date:20120518

Re: [Freesurfer] Inter-hemispheric registration issue

2012-05-18 Thread Irene Altarelli

Thanks for your help, Doug. 

It seems as if there is another script problem then, because when
running the command I get the following error message (log also
attached):
ERROR: Option --keep-precision unknown

I'm using Fs version 5, and the version of xhemireg I have downloaded
is: v 1.22 2012/01/20 20:12:32.

Should that --keep-precision option be removed from the script?

Thank you,
Irene



Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit :
> Irene, this is a problem with the script. The work-around is to run 
> xhemireg before running surfreg with the --xhemi option.
> 
> doug
> 
> On 05/16/2012 01:56 AM, Irene Altarelli wrote:
> > Dear Doug,
> >
> > here is what I get.
> >
> > First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the
> > attached log file. Here is the terminal output:
> >
> > setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/
> > cd /home/ialtarelli
> > /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym
> > --lh
> >
> > Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012
> > x86_64 GNU/Linux
> > #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200)
> > #CMD# mris_register -curv -annot
> > aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere 
> > /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif 
> > /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg
> > using smoothwm curvature for final alignment
> > zeroing medial wall in aparc.annot
> > $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $
> >$Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $
> > reading surface
> > from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere...
> > reading colortable from annotation file...
> > colortable with 36 entries read
> > (originally 
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > reading template parameterization
> > from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif...
> > ripping medial wall...
> > writing registered surface
> > to 
> > /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg...
> > curvature mean = 0.007, std = 0.603
> > curvature mean = 0.030, std = 0.806
> > curvature mean = 0.024, std = 0.853
> > curvature mean = 0.009, std = 0.826
> > curvature mean = 0.011, std = 0.936
> > curvature mean = 0.003, std = 0.836
> > curvature mean = 0.005, std = 0.972
> > curvature mean = 0.001, std = 0.837
> > curvature mean = 0.001, std = 0.988
> > curvature mean = -0.032, std = 0.312
> > curvature mean = 0.032, std = 0.124
> > curvature mean = 0.079, std = 0.315
> > curvature mean = 0.031, std = 0.151
> > curvature mean = 0.049, std = 0.489
> > curvature mean = 0.031, std = 0.165
> > curvature mean = 0.028, std = 0.631
> > curvature mean = 0.031, std = 0.171
> > curvature mean = 0.011, std = 0.749
> > 159: 0 negative triangles
> > surfreg-Run-Time-Hours aa_tris lh 0 0,90
> > mardi 15 mai 2012, 20:17:58 (UTC+0200)
> > surfreg done
> >
> > Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the
> > terminal output is just:
> >
> > ERROR: cannot
> > find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere
> >
> > without any log file, at least I can't find any modified file in the
> > subject's folder.
> >
> >
> > Hope this helps make things clearer.
> > Many thanks in advance!
> > Irene
> >
> >
> > Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit :
> >> Can you send me the command line and terminal output? Did you run
> >> xhemireg first? Should not have had to ...
> >>
> >> On 05/15/2012 03:02 PM, irene.altare...@ens.fr wrote:
> >>> Dear Doug,
> >>>
> >>> where would that log file be? As the /subject/xhemi fails to be created 
> >>> the log
> >>> normally appearing in there cannot be found.. Sorry if I misunderstood
> >>> something.
> >>>
> >>> Thanks,
> >>> Irene
> >>>
> >>>
> >>> Selon Douglas N Greve:
> >>>
>  Hi Irene, can you send the log file for the command that is failing?
>  doug
> 
>  On 05/15/2012 01:28 PM, Irene Altarelli wrote:
> > Dear all,
> >
> > I'm trying to use the new script for the inter-hemisphere analysis, in
> > Fs version 5.0. I have downloaded the files as suggested
> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html).
> >
> > Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym
> > --lh), but I have problems then with the --xhemi option. Some files
> > appear to be missing, I get the following error messages:
> >
> > ERROR: cannot find /path/subject/xhemi/surf/lh.sphere
> > ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm
> > ERROR: cannot find /path/subject/xhemi/surf/lh.sphere
> > ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot
> >
> > lh.fsaverage_sym.sphere.reg is created in $subject as it should (please
> > find the surfreg log below).
> >
> > T

Re: [Freesurfer] make check => mris_expand FAILED

2012-05-18 Thread Akio Yamamoto

I could solve this problem by myself.  Thanks,

(2012/05/18 14:31), Akio Yamamoto wrote:
> Hi,
>
> When I run 'make check' after successfully completing 'make' command, I
> get the following message:
>
> ..
>
> ./mris_expand -v 111706 -thickness lh.white 0.5 lh.midgray
>
> mris_expand FAILED
> FAIL: test_mris_expand
> =
> 1 of 1 tests failed
> Please report to freesurfer@nmr.mgh.harvard.edu
> =
>
>
> How can I fix this error? Any help would be appreciated.
>
> Thanks,
> --
> Akio Yamamoto
> The University of Tokyo
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>
>
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> at
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[Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Inês Violante

Hi,

I need to know the surface area of the structures in the aparc file
but I want to obtain this measurement from the pial surface and not
the white matter surface.
How can I do that?

Thank you a lot for your help.

ines
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Re: [Freesurfer] MEMPRAGE sequence.

2012-05-18 Thread Bruce Fischl

Andre or Dylan (both ccd) can help

cheers
Bruce
On Fri, 18 May 2012, Zheng Hui wrote:

> Hi all,
> 
> We did a scanner software upgrade to BV17 (Siemens) and lost the multi-echo
> MPRAGE sequence. Does anyone have any idea where to get the sequence? The
> scanner we have is a Siemens Tim Trio.
> 
> Any help will be appreciated!
> 
> Thank you,
> Zheng Hui
> 
>
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Re: [Freesurfer] make check => mris_expand FAILED

2012-05-18 Thread Bruce Fischl

Hi Akio

the test is wrong. Not sure how it happened, but we fixed this recently in 
dev so you'll need to grab the new test data.

cheers
Bruce

On Fri, 18 May 2012, Akio Yamamoto wrote:

> Hi,
>
> When I run 'make check' after successfully completing 'make' command, I
> get the following message:
>
> ..
>
> ./mris_expand -v 111706 -thickness lh.white 0.5 lh.midgray
>
> mris_expand FAILED
> FAIL: test_mris_expand
> =
> 1 of 1 tests failed
> Please report to freesurfer@nmr.mgh.harvard.edu
> =
>
>
> How can I fix this error? Any help would be appreciated.
>
> Thanks,
> --
> Akio Yamamoto
> The University of Tokyo
> ___
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>
>
>
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Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Michael Harms


The last argument of mris_anatomical_stats allows you to specify the
surface to use (pial in your case)

cheers,
-MH


NAME
mris_anatomical_stats

SYNOPSIS
mris_anatomical_stats [options]  
[]


On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
> Hi,
> 
> I need to know the surface area of the structures in the aparc file
> but I want to obtain this measurement from the pial surface and not
> the white matter surface.
> How can I do that?
> 
> Thank you a lot for your help.
> 
> ines
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Inês Violante

Hi,

Thanks Michael.
However, when I try to do this using the aparc.annot file:

mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial

I receive this error:

mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot

I imagine this happens because the mris_anatomical_stats is waiting
for a .label file

What I aim is the output of the aparcstats2table for the surface area
using the pial surface.

