displacement volumes 
because some of them work and some of them don't. All the displacement 
volumes are non-zero, so I wonder if the averaging can produce values that 
cause problems for the mincresample operation.
Any ideas?

Thanks in advance
Oliver

From auzias at chups.jussieu.fr  Wed Jul  4 07:52:57 2007
From: auzias at chups.jussieu.fr (auzias@chups.jussieu.fr)
Date: Wed,  4 Jul 2007 13:52:57 +0200
Subject: [MINC-users] apply a transformation to a tesselation
Message-ID: <20070704135257.rqkj8lc68k0o08so@webmail.upmc.fr>

Hi,
is there an "easy way" to apply a transformation (.xfm) to a list of vertices?

I deal with tesselations from BranVISA plateform, which give me tesselations as
.mesh files,  with specific referentials.

I obtained the .xfm transformation with MRITOTAL from mri, and i would now
register the corresponding tesselations.
I tried to apply the scaling and translation from the matrice in the .xfm, but
it seems to be more complicated (center of the rotation,...).
So, i m watching to convert .mesh to .obj, but is there any easier way?

Thanks for your attention,

Guillaume Auzias,
PhD student in Paris, France.


From a.janke at gmail.com  Wed Jul  4 08:00:06 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 4 Jul 2007 22:00:06 +1000
Subject: [MINC-users] averaging displacement -> black slices
In-Reply-To: <200707041039.36237.oliver.gress@medizin.uni-leipzig.de>
References: <200707041039.36237.oliver.gress@medizin.uni-leipzig.de>
Message-ID: <d747ed50707040500j39d1cc75hd4d42fade6377a92@mail.gmail.com>

On 7/4/07, oliver.gress at medizin.uni-leipzig.de
<oliver.gress at medizin.uni-leipzig.de> wrote:
>
> I'm registering histological slices (minc volumes with z-depth=1) with
> hierarchical non-linear fitting using minctracc. I register each slice
> to its predecessor and successor. I get two minc files for the
> displacement volumes, which I average by mincaverage.
>
> My problem now is that after applying the averaged displacement to the slices
> by mincresample, almost every second slice just contains 'zero'-values, so
> they appear black. The problem seem to be the averaged displacement volumes
> because some of them work and some of them don't. All the displacement
> volumes are non-zero, so I wonder if the averaging can produce values that
> cause problems for the mincresample operation.

Hi Oliver,


My guess would be that you are getting displacements in the "z"
direction or at least the direction that is perpendicular to the
slices.  When you then transform the data this wil result in black
holes as the data is moved out of the plane. Are you setting the
deformation in this direction to 0?


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

From Michel.Audette at medizin.uni-leipzig.de  Wed Jul  4 08:04:13 2007
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Wed, 4 Jul 2007 14:04:13 +0200
Subject: [MINC-users] averaging displacement -> black slices
References: <200707041039.36237.oliver.gress@medizin.uni-leipzig.de>
	<d747ed50707040500j39d1cc75hd4d42fade6377a92@mail.gmail.com>
Message-ID: <160E3DD4FB702C4CB860C65186686E6901145500@MRZS152229.medizin.uni-leipzig.de>

Dear Andrew, 

thanks for the kind and prompt reply. Makes perfect sense! I have not looked at Oliver's script recently, but it would nice if it were that. 

Cheers,

Michel




-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke
Sent: Wed 7/4/2007 2:00 PM
To: MINC users mailing list
Subject: Re: [MINC-users] averaging displacement -> black slices
 
On 7/4/07, oliver.gress at medizin.uni-leipzig.de
<oliver.gress at medizin.uni-leipzig.de> wrote:
>
> I'm registering histological slices (minc volumes with z-depth=1) with
> hierarchical non-linear fitting using minctracc. I register each slice
> to its predecessor and successor. I get two minc files for the
> displacement volumes, which I average by mincaverage.
>
> My problem now is that after applying the averaged displacement to the slices
> by mincresample, almost every second slice just contains 'zero'-values, so
> they appear black. The problem seem to be the averaged displacement volumes
> because some of them work and some of them don't. All the displacement
> volumes are non-zero, so I wonder if the averaging can produce values that
> cause problems for the mincresample operation.

Hi Oliver,


My guess would be that you are getting displacements in the "z"
direction or at least the direction that is perpendicular to the
slices.  When you then transform the data this wil result in black
holes as the data is moved out of the plane. Are you setting the
deformation in this direction to 0?