Perhaps I am not using the correct command

Thanks for the help.

ines


On Fri, May 18, 2012 at 3:41 PM, Michael Harms  wrote:
>
> The last argument of mris_anatomical_stats allows you to specify the
> surface to use (pial in your case)
>
> cheers,
> -MH
>
>
> NAME
>        mris_anatomical_stats
>
> SYNOPSIS
>        mris_anatomical_stats [options]  
> []
>
>
> On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
>> Hi,
>>
>> I need to know the surface area of the structures in the aparc file
>> but I want to obtain this measurement from the pial surface and not
>> the white matter surface.
>> How can I do that?
>>
>> Thank you a lot for your help.
>>
>> ines
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>

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Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Michael Harms


You should be able to get the correct syntax by checking the recon-
all.log file for an example.

cheers,
-MH

On Fri, 2012-05-18 at 15:48 +0100, Inês Violante wrote:
> Hi,
> 
> Thanks Michael.
> However, when I try to do this using the aparc.annot file:
> 
> mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial
> 
> I receive this error:
> 
> mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot
> 
> I imagine this happens because the mris_anatomical_stats is waiting
> for a .label file
> 
> What I aim is the output of the aparcstats2table for the surface area
> using the pial surface.
> 
> Perhaps I am not using the correct command
> 
> Thanks for the help.
> 
> ines
> 
> 
> On Fri, May 18, 2012 at 3:41 PM, Michael Harms  wrote:
> >
> > The last argument of mris_anatomical_stats allows you to specify the
> > surface to use (pial in your case)
> >
> > cheers,
> > -MH
> >
> >
> > NAME
> >mris_anatomical_stats
> >
> > SYNOPSIS
> >mris_anatomical_stats [options]  
> > []
> >
> >
> > On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
> >> Hi,
> >>
> >> I need to know the surface area of the structures in the aparc file
> >> but I want to obtain this measurement from the pial surface and not
> >> the white matter surface.
> >> How can I do that?
> >>
> >> Thank you a lot for your help.
> >>
> >> ines
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to whom it 
> >> is
> >> addressed. If you believe this e-mail was sent to you in error and the 
> >> e-mail
> >> contains patient information, please contact the Partners Compliance 
> >> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> >> error
> >> but does not contain patient information, please contact the sender and 
> >> properly
> >> dispose of the e-mail.
> >

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Re: [Freesurfer] Inter-hemispheric registration issue

2012-05-18 Thread Douglas N Greve

You'll need a new version of mri_vol2vol, which I have put on that ftp site.
doug

On 05/18/2012 04:25 AM, Irene Altarelli wrote:
> Thanks for your help, Doug.
>
> It seems as if there is another script problem then, because when
> running the command I get the following error message (log also
> attached):
> ERROR: Option --keep-precision unknown
>
> I'm using Fs version 5, and the version of xhemireg I have downloaded
> is: v 1.22 2012/01/20 20:12:32.
>
> Should that --keep-precision option be removed from the script?
>
> Thank you,
> Irene
>
>
>
> Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit :
>> Irene, this is a problem with the script. The work-around is to run
>> xhemireg before running surfreg with the --xhemi option.
>>
>> doug
>>
>> On 05/16/2012 01:56 AM, Irene Altarelli wrote:
>>> Dear Doug,
>>>
>>> here is what I get.
>>>
>>> First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the
>>> attached log file. Here is the terminal output:
>>>
>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/
>>> cd /home/ialtarelli
>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym
>>> --lh
>>>
>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012
>>> x86_64 GNU/Linux
>>> #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200)
>>> #CMD# mris_register -curv -annot
>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere 
>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif 
>>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg
>>> using smoothwm curvature for final alignment
>>> zeroing medial wall in aparc.annot
>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $
>>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $
>>> reading surface
>>> from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere...
>>> reading colortable from annotation file...
>>> colortable with 36 entries read
>>> (originally 
>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>>> reading template parameterization
>>> from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif...
>>> ripping medial wall...
>>> writing registered surface
>>> to 
>>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg...
>>> curvature mean = 0.007, std = 0.603
>>> curvature mean = 0.030, std = 0.806
>>> curvature mean = 0.024, std = 0.853
>>> curvature mean = 0.009, std = 0.826
>>> curvature mean = 0.011, std = 0.936
>>> curvature mean = 0.003, std = 0.836
>>> curvature mean = 0.005, std = 0.972
>>> curvature mean = 0.001, std = 0.837
>>> curvature mean = 0.001, std = 0.988
>>> curvature mean = -0.032, std = 0.312
>>> curvature mean = 0.032, std = 0.124
>>> curvature mean = 0.079, std = 0.315
>>> curvature mean = 0.031, std = 0.151
>>> curvature mean = 0.049, std = 0.489
>>> curvature mean = 0.031, std = 0.165
>>> curvature mean = 0.028, std = 0.631
>>> curvature mean = 0.031, std = 0.171
>>> curvature mean = 0.011, std = 0.749
>>> 159: 0 negative triangles
>>> surfreg-Run-Time-Hours aa_tris lh 0 0,90
>>> mardi 15 mai 2012, 20:17:58 (UTC+0200)
>>> surfreg done
>>>
>>> Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the
>>> terminal output is just:
>>>
>>> ERROR: cannot
>>> find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere
>>>
>>> without any log file, at least I can't find any modified file in the
>>> subject's folder.
>>>
>>>
>>> Hope this helps make things clearer.
>>> Many thanks in advance!
>>> Irene
>>>
>>>
>>> Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit :
 Can you send me the command line and terminal output? Did you run
 xhemireg first? Should not have had to ...

 On 05/15/2012 03:02 PM, irene.altare...@ens.fr wrote:
> Dear Doug,
>
> where would that log file be? As the /subject/xhemi fails to be created 
> the log
> normally appearing in there cannot be found.. Sorry if I misunderstood
> something.
>
> Thanks,
> Irene
>
>
> Selon Douglas N Greve:
>
>> Hi Irene, can you send the log file for the command that is failing?
>> doug
>>
>> On 05/15/2012 01:28 PM, Irene Altarelli wrote:
>>> Dear all,
>>>
>>> I'm trying to use the new script for the inter-hemisphere analysis, in
>>> Fs version 5.0. I have downloaded the files as suggested
>>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html).
>>>
>>> Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym
>>> --lh), but I have problems then with the --xhemi option. Some files
>>> appear to be missing, I get the following error messages:
>>>
>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere
>>> ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm
>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere
>>> ERROR: cannot find /path/subject/xhemi/l

Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Douglas N Greve

And you can get the full command line from the 
$subject/scripts/recon-all.log file
doug

On 05/18/2012 10:41 AM, Michael Harms wrote:
> The last argument of mris_anatomical_stats allows you to specify the
> surface to use (pial in your case)
>
> cheers,
> -MH
>
>
> NAME
>  mris_anatomical_stats
>
> SYNOPSIS
>  mris_anatomical_stats [options]  
> []
>
>
> On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
>> Hi,
>>
>> I need to know the surface area of the structures in the aparc file
>> but I want to obtain this measurement from the pial surface and not
>> the white matter surface.
>> How can I do that?
>>
>> Thank you a lot for your help.
>>
>> ines
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Inês Violante

Thank you.

I've tried this command:

mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial

Would this be appropriate?


ines

On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve
 wrote:
> And you can get the full command line from the
> $subject/scripts/recon-all.log file
> doug
>
> On 05/18/2012 10:41 AM, Michael Harms wrote:
>> The last argument of mris_anatomical_stats allows you to specify the
>> surface to use (pial in your case)
>>
>> cheers,
>> -MH
>>
>>
>> NAME
>>          mris_anatomical_stats
>>
>> SYNOPSIS
>>          mris_anatomical_stats [options]  
>> []
>>
>>
>> On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
>>> Hi,
>>>
>>> I need to know the surface area of the structures in the aparc file
>>> but I want to obtain this measurement from the pial surface and not
>>> the white matter surface.
>>> How can I do that?
>>>
>>> Thank you a lot for your help.
>>>
>>> ines
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Douglas N Greve

yes, but you might want to change the name of the stats file so that you 
don't overwrite the one that is there
doug

On 05/18/2012 11:39 AM, Inês Violante wrote:
> Thank you.
>
> I've tried this command:
>
> mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
> AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial
>
> Would this be appropriate?
>
>
> ines
>
> On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve
>   wrote:
>> And you can get the full command line from the
>> $subject/scripts/recon-all.log file
>> doug
>>
>> On 05/18/2012 10:41 AM, Michael Harms wrote:
>>> The last argument of mris_anatomical_stats allows you to specify the
>>> surface to use (pial in your case)
>>>
>>> cheers,
>>> -MH
>>>
>>>
>>> NAME
>>>   mris_anatomical_stats
>>>
>>> SYNOPSIS
>>>   mris_anatomical_stats [options]
>>> []
>>>
>>>
>>> On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
 Hi,

 I need to know the surface area of the structures in the aparc file
 but I want to obtain this measurement from the pial surface and not
 the white matter surface.
 How can I do that?