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


From jason at bic.mni.mcgill.ca  Wed Jul  4 08:14:57 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 4 Jul 2007 08:14:57 -0400
Subject: [MINC-users] apply a transformation to a tesselation
In-Reply-To: <20070704135257.rqkj8lc68k0o08so@webmail.upmc.fr>
References: <20070704135257.rqkj8lc68k0o08so@webmail.upmc.fr>
Message-ID: <353A0495-FEA7-48CD-BE09-01CC080F54F1@bic.mni.mcgill.ca>

You want transform_objects - it takes an obj file, a transform (xfm),  
and applies the transform to the tessellation.

Jason

On 4-Jul-07, at 7:52 AM, auzias at chups.jussieu.fr wrote:

> Hi,
> is there an "easy way" to apply a transformation (.xfm) to a list  
> of vertices?
>
> I deal with tesselations from BranVISA plateform, which give me  
> tesselations as
> .mesh files,  with specific referentials.
>
> I obtained the .xfm transformation with MRITOTAL from mri, and i  
> would now
> register the corresponding tesselations.
> I tried to apply the scaling and translation from the matrice in  
> the .xfm, but
> it seems to be more complicated (center of the rotation,...).
> So, i m watching to convert .mesh to .obj, but is there any easier  
> way?
>
> Thanks for your attention,
>
> Guillaume Auzias,
> PhD student in Paris, France.
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From vanerp at LifeSci.UCLA.EDU  Thu Jul  5 02:16:07 2007
From: vanerp at LifeSci.UCLA.EDU (Theo van Erp)
Date: Wed, 04 Jul 2007 23:16:07 -0700
Subject: [MINC-users] MINC-users Digest, Vol 23, Issue 8
In-Reply-To: <mailman.1.1183219217.697721.minc-users@bic.mni.mcgill.ca>
Message-ID: <C2B1DAB7.1B87B%vanerp@zetapup.lifesci.ucla.edu>

Thanks for your responses Jason and Andrew,

With regard to the following error when loading .obj files created under
IRIX and Displaying on intel mac OS X or Linux:

/usr/local/Display-1.4.1/Display  003_nu_4400_L.obj
Inputting 003_nu_4400_L.obj.
Error inputting binary data.
     (305839 out of 33554688 items of size 12).
System message: No such file or directory
Error loading 003_nu_4400_L.obj

I just wanted to let you know that Jason's solution (using ascii_binary, see
below) worked.

> The binary versions of obj files are endian dependent - so if they were
> created on a different endian machine (say a MIPS processor IRIX machine
> creates them and then a i386 linux box tries to read them) you'll get
> that error. Convert the files to ascii (using ascii_binary) on the
> machine that created the surfaces and you'll be all set.
> 
> Jason

Andrew I also tried what you suggested below, but it did not solve this
problem.

> This may be an interesting "feature" of the OSX GLUT implementation
> biting you.  I would be interested to know if this works if you give
> the full .obj file name.  ie: /home/theo/blah/bue/foo.obj
>
> If so then start Display by itself with no filename and then under
> File->Preferences set the Current working Directory option and then
> Quit using the file menu.
> 
> Then try again with a relative path.
>
> a

Best, Theo

_____________________________________________________________
Theo G.M. van Erp, PhD

Clinical Neuroscience Lab
Department of Psychology                vanerp at psych.ucla.edu
University of California Los Angeles    voice (310) 794-9673
1285 Franz Hall, room 5556              fax (310) 794-9740
Los Angeles, California,  90095-1563
http://www.bol.ucla.edu/~vanerp
_____________________________________________________________





From auzias at chups.jussieu.fr  Tue Jul 10 07:55:29 2007
From: auzias at chups.jussieu.fr (auzias@chups.jussieu.fr)
Date: Tue, 10 Jul 2007 13:55:29 +0200
Subject: [MINC-users] apply a transformation to a tesselation
In-Reply-To: <353A0495-FEA7-48CD-BE09-01CC080F54F1@bic.mni.mcgill.ca>
References: <20070704135257.rqkj8lc68k0o08so@webmail.upmc.fr>
	<353A0495-FEA7-48CD-BE09-01CC080F54F1@bic.mni.mcgill.ca>
Message-ID: <20070710135529.g7lvigbwu8koocw0@webmail.upmc.fr>

Thank you for your answer.
Don t you know any format converter to obtain a .obj from .mesh (BrainVisa
format)?

Thanks,
Guillaume.