 Thank you a lot for your help.

 ines
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Kiely Madhavan

That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error
that the control points are not within the mask. THis happens for all
tracts.

Thanks,

Kiely

On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> The .mat registration matrix should be saved under dmri/xfms/.
>
>
>
> On Wed, 16 May 2012, Kiely Donnelly wrote:
>
>  I tried using corratio and it seems to have fixed the registration issue.
>> I'm very new to this so just want to make sure I did it correctly before I
>> move forward. Should the command line look something like this if I am
>> running it in this individuals dmri directory:
>>
>> flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out
>> lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio
>>
>>
>> Thanks so much for your help.
>>
>> Kiely
>>
>> On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
>>  wrote:
>>  you have to run flirt commandline separately to check if it
>>  solves your
>>  problem.
>>
>>
>>  > Is this something I can change in my dmrirc file or do I need
>>  to run flirt
>>  > on it's own?
>>  >
>>  > Thanks,
>>  >
>>  > Kiely
>>  >
>>  > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan <
>>  > rspr...@nmr.mgh.harvard.edu> wrote:
>>  >
>>  >> Kiely, For flirt, try using corratio, cost function instead
>>  of
>>  >> mutualinfo
>>  >> (which is the default in trac-all) to see if that solves your
>>  >> registration
>>  >> problem.
>>  >>
>>  >>
>>  >> > Hi Kiely - Looks like you used flirt for the intra-subject
>>  >> registration,
>>  >> > so you can look in trac-all.log for the flirt command line
>>  that
>>  >> registers
>>  >> > diffusion to anatomical and play around with the
>>  parameters.
>>  >> >
>>  >> > You can also use bbregister instead of flirt for the
>>  intra-subject
>>  >> > registration - it has the option to initialize with flirt
>>  or with SPM.
>>  >> >
>>  >> > Hope this helps,
>>  >> > a.y
>>  >> >
>>  >> > On Wed, 16 May 2012, Kiely Donnelly wrote:
>>  >> >
>>  >> >> Hi Priti - Thanks for your help. The inter-subject
>>  registration seems
>>  >> to
>>  >> >> have run OK, but there must be something wrong with the
>>  intra-subject
>>  >> >> registration. When I try to view it using freeview, it's
>>  completely
>>  >> dark
>>  >> >> - I
>>  >> >> don't see a brain at all. Is there a way to troubleshoot
>>  this?
>>  >> >> Thanks,
>>  >> >>
>>  >> >> Kiely
>>  >> >>
>>  >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
>>  >> >>  wrote:
>>  >> >>   Hi Kiely,
>>  >> >>
>>  >> >>   Have you checked your inter and intra subject
>>  registrations?
>>  >> The
>>  >> >>   control
>>  >> >>   points going off the dwi is not only for one paths
>>  but for all
>>  >> >>   the paths.
>>  >> >>   If the registration goes terribly wrong, this can
>>  happen. You
>>  >> >>   can take a
>>  >> >>   look at
>>  >> >>
>>  >> >>   /dmri/lowb_brain_anat.flt.nii.**gz (For intra subject
>>  >> registration
>>  >> >>   diff-anat)
>>  >> >>
>>  >> >>   and
>>  >> >>
>>  >> >>   /dmri/brain_anat_mni.nii.gz (For inter-subject
>>  registration
>>  >> >>   anat-mni)
>>  >> >>
>>  >> >>   I would start by checking that first.
>>  >> >>
>>  >> >>   Priti
>>  >> >>
>>  >> >>   > Hello--
>>  >> >>   >
>>  >> >>   > I have run Tracula successfully for ~75 healthy
>>  subjects.
>>  >> >>   However, the
>>  >> >>   > pathway reconstruction seems to fail for a handful
>>  of people.
>>  >> >>   I've
>>  >> >>   > attached
>>  >> >>   > the log file for one of these subjects. It appears
>>  that the
>>  >> >>   control points
>>  >> >>   > are not within the dwi. A similar problem occurred
>>  in a
>>  >> >>   subject with
>>  >> >>   > substantial signal loss in the dwi, but that
>>  doesn't seem to
>>  >> >>   be the case
>>  >> >>   > for this particular person. I have been creating
>>  the entire
>>  >> >>   set of tracts,
>>  >> >>   > but at this point, I'm only interested in the SLFt
>>  and SLFp.
>>  >> >>   >
>>  >> >>   > Thanks,
>>  >> >>   >
>>  >> >>   > Kiely
>>  >> >> > __**_
>>  >> >> > Freesurfer mailing list
>>  >> >> > Freesurfer@nmr.mgh.harvard.edu
>>  >> >> >
>>  
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer

Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Douglas N Greve

Hi Ines, this is a good thing to post to the list since there are others 
that might know better than me. Also, please include the  full terminal 
output.
thanks
doug



On 05/18/2012 11:51 AM, Inês Violante wrote:
> Thanks a lot!
>
> Just another question:
> I get this message for one of my subjects using the previous command:
>
> ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
>
> I must have done something wrong. Is there a way to correct this
> without having to run the whole recon-all again?
>
> All the best,
>
> ines
>
>
> On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve
>   wrote:
>> yes, but you might want to change the name of the stats file so that you
>> don't overwrite the one that is there
>> doug
>>
>>
>> On 05/18/2012 11:39 AM, Inęs Violante wrote:
>>> Thank you.
>>>
>>> I've tried this command:
>>>
>>> mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
>>> AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial
>>>
>>> Would this be appropriate?
>>>
>>>
>>> ines
>>>
>>> On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve
>>> wrote:
 And you can get the full command line from the
 $subject/scripts/recon-all.log file
 doug

 On 05/18/2012 10:41 AM, Michael Harms wrote:
> The last argument of mris_anatomical_stats allows you to specify the
> surface to use (pial in your case)
>
> cheers,
> -MH
>
>
> NAME
>   mris_anatomical_stats
>
> SYNOPSIS
>   mris_anatomical_stats [options]  
> []
>
>
> On Fri, 2012-05-18 at 15:18 +0100, Inęs Violante wrote:
>> Hi,
>>
>> I need to know the surface area of the structures in the aparc file
>> but I want to obtain this measurement from the pial surface and not
>> the white matter surface.
>> How can I do that?
>>
>> Thank you a lot for your help.
>>
>> ines
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Anastasia Yendiki



Were the old .mat files replaced with the new ones?

On Fri, 18 May 2012, Kiely Madhavan wrote:


That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error that
the control points are not within the mask. THis happens for all tracts.
Thanks,

Kiely

On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
 wrote:

  The .mat registration matrix should be saved under dmri/xfms/.


  On Wed, 16 May 2012, Kiely Donnelly wrote:

I tried using corratio and it seems to have fixed
the registration issue.
I'm very new to this so just want to make sure I did
it correctly before I
move forward. Should the command line look something
like this if I am
running it in this individuals dmri directory: 

flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
-out
lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
-cost corratio


Thanks so much for your help.

Kiely

On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
 wrote:
     you have to run flirt commandline separately to
check if it
     solves your
     problem.