> You want transform_objects - it takes an obj file, a transform (xfm),
> and applies the transform to the tessellation.
>
> Jason
>
> On 4-Jul-07, at 7:52 AM, auzias at chups.jussieu.fr wrote:
>
>> Hi,
>> is there an "easy way" to apply a transformation (.xfm) to a list
>> of vertices?
>>
>> I deal with tesselations from BranVISA plateform, which give me
>> tesselations as
>> .mesh files,  with specific referentials.
>>
>> I obtained the .xfm transformation with MRITOTAL from mri, and i
>> would now
>> register the corresponding tesselations.
>> I tried to apply the scaling and translation from the matrice in
>> the .xfm, but
>> it seems to be more complicated (center of the rotation,...).
>> So, i m watching to convert .mesh to .obj, but is there any easier
>> way?
>>
>> Thanks for your attention,
>>
>> Guillaume Auzias,
>> PhD student in Paris, France.
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>




From tpb1 at ualberta.ca  Tue Jul 10 11:50:30 2007
From: tpb1 at ualberta.ca (tpb1@ualberta.ca)
Date: Tue, 10 Jul 2007 09:50:30 -0600
Subject: [MINC-users] tpb1@ualberta.ca (Thomas Bouchard): Error saving mnc
	but not tag	labels
Message-ID: <20070710095030.13z1g1m4g4400gos@webmail.ualberta.ca>

Hi Everyone,
I'm running into a snag when trying to save .mnc labels on an external  
drive.  Saving using absolute or relative paths doesn't make a  
difference, e.g.

Enter filename to save: /media/usbdisk/labels.mnc
nccreate: filename "/media/usbdisk/labels.mnc": Operation not permitted
micreate: MINC package entry point
Error: opening MINC file "/media/usbdisk/labels.mnc".

###############################################
#                                             #
#  Error:  Labels were NOT saved.             #
#                                             #
###############################################

However, .tag files can be saved just fine.  The external drive is not  
read-only, so that's not the problem.  Of course, I could use the .tag  
format, but to save space, I'd like to figure out what's wrong with  
saving in the .mnc format.  Labels save in either format when saving  
to the local disk drive, just not to the external drive.

Thanks in advance for your help,
Thomas


From a.janke at gmail.com  Tue Jul 10 20:28:37 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 11 Jul 2007 10:28:37 +1000
Subject: [MINC-users] tpb1@ualberta.ca (Thomas Bouchard): Error saving
	mnc but not tag labels
In-Reply-To: <20070710095030.13z1g1m4g4400gos@webmail.ualberta.ca>
References: <20070710095030.13z1g1m4g4400gos@webmail.ualberta.ca>
Message-ID: <d747ed50707101728l24dc400fxf5e0a9cc6eca220b@mail.gmail.com>

Hi Thomas,

This is indeed most interesting,   I am guessing that you are running
some linux variant (Ubuntu? -- given the /media path) and that the
external disk is FAT32?

Does it work if you save the .tag file to /tmp/fred.tag ?

a

On 7/11/07, tpb1 at ualberta.ca <tpb1 at ualberta.ca> wrote:
> Hi Everyone,
> I'm running into a snag when trying to save .mnc labels on an external
> drive.  Saving using absolute or relative paths doesn't make a
> difference, e.g.
>
> Enter filename to save: /media/usbdisk/labels.mnc
> nccreate: filename "/media/usbdisk/labels.mnc": Operation not permitted
> micreate: MINC package entry point
> Error: opening MINC file "/media/usbdisk/labels.mnc".
>
> ###############################################
> #                                             #
> #  Error:  Labels were NOT saved.             #
> #                                             #
> ###############################################
>
> However, .tag files can be saved just fine.  The external drive is not
> read-only, so that's not the problem.  Of course, I could use the .tag
> format, but to save space, I'd like to figure out what's wrong with
> saving in the .mnc format.  Labels save in either format when saving
> to the local disk drive, just not to the external drive.
>
> Thanks in advance for your help,
> Thomas
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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

From penhunelab at gmail.com  Wed Jul 11 14:23:58 2007
From: penhunelab at gmail.com (Penhune Lab)
Date: Wed, 11 Jul 2007 14:23:58 -0400
Subject: [MINC-users] 1.0 mm icbm 152 template
Message-ID: <c983d2410707111123j4ee7def6gf0663a177490ea1d@mail.gmail.com>

Hello, could someone please point me in the direction of the 1.00 mm ICBM
152 template? I can't seem to find it...

Thanks,
Chris
-- 
Laboratory for Motor Learning and Neural Plasticity
Directed by Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC  H4B 1R6  Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From sylvain at bic.mni.mcgill.ca  Wed Jul 11 14:44:39 2007
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Wed, 11 Jul 2007 14:44:39 -0400
Subject: [MINC-users] 1.0 mm icbm 152 template
In-Reply-To: <c983d2410707111123j4ee7def6gf0663a177490ea1d@mail.gmail.com>
References: <c983d2410707111123j4ee7def6gf0663a177490ea1d@mail.gmail.com>
Message-ID: <Pine.SGI.4.58.0707111444210.69694985@yorick.bic.mni.mcgill.ca>


/data/avgbrain/avgbrain1/brain/images/icbm*

On Wed, 11 Jul 2007, Penhune Lab wrote:

> Hello, could someone please point me in the direction of the 1.00 mm ICBM
> 152 template? I can't seem to find it...
>
> Thanks,
> Chris
> --
> Laboratory for Motor Learning and Neural Plasticity
> Directed by Dr. Virginia Penhune
> Department of Psychology, Concordia University
> SP-A 244, 7141 Sherbrooke St. W
> Montreal, QC  H4B 1R6  Canada
> (514)848-2424 ext. 7567
> http://psychology.concordia.ca/fac/penhune/winindex.html
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4

From a.janke at gmail.com  Wed Jul 11 20:05:17 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 12 Jul 2007 10:05:17 +1000
Subject: [MINC-users] 1.0 mm icbm 152 template
In-Reply-To: <Pine.SGI.4.58.0707111444210.69694985@yorick.bic.mni.mcgill.ca>
References: <c983d2410707111123j4ee7def6gf0663a177490ea1d@mail.gmail.com>
	<Pine.SGI.4.58.0707111444210.69694985@yorick.bic.mni.mcgill.ca>
Message-ID: <d747ed50707111705v3279957do6cdc1b4fda37d9f1@mail.gmail.com>

Either that or in this package:

   http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-lin-1.0.tar.gz

a

On 7/12/07, Sylvain MILOT <sylvain at bic.mni.mcgill.ca> wrote:
> /data/avgbrain/avgbrain1/brain/images/icbm*
>
> On Wed, 11 Jul 2007, Penhune Lab wrote:
> > Hello, could someone please point me in the direction of the 1.00 mm ICBM
> > 152 template? I can't seem to find it...
>

From dfwang at cse.cuhk.edu.hk  Fri Jul 20 16:26:57 2007
From: dfwang at cse.cuhk.edu.hk (Defeng WANG)
Date: Sat, 21 Jul 2007 04:26:57 +0800
Subject: [MINC-users] where to download the cortical_surface package?
References: <c983d2410707111123j4ee7def6gf0663a177490ea1d@mail.gmail.com><Pine.SGI.4.58.0707111444210.69694985@yorick.bic.mni.mcgill.ca>
	<d747ed50707111705v3279957do6cdc1b4fda37d9f1@mail.gmail.com>
Message-ID: <00bf01c7cb0c$55201340$a459bd89@PC89164>

Dear Minc Users,

Is there anybody who knows where to download the pakcage cortical_surface?

Actually the command I want to use is deform_surface, which should be in the
cortical_surface package.

Any comment will be greatly appreciated.

Regards,
Defeng


From a.janke at gmail.com  Sun Jul 22 21:47:42 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 23 Jul 2007 11:47:42 +1000
Subject: [MINC-users] where to download the cortical_surface package?
In-Reply-To: <00bf01c7cb0c$55201340$a459bd89@PC89164>
References: <c983d2410707111123j4ee7def6gf0663a177490ea1d@mail.gmail.com>
	<Pine.SGI.4.58.0707111444210.69694985@yorick.bic.mni.mcgill.ca>
	<d747ed50707111705v3279957do6cdc1b4fda37d9f1@mail.gmail.com>
	<00bf01c7cb0c$55201340$a459bd89@PC89164>
Message-ID: <d747ed50707221847r67d8b169o6d336dcfe3eaa804@mail.gmail.com>

On 7/21/07, Defeng WANG <dfwang at cse.cuhk.edu.hk> wrote:
> Is there anybody who knows where to download the package cortical_surface?
>
> Actually the command I want to use is deform_surface, which should be in the
> cortical_surface package.