     > Is this something I can change in my dmrirc
file or do I need
     to run flirt
     > on it's own?
     >
     > Thanks,
     >
     > Kiely
     >
     > On Wed, May 16, 2012 at 9:27 AM, Priti
Srinivasan <
     > rspr...@nmr.mgh.harvard.edu> wrote:
     >
     >> Kiely, For flirt, try using corratio, cost
function instead
     of
     >> mutualinfo
     >> (which is the default in trac-all) to see if
that solves your
     >> registration
     >> problem.
     >>
     >>
     >> > Hi Kiely - Looks like you used flirt for
the intra-subject
     >> registration,
     >> > so you can look in trac-all.log for the
flirt command line
     that
     >> registers
     >> > diffusion to anatomical and play around
with the
     parameters.
     >> >
     >> > You can also use bbregister instead of
flirt for the
     intra-subject
     >> > registration - it has the option to
initialize with flirt
     or with SPM.
     >> >
     >> > Hope this helps,
     >> > a.y
     >> >
     >> > On Wed, 16 May 2012, Kiely Donnelly wrote:
     >> >
     >> >> Hi Priti - Thanks for your help. The
inter-subject
     registration seems
     >> to
     >> >> have run OK, but there must be something
wrong with the
     intra-subject
     >> >> registration. When I try to view it using
freeview, it's
     completely
     >> dark
     >> >> - I
     >> >> don't see a brain at all. Is there a way
to troubleshoot
     this?
     >> >> Thanks,
     >> >>
     >> >> Kiely
     >> >>
     >> >> On Wed, May 9, 2012 at 2:08 PM, Priti
Srinivasan
     >> >>  wrote:
     >> >>       Hi Kiely,
     >> >>
     >> >>       Have you checked your inter and
intra subject
     registrations?
     >> The
     >> >>       control
     >> >>       points going off the dwi is not
only for one paths
     but for all
     >> >>       the paths.
     >> >>       If the registration goes terribly
wrong, this can
     happen. You
     >> >>       can take a
     >> >>       look at
     >> >>
     >> >>       /dmri/lowb_brain_anat.flt.nii.gz
(For intra subject
     >> registration
     >> >>       diff-anat)
     >> >>
     >> >>       and
     >> >>
     >> >>       /dmri/brain_anat_mni.nii.gz (For
inter-subject
     registration
     >> >>       anat-mni)
     >> >>
     >> >>       I would start by checking that
first.
     >> >>
     >> >>       Priti
     >> >>
     >> >>       > Hello--
     >> >>       >

Re: [Freesurfer] Surface Area aparc from pial surface

2012-05-18 Thread Inês Violante

Hi,

It repeats this several times and

MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file: CS/label/lh.aparc.annot
MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file: CS/label/lh.aparc.annot
MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file: CS/label/lh.aparc.annot

(...)

ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!


On Fri, May 18, 2012 at 4:53 PM, Douglas N Greve
 wrote:
> Hi Ines, this is a good thing to post to the list since there are others
> that might know better than me. Also, please include the  full terminal
> output.
> thanks
> doug
>
>
>
>
> On 05/18/2012 11:51 AM, Inês Violante wrote:
>>
>> Thanks a lot!
>>
>> Just another question:
>> I get this message for one of my subjects using the previous command:
>>
>> ERROR: Too many out-of-range vertex indices in
>> MRISreadAnnotationIntoArray!
>>
>> I must have done something wrong. Is there a way to correct this
>> without having to run the whole recon-all again?
>>
>> All the best,
>>
>> ines
>>
>>
>> On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve
>>   wrote:
>>>
>>> yes, but you might want to change the name of the stats file so that you
>>> don't overwrite the one that is there
>>> doug
>>>
>>>
>>> On 05/18/2012 11:39 AM, Inęs Violante wrote:

 Thank you.

 I've tried this command:

 mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
 AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial

 Would this be appropriate?


 ines

 On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve
     wrote:
>
> And you can get the full command line from the
> $subject/scripts/recon-all.log file
> doug
>
> On 05/18/2012 10:41 AM, Michael Harms wrote:
>>
>> The last argument of mris_anatomical_stats allows you to specify the
>> surface to use (pial in your case)
>>
>> cheers,
>> -MH
>>
>>
>> NAME
>>          mris_anatomical_stats
>>
>> SYNOPSIS
>>          mris_anatomical_stats [options]      
>> []
>>
>>
>> On Fri, 2012-05-18 at 15:18 +0100, Inęs Violante wrote:
>>>
>>> Hi,
>>>
>>> I need to know the surface area of the structures in the aparc file
>>> but I want to obtain this measurement from the pial surface and not
>>> the white matter surface.
>>> How can I do that?
>>>
>>> Thank you a lot for your help.
>>>
>>> ines
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>>> whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and
>>> the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>> you
>>> in error
>>> but does not contain patient information, please contact the sender
>>> and
>>> properly
>>> dispose of the e-mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Kiely Madhavan

I only created a diff2anat.flt.mat file which replaced the old one. Do they
all need to be recreated? If so, is that something I add to the command
line?

On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Were the old .mat files replaced with the new ones?
>
>
> On Fri, 18 May 2012, Kiely Madhavan wrote:
>
>  That seemed to fix the registration issue, but I'm still unable to
>> reconstruct the tracts using trac-all -path. I'm getting the same error
>> that
>> the control points are not within the mask. THis happens for all tracts.
>> Thanks,
>>
>> Kiely
>>
>> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
>>  wrote:
>>
>>  The .mat registration matrix should be saved under dmri/xfms/.
>>
>>
>>  On Wed, 16 May 2012, Kiely Donnelly wrote:
>>
>>I tried using corratio and it seems to have fixed
>>the registration issue.
>>I'm very new to this so just want to make sure I did
>>it correctly before I
>>move forward. Should the command line look something
>>like this if I am
>>running it in this individuals dmri directory:
>>
>>flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
>>-out
>>lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
>>-cost corratio
>>
>>
>>Thanks so much for your help.
>>
>>Kiely
>>
>>On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
>> wrote:
>> you have to run flirt commandline separately to
>>check if it
>> solves your
>> problem.
>>
>>
>> > Is this something I can change in my dmrirc
>>file or do I need
>> to run flirt
>> > on it's own?
>> >
>> > Thanks,
>> >
>> > Kiely
>> >
>> > On Wed, May 16, 2012 at 9:27 AM, Priti
>>Srinivasan <
>> > rspr...@nmr.mgh.harvard.edu> wrote:
>> >
>> >> Kiely, For flirt, try using corratio, cost
>>function instead
>> of
>> >> mutualinfo
>> >> (which is the default in trac-all) to see if
>>that solves your
>> >> registration
>> >> problem.
>> >>
>> >>
>> >> > Hi Kiely - Looks like you used flirt for
>>the intra-subject
>> >> registration,
>> >> > so you can look in trac-all.log for the
>>flirt command line
>> that
>> >> registers
>> >> > diffusion to anatomical and play around
>>with the
>> parameters.
>> >> >
>> >> > You can also use bbregister instead of
>>flirt for the
>> intra-subject
>> >> > registration - it has the option to
>>initialize with flirt
>> or with SPM.
>> >> >
>> >> > Hope this helps,
>> >> > a.y
>> >> >
>> >> > On Wed, 16 May 2012, Kiely Donnelly wrote:
>> >> >
>> >> >> Hi Priti - Thanks for your help. The
>>inter-subject
>> registration seems
>> >> to
>> >> >> have run OK, but there must be something
>>wrong with the
>> intra-subject
>> >> >> registration. When I try to view it using
>>freeview, it's
>> completely
>> >> dark
>> >> >> - I
>> >> >> don't see a brain at all. Is there a way
>>to troubleshoot
>> this?
>> >> >> Thanks,
>> >> >>
>> >> >> Kiely
>> >> >>
>> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti
>>Srinivasan
>> >> >>  wrote:
>> >> >>   Hi Kiely,
>> >> >>
>> >> >>   Have you checked your inter and
>>intra subject
>> registrations?
>> >> The
>> >> >>   control
>> >> >>   points going off the dwi is not
>>only for one paths
>> but for all
>> >> >>   the paths.
>> >> >>   If the registration goes terribly
>>wrong, this can
>> happen. You
>> >> >>   can take a
>> >> >>   look at
>> >> >>
>> >> >>   /dmri/lowb_brain_anat.flt.nii.**gz
>>(For intra subject
>> >> registration
>> >>

Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Anastasia Yendiki

The other registration files depend on diff2anat. For example, diff2mni is 
composed of diff2anat and anat2mni. If you're using the old diff2mni, 
it's like you didn't change anything.