Hi Defeng

The cortical surface extraction tools are not publicly released (just
yet) but they are available to a number of labs based on
collaborations that Alan Evans (the head of the group that developed
these tools) has.

I would suggest you contact Alan directly regarding this, his web page is here:

   http://www.bic.mni.mcgill.ca/~alan/


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

From Michel.Audette at medizin.uni-leipzig.de  Tue Jul 31 11:30:49 2007
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Tue, 31 Jul 2007 17:30:49 +0200
Subject: [MINC-users] rawtominc difficulties
References: <160E3DD4FB702C4CB860C65186686E69011455D7@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011455D8@MRZS152229.medizin.uni-leipzig.de>

Dear all, 

when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
See below: 

maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
rawtominc: Premature end of file.

maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 1 489 366 -input HumanS16885_Stack.raw
maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 2 489 366 -input HumanS16885_Stack.raw
rawtominc: Premature end of file.

The following is my tiffinfo result, for the tiff file that produced the raw file. 

maudette at icaw164201:~/data/ENTdata> !tiff
tiffinfo HumanS16885_Stack.tiff
TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: unknown field with tag 43314 (0xa932) encountered.
TIFF Directory at offset 0x8
  Subfile Type: (0 = 0x0)
  Image Width: 489 Image Length: 366
  Bits/Sample: 8
  Compression Scheme: None
  Photometric Interpretation: min-is-white
  Samples/Pixel: 1
  Rows/Strip: 366
  Planar Configuration: single image plane
  Tag 43314: 18768,18755,18765,16711,366,489,162,768,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,65535,0,0,0,65535,0,0,0,65535,65535,65535,0,0,65535,65535,65535,0,65535,0,255,0,0,0,0,0,0,0,14,0,0,255,255,0,2,16605,15543,42740,56988,49245,30630,62686,39891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,100,150,16256,0,340,0,0,4,0,0,16256,0,0,255,256,65535,65535,65535,0,0,0,3,0,1392,27000,25964,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength.
TIFF Directory at offset 0x3a086d8
  Subfile Type: (0 = 0x0)
  Image Width: 489 Image Length: 366
  Bits/Sample: 8

When I did a tiff2pdf I saw that the pdf file looked fine, and had 340 pages. 

Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?

Thanks for your kind consideration. 

Cheers, 

Michel

Michel Audette, Ph.D. 
Innovation Center Computer Assisted Surgery (ICCAS) 
Philipp-Rosenthal-Strasse 55
Leipzig, Germany
Phone: ++49 (0) 341 / 97 - 1 20 13
Fax: ++49 (0) 341 / 97 - 1 20 09




From jason at bic.mni.mcgill.ca  Tue Jul 31 11:27:27 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Tue, 31 Jul 2007 11:27:27 -0400
Subject: [MINC-users] rawtominc difficulties
In-Reply-To: <160E3DD4FB702C4CB860C65186686E69011455D8@MRZS152229.medizin.uni-leipzig.de>
References: <160E3DD4FB702C4CB860C65186686E69011455D7@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <46AF54DF.9090902@bic.mni.mcgill.ca>

Try something like the following:

convert -depth 8 tifffile.tif rawfile.gray
cat rawfile.gray | rawtominc -clobber output.mnc 489 366 340

(the -depth in convert is often key)

Jason

Audette, Michel wrote:
> Dear all, 
>
> when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> See below: 
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 1 489 366 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 2 489 366 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> The following is my tiffinfo result, for the tiff file that produced the raw file. 
>
> maudette at icaw164201:~/data/ENTdata> !tiff
> tiffinfo HumanS16885_Stack.tiff
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: unknown field with tag 43314 (0xa932) encountered.
> TIFF Directory at offset 0x8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>   Compression Scheme: None
>   Photometric Interpretation: min-is-white
>   Samples/Pixel: 1
>   Rows/Strip: 366
>   Planar Configuration: single image plane
>   Tag 43314: 18768,18755,18765,16711,366,489,162,768,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,65535,0,0,0,65535,0,0,0,65535,65535,65535,0,0,65535,65535,65535,0,65535,0,255,0,0,0,0,0,0,0,14,0,0,255,255,0,2,16605,15543,42740,56988,49245,30630,62686,39891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,100,150,16256,0,340,0,0,4,0,0,16256,0,0,255,256,65535,65535,65535,0,0,0,3,0,1392,27000,25964,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength.
> TIFF Directory at offset 0x3a086d8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>
> When I did a tiff2pdf I saw that the pdf file looked fine, and had 340 pages. 
>
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
> Thanks for your kind consideration. 
>
> Cheers, 
>
> Michel
>
> Michel Audette, Ph.D. 
> Innovation Center Computer Assisted Surgery (ICCAS) 
> Philipp-Rosenthal-Strasse 55
> Leipzig, Germany
> Phone: ++49 (0) 341 / 97 - 1 20 13
> Fax: ++49 (0) 341 / 97 - 1 20 09
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From a.janke at gmail.com  Tue Jul 31 11:39:03 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 1 Aug 2007 01:39:03 +1000
Subject: [MINC-users] rawtominc difficulties
In-Reply-To: <46AF54DF.9090902@bic.mni.mcgill.ca>
References: <160E3DD4FB702C4CB860C65186686E69011455D8@MRZS152229.medizin.uni-leipzig.de>
	<46AF54DF.9090902@bic.mni.mcgill.ca>
Message-ID: <d747ed50707310839lb319d14qa8f4a71b5aba92d1@mail.gmail.com>