The -intra step creates all these. You need to edit the command that 
generates the diff2anat in your version of trac-preproc. Either comment 
that line out so that it runs everything but that, or change that line to 
the options that worked for you.

On Fri, 18 May 2012, Kiely Madhavan wrote:

I only created a diff2anat.flt.mat file which replaced the old one. Do they all 
need to be recreated? If so, is that something I
add to the command line?

On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki 
 wrote:

  Were the old .mat files replaced with the new ones?

  On Fri, 18 May 2012, Kiely Madhavan wrote:

That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same 
error that
the control points are not within the mask. THis happens for all 
tracts.
Thanks,

Kiely

On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
 wrote:

     The .mat registration matrix should be saved under dmri/xfms/.

     On Wed, 16 May 2012, Kiely Donnelly wrote:

           I tried using corratio and it seems to have fixed
           the registration issue.
           I'm very new to this so just want to make sure I did
           it correctly before I
           move forward. Should the command line look something
           like this if I am
           running it in this individuals dmri directory: 

           flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
           -out
           lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
           -cost corratio

           Thanks so much for your help.

           Kiely

           On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
            wrote:
                you have to run flirt commandline separately to
           check if it
                solves your
                problem.

                > Is this something I can change in my dmrirc
           file or do I need
                to run flirt
                > on it's own?
                >
                > Thanks,
                >
                > Kiely
                >
                > On Wed, May 16, 2012 at 9:27 AM, Priti
           Srinivasan <
                > rspr...@nmr.mgh.harvard.edu> wrote:
                >
                >> Kiely, For flirt, try using corratio, cost
           function instead
                of
                >> mutualinfo
                >> (which is the default in trac-all) to see if
           that solves your
                >> registration
                >> problem.
                >>
                >>
                >> > Hi Kiely - Looks like you used flirt for
           the intra-subject
                >> registration,
                >> > so you can look in trac-all.log for the
           flirt command line
                that
                >> registers
                >> > diffusion to anatomical and play around
           with the
                parameters.
                >> >
                >> > You can also use bbregister instead of
           flirt for the
                intra-subject
                >> > registration - it has the option to
           initialize with flirt
                or with SPM.
                >> >
                >> > Hope this helps,
                >> > a.y
                >> >
                >> > On Wed, 16 May 2012, Kiely Donnelly wrote:
                >> >
                >> >> Hi Priti - Thanks for your help. The
           inter-subject
                registration seems
                >> to
                >> >> have run OK, but there must be something
           wrong with the
                intra-subject
                >> >> registration. When I try to view it using
           freeview, it's
                completely
                >> da

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

2012-05-18 Thread Matt Glasser

Another note on this:

Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag
is not set to 1 (it picks op a lot of options it shouldn't).  Thus, instead
of commenting out the flag, it is better to set it to zero after the 

set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*`

Line.  Then one gets the best of both worlds.  

Peace,

Matt.

-Original Message-
From: Matt Glasser [mailto:m...@ma-tea.com] 
Sent: Thursday, March 22, 2012 5:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)

I'm dredging this 2 year old post up for the benefit of Google and anyone
else who wonders about the cause of this.  It is a non-fatal error (for
FreeSurfer, but perhaps not other things) that is caused by having set the
variable:

POSIXLY_CORRECT=1

It causes bc (on Debian/Ubuntu) systems to fail when making comparisons
like:

echo '3.5 > 2.5' | bc -l

I am guessing (because this is what I was doing) that the poster was using
fsl_sub to launch FreeSurfer jobs in SGE.  fsl_sub sets this flag for some
reason, but commenting it out seems not to cause any problems.

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng
Sent: Sunday, March 14, 2010 1:37 PM
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

Thanks! I would check them later.

On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl
 wrote:
> if it was a syntax error then recon-all wouldn't have finished, so I'm not
> sure what's going on. You should visually inspect the surfaces and
> segmentations to make sure they are all ok.
>
> cheers,
> Bruce
>
> On Mon, 15 Mar 2010, Xue, Feng wrote:
>
>> Sorry, I didn't notice that the reply address was not the list, I've
>> done re-post it.
>>
>> Is there any method to check whether it is ok? For SGE, it might only
>> write errors to dot e files instead of warnings.
>>
>> It seemed like a shell syntax error, however, I don't have that
>> experience to check the recon-all script.
>>
>> On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl
>>  wrote:
>>>
>>> can you post this to the list? There are others better qualified to say
>>> what's going on. But if everything finished ok is there really a
problem?
>>> Maybe this is just a warning?
>>> On Sun, 14 Mar 2010, Xue, Feng wrote:
>>>
 Hi Bruce,

 Thanks for your reply. The recon-all.log said it finished without
 error. please find the whole scripts root in the attachment.
 I'm also running a raw testing with one subject and without
SGEMaybe
 I can report the result the day after tomorrow.

 BTW, I found in my 64bit Debian nodes, I repeated got the error as
below
 (standard_in) 2: Error: comparison in expression
 but in 32bit, I met both.

 for the GMail security restriction, I changed recon-all.cmd in the
 attachment to recon-all.cmds.

 On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl
  wrote:
>
> what does the recon-all.log say? Did the recon finish correctly? Does
> this
> happen if you just run it on the command line?
> Bruce
>
> On Sat, 13 Mar 2010, Xue, Feng wrote:
>
>> Dear Bruce & FS experts,
>>
>> Please forgive my re-post, for I havn't got any response from last
>> post.
>> I do appreciate if anyone could give me a hint or suggestion.
>>
>> ++
>>
>> We are running freesurfer with Sun GridEngine. Currently, we
>> repeatedly got this error in SGE's job error log file on some data
>> when doing recon_all:
>>
>> $ cat recon_xf.e437
>> (standard_in) 2: Error: comparison in expression
>> $ cat recon_xf.e431
>> (standard_in) 2: comparison in expression
>>
>> I also checked the recon-all-status.log file, but not error was
found.
>>
>> Has anyone met this problem? Is it critical?
>> Thanks in advance.
>>
>> --
>> Best Regards
>>
>> Xue, Feng Phd. candidate
>> Major in Developmental Cognitive Neuroscience
>>
>> National Key Laboratory of Cognitive Neuroscience and Learning
>> Beijing Normal University
>> Beijing, China. 100875
>> Tel: +86-13810154455
>> web: http://psychbrain.bnu.edu.cn
>> ==
>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
>> telnet://bbs.mdjs.org
>> http://bbs.mdjs.org
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom
> it
> is
> addressed. If you believe this e-mail was sent to you in error and the

Re: [Freesurfer] surfaceRAS to Talairach

2012-05-18 Thread Douglas N Greve

What do you mean by "ras matlab subscripts"? Those looks like indices, 
not RAS. Assuming those are indices, then that looks right.
doug

On 05/18/2012 02:02 PM, Jordan L. Poppenk wrote:
> Dear Doug,
>
> To generalize from this earlier conversion question, to interpret the 
> coordinate space of a file loaded by freesufer/matlab/MRIread.m, would one 
> use the following transform to move from ras matlab subscripts (e.g., 
> 1:256,1:256,1:256) to mni coords?
>
> mni = talairach.xfm * vox2ras1 * [r a s 1]
>
> The coordinates I get out of this transform do not seem quite right.
>
> Cheers,
> Jordan
>
>
> On May 3, 2012, at 5:40 PM, Jordan Poppenk wrote:
>
>> Dear Douglas,
>>
>> That's exactly the information I was looking for. This worked perfectly. 
>> Thank you for your help!
>>
>> Cheers,
>> Jordan
>>
>>
>>> Here's how to convert from surface RAS to mni305
>>>
>>> mni305ras =  X*S*inv(K)*ras
>>> X = talairach.xfm
>>> S = scanner vox2ras (mri_info --vox2ras orig.mgz)
>>> K = tkreg vox2ras   (mri_info --vox2ras-tkr orig.mgz)
>>> ras = surface ras
>>>
>>> If you want to go from mni305 to approximate talairach, you can use this
>>> transform from Matthew Brett:
>>>
>>>
>>> function outpoints = mni2tal(inpoints)
>>> % Converts coordinates from MNI brain to best guess
>>> % for equivalent Talairach coordinates
>>> % FORMAT outpoints = mni2tal(inpoints)
>>> % Where inpoints is N by 3 or 3 by N matrix of coordinates
>>> %  (N being the number of points)
>>> % outpoints is the coordinate matrix with Talairach points
>>> % Matthew Brett 10/8/99
>>>
>>> dimdim = find(size(inpoints) == 3);
>>> if isempty(dimdim)
>>>error('input must be a N by 3 or 3 by N matrix')
>>> end
>>> if dimdim == 2
>>>inpoints = inpoints'; %'
>>> end
>>>
>>> % Transformation matrices, different zooms above/below AC
>>> upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]);
>>> downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]);
>>>
>>> tmp = inpoints(3,:)<0;  % 1 if below AC
>>> inpoints = [inpoints; ones(1, size(inpoints, 2))];
>>> inpoints(:, tmp) = downT * inpoints(:, tmp);
>>> inpoints(:, ~tmp) = upT * inpoints(:, ~tmp);
>>> outpoints = inpoints(1:3, :);
>>> if dimdim == 2
>>>outpoints = outpoints'; %'
>>> end
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 05/02/2012 12:54 PM, Jordan Poppenk wrote:
>>> Dear FreeSurfer experts,
>>>

>>> How does one properly convert from surfaceRAS coords, as provided by 
>>> fs_read_surf.m, to talairach coords? I have tried using 
>>> freesurfer_surf2tal.m posted on the web by Darren Weber, supplying it with 
>>> transform data from transforms/talairach.xfm, but the values returned often 
>>> differ from those in tksurfer by as much as 20mm (and are clearly wrong). 
>>> What I would like to do is match the coordinate system in tksurfer (which 
>>> is clearly right). How does tksurfer do it?
>>>

>>> Cheers,
>>>
>>> Jordan
>>>


>>> ___
>>>
>>> Freesurfer mailing list
>>>
 Freesurfer at nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> -- 
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>>
>>> greve at nmr.mgh.harvard.edu
>>>
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Kiely Madhavan

OK - Can you point me in the direction of the trac-preproc file that I
should edit?

On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> The other registration files depend on diff2anat. For example, diff2mni is
> composed of diff2anat and anat2mni. If you're using the old diff2mni, it's
> like you didn't change anything.
>
> The -intra step creates all these. You need to edit the command that
> generates the diff2anat in your version of trac-preproc. Either comment
> that line out so that it runs everything but that, or change that line to
> the options that worked for you.
>
>
>
> On Fri, 18 May 2012, Kiely Madhavan wrote:
>
>  I only created a diff2anat.flt.mat file which replaced the old one. Do
>> they all need to be recreated? If so, is that something I
>> add to the command line?
>>
>> On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>  Were the old .mat files replaced with the new ones?
>>
>>  On Fri, 18 May 2012, Kiely Madhavan wrote:
>>
>>That seemed to fix the registration issue, but I'm still
>> unable to
>>reconstruct the tracts using trac-all -path. I'm getting the
>> same error that
>>the control points are not within the mask. THis happens for
>> all tracts.
>>Thanks,
>>
>>Kiely
>>
>>On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
>> wrote:
>>
>>á á áThe .mat registration matrix should be saved under
>> dmri/xfms/.
>>
>>
>>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:
>>
>>á á á á á áI tried using corratio and it seems to have fixed
>>á á á á á áthe registration issue.
>>á á á á á áI'm very new to this so just want to make sure I did
>>á á á á á áit correctly before I
>>á á á á á ámove forward. Should the command line look something
>>á á á á á álike this if I am
>>á á á á á árunning it in this individuals dmri directory:á
>>
>>á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
>>á á á á á á-out
>>á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
>>á á á á á á-cost corratio
>>
>>
>>á á á á á áThanks so much for your help.
>>
>>á á á á á áKiely
>>
>>á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
>>á á á á á á wrote:
>>á á á á á áá á áyou have to run flirt commandline separately to
>>á á á á á ácheck if it
>>á á á á á áá á ásolves your
>>á á á á á áá á áproblem.
>>
>>
>>á á á á á áá á á> Is this something I can change in my dmrirc
>>á á á á á áfile or do I need
>>á á á á á áá á áto run flirt
>>á á á á á áá á á> on it's own?
>>á á á á á áá á á>
>>á á á á á áá á á> Thanks,
>>á á á á á áá á á>
>>á á á á á áá á á> Kiely
>>á á á á á áá á á>
>>á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti
>>á á á á á áSrinivasan <
>>á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote:
>>á á á á á áá á á>
>>á á á á á áá á á>> Kiely, For flirt, try using corratio, cost
>>á á á á á áfunction instead
>>á á á á á áá á áof
>>á á á á á áá á á>> mutualinfo
>>á á á á á áá á á>> (which is the default in trac-all) to see if
>>á á á á á áthat solves your
>>á á á á á áá á á>> registration
>>á á á á á áá á á>> problem.
>>á á á á á áá á á>>
>>á á á á á áá á á>>
>>á á á á á áá á á>> > Hi Kiely - Looks like you used flirt for
>>á á á á á áthe intra-subject
>>á á á á á áá á á>> registration,
>>á á á á á áá á á>> > so you can look in trac-all.log for the
>>á á á á á áflirt command line
>>á á á á á áá á áthat
>>á á á á á áá á á>> registers
>>á á á á á áá á á>> > diffusion to anatomical and play around
>>á á á á á áwith the
>>á á á á á áá á áparameters.
>>á á á á á áá á á>> >
>>á á á á á áá á á>> > You can also use bbregister instead of
>>á á á á á áflirt for the
>>á á á á á áá á áintra-subject
>>á á á á á áá á á>> > registration - it has the option to
>>á á á á á áinitialize with flirt
>>á á á á á áá á áor with SPM.
>>á á á á á áá á á>> >
>>á á á á á áá á á>> > Hope this helps,
>>á á á á á áá á á>> > a.y
>>á á á á á áá á á>> >
>>á á á á á áá á á>> > On Wed, 16 May 2012, Kiely Donnelly wrote:
>>á á á á á áá á á>> >
>>á á á á á áá á á>> >> Hi Priti - Thanks for your help. The
>>á á á á á ái

Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Anastasia Yendiki



This is a script, it's in the directory where all freesurfer scripts are. 
You can find it by doing "which trac-preproc".


On Fri, 18 May 2012, Kiely Madhavan wrote:


OK - Can you point me in the direction of the trac-preproc file that I should 
edit? 

On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki 
 wrote:

  The other registration files depend on diff2anat. For example, diff2mni 
is composed of diff2anat and anat2mni. If
  you're using the old diff2mni, it's like you didn't change anything.

  The -intra step creates all these. You need to edit the command that 
generates the diff2anat in your version of
  trac-preproc. Either comment that line out so that it runs everything but 
that, or change that line to the options
  that worked for you.


  On Fri, 18 May 2012, Kiely Madhavan wrote:

  I only created a diff2anat.flt.mat file which replaced the old one. Do 
they all need to be recreated? If so,
  is that something I
  add to the command line?

  On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki 
 wrote:

       Were the old .mat files replaced with the new ones?

       On Fri, 18 May 2012, Kiely Madhavan wrote:

             That seemed to fix the registration issue, but I'm still 
unable to
             reconstruct the tracts using trac-all -path. I'm getting the 
same error that
             the control points are not within the mask. THis happens for 
all tracts.
             Thanks,

             Kiely

             On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
              wrote:

           á á áThe .mat registration matrix should be saved under dmri/xfms/.