Also, be careful of imagemagick, it can be compiled with either 8 or
16 bit quanta on different machines.  Meaning that you get either a
short or a float.  Have dig in the perl guts of mincpik for an idea of
what is going on.  (the same as what jason has given below).

I think man convert will tell you which it has been compiled with.  (IIRC!)

a

On 8/1/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> Try something like the following:
>
> convert -depth 8 tifffile.tif rawfile.gray
> cat rawfile.gray | rawtominc -clobber output.mnc 489 366 340
>
> (the -depth in convert is often key)
>
> Jason
>
> Audette, Michel wrote:
> > Dear all,
> >
> > when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> > See below:
> >
> > maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> > maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> > rawtominc: Premature end of file.
> >
> > maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 1 489 366 -input HumanS16885_Stack.raw
> > maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 2 489 366 -input HumanS16885_Stack.raw
> > rawtominc: Premature end of file.
> >
> > The following is my tiffinfo result, for the tiff file that produced the raw file.
> >
> > maudette at icaw164201:~/data/ENTdata> !tiff
> > tiffinfo HumanS16885_Stack.tiff
> > TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: unknown field with tag 43314 (0xa932) encountered.
> > TIFF Directory at offset 0x8
> >   Subfile Type: (0 = 0x0)
> >   Image Width: 489 Image Length: 366
> >   Bits/Sample: 8
> >   Compression Scheme: None
> >   Photometric Interpretation: min-is-white
> >   Samples/Pixel: 1
> >   Rows/Strip: 366
> >   Planar Configuration: single image plane
> >   Tag 43314: 18768,18755,18765,16711,366,489,162,768,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,65535,0,0,0,65535,0,0,0,65535,65535,65535,0,0,65535,65535,65535,0,65535,0,255,0,0,0,0,0,0,0,14,0,0,255,255,0,2,16605,15543,42740,56988,49245,30630,62686,39891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,100,150,16256,0,340,0,0,4,0,0,16256,0,0,255,256,65535,65535,65535,0,0,0,3,0,1392,27000,25964,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
> > TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength.
> > TIFF Directory at offset 0x3a086d8
> >   Subfile Type: (0 = 0x0)
> >   Image Width: 489 Image Length: 366
> >   Bits/Sample: 8
> >
> > When I did a tiff2pdf I saw that the pdf file looked fine, and had 340 pages.
> >
> > Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
> >
> > Thanks for your kind consideration.
> >
> > Cheers,
> >
> > Michel
> >
> > Michel Audette, Ph.D.
> > Innovation Center Computer Assisted Surgery (ICCAS)
> > Philipp-Rosenthal-Strasse 55
> > Leipzig, Germany
> > Phone: ++49 (0) 341 / 97 - 1 20 13
> > Fax: ++49 (0) 341 / 97 - 1 20 09
> >
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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

From vladimir.fonov at gmail.com  Tue Jul 31 12:00:30 2007
From: vladimir.fonov at gmail.com (Vladimir FONOV)
Date: Tue, 31 Jul 2007 12:00:30 -0400
Subject: [MINC-users] rawtominc difficulties
In-Reply-To: <160E3DD4FB702C4CB860C65186686E69011455D8@MRZS152229.medizin.uni-leipzig.de>
References: <160E3DD4FB702C4CB860C65186686E69011455D7@MRZS152229.medizin.uni-leipzig.de>
	<160E3DD4FB702C4CB860C65186686E69011455D8@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <ea3878950707310900v6c0108b4qb9449fdc08c731e0@mail.gmail.com>

Hello,

On 7/31/07, Audette, Michel <Michel.Audette at medizin.uni-leipzig.de> wrote:
> when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> See below:
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
You can check the size of the file , for example. If there are no
headers, it should be
X*Y*Z bytes long .