           á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:

           á á á á á áI tried using corratio and it seems to have fixed
           á á á á á áthe registration issue.
           á á á á á áI'm very new to this so just want to make sure I did
           á á á á á áit correctly before I
           á á á á á ámove forward. Should the command line look something
           á á á á á álike this if I am
           á á á á á árunning it in this individuals dmri directory:á

           á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
           á á á á á á-out
           á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
           á á á á á á-cost corratio


           á á á á á áThanks so much for your help.

           á á á á á áKiely

           á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
           á á á á á á wrote:
           á á á á á áá á áyou have to run flirt commandline separately to
           á á á á á ácheck if it
           á á á á á áá á ásolves your
           á á á á á áá á áproblem.


           á á á á á áá á á> Is this something I can change in my dmrirc
           á á á á á áfile or do I need
           á á á á á áá á áto run flirt
           á á á á á áá á á> on it's own?
           á á á á á áá á á>
           á á á á á áá á á> Thanks,
           á á á á á áá á á>
           á á á á á áá á á> Kiely
           á á á á á áá á á>
           á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti
           á á á á á áSrinivasan <
           á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote:
           á á á á á áá á á>
           á á á á á áá á á>> Kiely, For flirt, try using corratio, cost
           á á á á á áfunction instead
           á á á á á áá á áof
           á á á á á áá á á>> mutualinfo
           á á á á á áá á á>> (which is the default in trac-all) to see if
           á á á á á áthat solves your
           á á á á á áá á á>> registration
           á á á á á áá á á>> problem.
           á á á á á áá á á>>
           á á á á á áá á á>>
           á á á á á áá á á>> > Hi Kiely - Looks like you used flirt for
           á á á á á áthe intra-subject
           á á á á á áá á á>> registration,
           á á á á á áá á á>> > so you can look in trac-all.log for the
           á á á á á áflirt command line
           á á á á á áá á áthat
           á á á á á áá á á>> registers
           á á á á á áá á á>> > diffusion to anatomical and play around
           á á á á á áwith the
           á á á á á áá á áparameters.
           á á á á á áá á á>> >
           á á á á á áá á á>> > You can also use bbregister instead of
           á á á á á áflirt for the
           á á á á á áá á áintra-subject
           á á á á á áá á á>> > registration - it has the option to
           á á á á á áinitialize with flirt
           á á á á á áá á áor with SPM.
           á á á á á áá á á>> >
           á á á á á áá á á>> > Hope this helps,
           á á á á á áá á á>> > a.y
           á á á á á áá á á>> >
           á á á á á áá á á>> > On Wed, 16 May 2012, Kiely Donnelly wrote:
           á á á á á áá á á>> >
           á á á á á áá á á>> >> Hi Priti - Thanks for your help. The
           á á á á á áinter-subject
           á á á á á áá á áregistration seems
           á á á á á áá á

Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Kiely Madhavan

That's where I looked, but all I see is the following (I don't see the
command line that creates the diff2anat for me to edit):


Last login: Fri May 18 13:45:47 on ttys000
/Applications/freesurfer/bin/trac-preproc ; exit;
Kielys-MacBook-Air:~ kielydonnelly$
/Applications/freesurfer/bin/trac-preproc ; exit;

USAGE: trac-preproc

Required arguments:
  -c   : dmrirc file (see dmrirc.example)

Other arguments:
  -log : default is trac-all.log in the same dir as dmrirc
  -nolog : do not save a log file
  -cmd : default is trac-all.cmd in the same dir as dmrirc
  -nocmd : do not save a cmd file
  -no-isrunning  : do not check whether this subject is currently being
processed
  -umask umask   : set unix file permission mask (default 002)
  -grp groupid   : check that current group is alpha groupid
  -allowcoredump : set coredump limit to unlimited
  -debug : generate much more output
  -dontrun   : do everything but execute each command
  -version   : print version of this script and exit
  -help  : print full contents of help

logout

[Process completed]

On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> This is a script, it's in the directory where all freesurfer scripts are.
> You can find it by doing "which trac-preproc".
>
>
> On Fri, 18 May 2012, Kiely Madhavan wrote:
>
>  OK - Can you point me in the direction of the trac-preproc file that I
>> should edit?
>>
>> On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>  The other registration files depend on diff2anat. For example,
>> diff2mni is composed of diff2anat and anat2mni. If
>>  you're using the old diff2mni, it's like you didn't change anything.
>>
>>  The -intra step creates all these. You need to edit the command that
>> generates the diff2anat in your version of
>>  trac-preproc. Either comment that line out so that it runs
>> everything but that, or change that line to the options
>>  that worked for you.
>>
>>
>>  On Fri, 18 May 2012, Kiely Madhavan wrote:
>>
>>  I only created a diff2anat.flt.mat file which replaced the old one.
>> Do they all need to be recreated? If so,
>>  is that something I
>>  add to the command line?
>>
>>  On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Were the old .mat files replaced with the new ones?
>>
>>   On Fri, 18 May 2012, Kiely Madhavan wrote:
>>
>> That seemed to fix the registration issue, but I'm still
>> unable to
>> reconstruct the tracts using trac-all -path. I'm getting
>> the same error that
>> the control points are not within the mask. THis happens
>> for all tracts.
>> Thanks,
>>
>> Kiely
>>
>> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
>>  wrote:
>>
>>á á áThe .mat registration matrix should be saved under
>> dmri/xfms/.
>>
>>
>>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:
>>
>>á á á á á áI tried using corratio and it seems to have fixed
>>á á á á á áthe registration issue.
>>á á á á á áI'm very new to this so just want to make sure I did
>>á á á á á áit correctly before I
>>á á á á á ámove forward. Should the command line look something
>>á á á á á álike this if I am
>>á á á á á árunning it in this individuals dmri directory:á
>>
>>á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
>>á á á á á á-out
>>á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
>>á á á á á á-cost corratio
>>
>>
>>á á á á á áThanks so much for your help.
>>
>>á á á á á áKiely
>>
>>á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
>>á á á á á á wrote:
>>á á á á á áá á áyou have to run flirt commandline separately to
>>á á á á á ácheck if it
>>á á á á á áá á ásolves your
>>á á á á á áá á áproblem.
>>
>>
>>á á á á á áá á á> Is this something I can change in my dmrirc
>>á á á á á áfile or do I need
>>á á á á á áá á áto run flirt
>>á á á á á áá á á> on it's own?
>>á á á á á áá á á>
>>á á á á á áá á á> Thanks,
>>á á á á á áá á á>
>>á á á á á áá á á> Kiely
>>á á á á á áá á á>
>>á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti
>>á á á á á áSrinivasan <
>>á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote:
>>á á á á á áá á á>
>>á á á á á áá á á>> Kiely, For flirt, try using corratio, cost
>>á á á á á áfunction instead
>>á á á á á áá á áof
>>á á á á á áá á á>> mutualinfo
>

Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Anastasia Yendiki



This is the help text that you get when you run the script. You need to 
open the script in a text editor.


On Fri, 18 May 2012, Kiely Madhavan wrote:


That's where I looked, but all I see is the following (I don't see the command 
line that creates the diff2anat for me to edit):

Last login: Fri May 18 13:45:47 on ttys000
/Applications/freesurfer/bin/trac-preproc ; exit;
Kielys-MacBook-Air:~ kielydonnelly$ /Applications/freesurfer/bin/trac-preproc ; 
exit;

USAGE: trac-preproc

Required arguments:
  -c       : dmrirc file (see dmrirc.example)

Other arguments:
  -log     : default is trac-all.log in the same dir as dmrirc
  -nolog         : do not save a log file
  -cmd     : default is trac-all.cmd in the same dir as dmrirc
  -nocmd         : do not save a cmd file
  -no-isrunning  : do not check whether this subject is currently being 
processed
  -umask umask   : set unix file permission mask (default 002)
  -grp groupid   : check that current group is alpha groupid 
  -allowcoredump : set coredump limit to unlimited
  -debug         : generate much more output
  -dontrun       : do everything but execute each command
  -version       : print version of this script and exit
  -help          : print full contents of help

logout

[Process completed]

On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki 
 wrote:

  This is a script, it's in the directory where all freesurfer scripts are. You 
can find it by doing "which
  trac-preproc".