Also, when i was using rawtominc i was explicitly specifying some things:
rawtominc -byte -range 0 255 -orange 0 255 -real_range 0 255 -unsigned
-zyx  ....



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

From Michel.Audette at medizin.uni-leipzig.de  Tue Jul 31 12:17:18 2007
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Tue, 31 Jul 2007 18:17:18 +0200
Subject: [MINC-users] rawtominc difficulties
References: <160E3DD4FB702C4CB860C65186686E69011455D7@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69011455D8@MRZS152229.medizin.uni-leipzig.de>
	<ea3878950707310900v6c0108b4qb9449fdc08c731e0@mail.gmail.com>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011455E1@MRZS152229.medizin.uni-leipzig.de>

Hi Vladimir, 

thanks to you too for the tip. 

Cheers, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Vladimir FONOV
Sent: Tue 7/31/2007 6:00 PM
To: MINC users mailing list
Subject: Re: [MINC-users] rawtominc difficulties
 
Hello,

On 7/31/07, Audette, Michel <Michel.Audette at medizin.uni-leipzig.de> wrote:
> when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> See below:
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
You can check the size of the file , for example. If there are no
headers, it should be
X*Y*Z bytes long .

Also, when i was using rawtominc i was explicitly specifying some things:
rawtominc -byte -range 0 255 -orange 0 255 -real_range 0 255 -unsigned
-zyx  ....



-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From Michel.Audette at medizin.uni-leipzig.de  Tue Jul 31 12:03:04 2007
From: Michel.Audette at medizin.uni-leipzig.de (Michel.Audette@medizin.uni-leipzig.de)
Date: Tue, 31 Jul 2007 18:03:04 +0200
Subject: [MINC-users] rawtominc difficulties
References: <160E3DD4FB702C4CB860C65186686E69011455D7@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011455DB@MRZS152229.medizin.uni-leipzig.de>

Dear Jason and Andrew, 

thanks for your kind and incredibly prompt replies. Jason, your advise was bang on, although I had to permute the sizes for the various axes. I have a volume, although it look like it can use some serious post-processing (one slice appears significantly corrupted, and the volume seems to exhibit quite a lot of intensity nonuniformity). 

Thanks again gents. 

Michel

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Jason Lerch
Sent: Tue 7/31/2007 5:27 PM
To: MINC users mailing list
Subject: Re: [MINC-users] rawtominc difficulties
 
Try something like the following:

convert -depth 8 tifffile.tif rawfile.gray
cat rawfile.gray | rawtominc -clobber output.mnc 489 366 340

(the -depth in convert is often key)

Jason

Audette, Michel wrote:
> Dear all, 
>
> when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> See below: 
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 1 489 366 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 2 489 366 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> The following is my tiffinfo result, for the tiff file that produced the raw file. 
>
> maudette at icaw164201:~/data/ENTdata> !tiff
> tiffinfo HumanS16885_Stack.tiff
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: unknown field with tag 43314 (0xa932) encountered.
> TIFF Directory at offset 0x8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>   Compression Scheme: None
>   Photometric Interpretation: min-is-white
>   Samples/Pixel: 1
>   Rows/Strip: 366
>   Planar Configuration: single image plane
>   Tag 43314: 18768,18755,18765,16711,366,489,162,768,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,65535,0,0,0,65535,0,0,0,65535,65535,65535,0,0,65535,65535,65535,0,65535,0,255,0,0,0,0,0,0,0,14,0,0,255,255,0,2,16605,15543,42740,56988,49245,30630,62686,39891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,100,150,16256,0,340,0,0,4,0,0,16256,0,0,255,256,65535,65535,65535,0,0,0,3,0,1392,27000,25964,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength.
> TIFF Directory at offset 0x3a086d8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>
> When I did a tiff2pdf I saw that the pdf file looked fine, and had 340 pages. 
>
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
> Thanks for your kind consideration. 
>
> Cheers, 
>
> Michel
>
> Michel Audette, Ph.D. 
> Innovation Center Computer Assisted Surgery (ICCAS) 
> Philipp-Rosenthal-Strasse 55
> Leipzig, Germany
> Phone: ++49 (0) 341 / 97 - 1 20 13
> Fax: ++49 (0) 341 / 97 - 1 20 09
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   

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


From Michel.Audette at medizin.uni-leipzig.de  Tue Jul 31 12:25:26 2007
From: Michel.Audette at medizin.uni-leipzig.de (Michel.Audette@medizin.uni-leipzig.de)
Date: Tue, 31 Jul 2007 18:25:26 +0200
Subject: [MINC-users] FW:  rawtominc difficulties
References: <160E3DD4FB702C4CB860C65186686E69011455D7@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011455E2@MRZS152229.medizin.uni-leipzig.de>

<160E3DD4FB702C4CB860C65186686E69011455D8 at MRZS152229.medizin.uni-leipzig.de> <46AF54DF.9090902 at bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E69011455DB at MRZS152229.medizin.uni-leipzig.de>
From: "Audette, Michel" <Michel.Audette at medizin.uni-leipzig.de>
To: <minc-users at bic.mni.mcgill.ca>

Dear Jason and Andrew, 

thanks for your kind and incredibly prompt replies. Jason, your advise was bang on, although I had to permute the sizes for the various axes. I have a volume, although it look like it can use some serious post-processing (one slice appears significantly corrupted, and the volume seems to exhibit quite a lot of intensity nonuniformity). 

Thanks again gents. 

Michel

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Jason Lerch
Sent: Tue 7/31/2007 5:27 PM
To: MINC users mailing list
Subject: Re: [MINC-users] rawtominc difficulties
 
Try something like the following:

convert -depth 8 tifffile.tif rawfile.gray
cat rawfile.gray | rawtominc -clobber output.mnc 489 366 340

(the -depth in convert is often key)

Jason

Audette, Michel wrote:
> Dear all, 
>
> when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> See below: 
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 1 489 366 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 2 489 366 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> The following is my tiffinfo result, for the tiff file that produced the raw file. 
>
> maudette at icaw164201:~/data/ENTdata> !tiff
> tiffinfo HumanS16885_Stack.tiff
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: unknown field with tag 43314 (0xa932) encountered.
> TIFF Directory at offset 0x8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>   Compression Scheme: None
>   Photometric Interpretation: min-is-white
>   Samples/Pixel: 1
>   Rows/Strip: 366
>   Planar Configuration: single image plane
>   Tag 43314: 18768,18755,18765,16711,366,489,162,768,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,65535,0,0,0,65535,0,0,0,65535,65535,65535,0,0,65535,65535,65535,0,65535,0,255,0,0,0,0,0,0,0,14,0,0,255,255,0,2,16605,15543,42740,56988,49245,30630,62686,39891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,100,150,16256,0,340,0,0,4,0,0,16256,0,0,255,256,65535,65535,65535,0,0,0,3,0,1392,27000,25964,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength.
> TIFF Directory at offset 0x3a086d8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>
> When I did a tiff2pdf I saw that the pdf file looked fine, and had 340 pages. 
>
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
> Thanks for your kind consideration. 
>
> Cheers, 
>
> Michel
>
> Michel Audette, Ph.D. 
> Innovation Center Computer Assisted Surgery (ICCAS) 
> Philipp-Rosenthal-Strasse 55
> Leipzig, Germany
> Phone: ++49 (0) 341 / 97 - 1 20 13
> Fax: ++49 (0) 341 / 97 - 1 20 09
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   

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




From marco.loggia at mail.mcgill.ca  Tue Jul 31 14:19:52 2007
From: marco.loggia at mail.mcgill.ca (Marco Loggia, Mr)
Date: Tue, 31 Jul 2007 14:19:52 -0400
Subject: [MINC-users] p values in stats_summary
Message-ID: <1C0EA32E98729E4B9162DFDF0E941CF30141842D@EXCHANGE2VS4.campus.mcgill.ca>

Hi,

 

I running stats_summary to identify significant clusters in my VBM
analysis, and in the column which reports (or should report?) the
P-values of local maxima (third column of the SUMMARY_PEAKS matrix
output) I obtain values up to 153.43.

 

Why is that?

 

Thanks,

Marco

 

 

Marco L. Loggia

Ph.D. Candidate, Neurological Sciences

McGill Centre for Research on Pain

3640 University St. Room M/19

Montreal, QC H3A 2B2

(514) 398-1271