  On Fri, 18 May 2012, Kiely Madhavan wrote:

OK - Can you point me in the direction of the trac-preproc file 
that I should edit? 

On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki 
 wrote:

     The other registration files depend on diff2anat. For example, 
diff2mni is composed of diff2anat
and anat2mni. If
     you're using the old diff2mni, it's like you didn't change 
anything.

     The -intra step creates all these. You need to edit the 
command that generates the diff2anat in
your version of
     trac-preproc. Either comment that line out so that it runs 
everything but that, or change that line
to the options
     that worked for you.


     On Fri, 18 May 2012, Kiely Madhavan wrote:

     I only created a diff2anat.flt.mat file which replaced the old 
one. Do they all need to be
recreated? If so,
     is that something I
     add to the command line?

     On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki 
 wrote:

          Were the old .mat files replaced with the new ones?

          On Fri, 18 May 2012, Kiely Madhavan wrote:

                That seemed to fix the registration issue, but I'm 
still unable to
                reconstruct the tracts using trac-all -path. I'm 
getting the same error that
                the control points are not within the mask. THis 
happens for all tracts.
                Thanks,

                Kiely

                On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
                 wrote:

           á á áThe .mat registration matrix should be saved under 
dmri/xfms/.


           á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:

           á á á á á áI tried using corratio and it seems to have 
fixed
           á á á á á áthe registration issue.
           á á á á á áI'm very new to this so just want to make 
sure I did
           á á á á á áit correctly before I
           á á á á á ámove forward. Should the command line look 
something
           á á á á á álike this if I am
           á á á á á árunning it in this individuals dmri 
directory:á

           á á á á á áflirt -in dwi_orig.nii.gz -ref 
brain_anat.nii.gz
           á á á á á á-out
           á á á á á álowb_brain_anat.flt.nii.gz -omat 
diff2anat.flt.mat
           á á á á á á-cost corratio


           á á á á á áThanks so much for your help.

           á á á á á áKiely

           á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti 
Srinivasan
           á á á á á á wrote:
           á á á á á áá á áyou have to run flirt commandline 
separately to
           á á á á á ácheck if it
           á á á á á áá á ásolves your
           á á á á á áá á áproblem.


           á á á á á áá á á> Is this something I can change in my 
dmrirc
           á á á á á áfile or do I need
           á á á á á áá á áto run flirt
           á á á á á áá á á> on it's own?
           á á á á á áá á á>
           á á á á á áá á á> Thanks,

Re: [Freesurfer] trac-all -path error

2012-05-18 Thread Priti Srinivasan

Hi Kiely,

In your terminal (after sourcing the freesurfer environment) type the
following:

gedit $FREESURFER_HOME/bin/trac-preproc (use pico if you're using mac, you
can also use other editors like vi or emacs)

This will open up trac-preproc script in a text editor.

you can scroll through to #--- Intra-subject registration #

in the script and look for the following lines:


  if ($doregflt) then
# Register low-b to anatomical using flirt
set cmd = flirt
set cmd = ($cmd -in $dwidir/lowb_brain.nii.gz)
set cmd = ($cmd -ref $dwidir/brain_anat.nii.gz)
set cmd = ($cmd -out $dwidir/lowb_brain_anat.flt.nii.gz)
set cmd = ($cmd -omat $xfmdir/diff2anat.flt.mat)
set cmd = ($cmd -cost mutualinfo)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
  $fs_time $cmd |& tee -a $LF
  if ($status) goto error_exit
endif

Change the mutualinfo in the above line to corratio

Re-run trac-all -intra -inter -masks -tensor -prior -c 
and then trac-all -path

Best,
Priti




> That's where I looked, but all I see is the following (I don't see the
> command line that creates the diff2anat for me to edit):
>
>
> Last login: Fri May 18 13:45:47 on ttys000
> /Applications/freesurfer/bin/trac-preproc ; exit;
> Kielys-MacBook-Air:~ kielydonnelly$
> /Applications/freesurfer/bin/trac-preproc ; exit;
>
> USAGE: trac-preproc
>
> Required arguments:
>   -c   : dmrirc file (see dmrirc.example)
>
> Other arguments:
>   -log : default is trac-all.log in the same dir as dmrirc
>   -nolog : do not save a log file
>   -cmd : default is trac-all.cmd in the same dir as dmrirc
>   -nocmd : do not save a cmd file
>   -no-isrunning  : do not check whether this subject is currently being
> processed
>   -umask umask   : set unix file permission mask (default 002)
>   -grp groupid   : check that current group is alpha groupid
>   -allowcoredump : set coredump limit to unlimited
>   -debug : generate much more output
>   -dontrun   : do everything but execute each command
>   -version   : print version of this script and exit
>   -help  : print full contents of help
>
> logout
>
> [Process completed]
>
> On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>>
>> This is a script, it's in the directory where all freesurfer scripts
>> are.
>> You can find it by doing "which trac-preproc".
>>
>>
>> On Fri, 18 May 2012, Kiely Madhavan wrote:
>>
>>  OK - Can you point me in the direction of the trac-preproc file that I
>>> should edit?
>>>
>>> On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki <
>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>
>>>  The other registration files depend on diff2anat. For example,
>>> diff2mni is composed of diff2anat and anat2mni. If
>>>  you're using the old diff2mni, it's like you didn't change
>>> anything.
>>>
>>>  The -intra step creates all these. You need to edit the command
>>> that
>>> generates the diff2anat in your version of
>>>  trac-preproc. Either comment that line out so that it runs
>>> everything but that, or change that line to the options
>>>  that worked for you.
>>>
>>>
>>>  On Fri, 18 May 2012, Kiely Madhavan wrote:
>>>
>>>  I only created a diff2anat.flt.mat file which replaced the old
>>> one.
>>> Do they all need to be recreated? If so,
>>>  is that something I
>>>  add to the command line?
>>>
>>>  On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki <
>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>
>>>   Were the old .mat files replaced with the new ones?
>>>
>>>   On Fri, 18 May 2012, Kiely Madhavan wrote:
>>>
>>> That seemed to fix the registration issue, but I'm
>>> still
>>> unable to
>>> reconstruct the tracts using trac-all -path. I'm
>>> getting
>>> the same error that
>>> the control points are not within the mask. THis
>>> happens
>>> for all tracts.
>>> Thanks,
>>>
>>> Kiely
>>>
>>> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
>>>  wrote:
>>>
>>>á á áThe .mat registration matrix should be saved under
>>> dmri/xfms/.
>>>
>>>
>>>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:
>>>
>>>á á á á á áI tried using corratio and it seems to have fixed
>>>á á á á á áthe registration issue.
>>>á á á á á áI'm very new to this so just want to make sure I
>>> did
>>>á á á á á áit correctly before I
>>>á á á á á ámove forward. Should the command line look
>>> something
>>>á á á á á álike this if I am
>>>á á á á á árunning it in this individuals dmri directory:á
>>>
>>>á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
>>>á á á á á á-out
>>>á á á á á álowb_brain_anat.flt.nii.gz -omat
>>> diff2anat.flt.mat
>>>á á á á á á-cost corratio
>

Re: [Freesurfer] Question about DODS model and DOSS model

2012-05-18 Thread Douglas N Greve

Yes, use the DODS model to look for an interaction. In your case, you 
will have four regressors: Group1 Intercept, G2 Intercept, G1 slope, G2 
slope, so test the interaction with the contrast [0 0 1 -1]. If there is 
no interaction, then run with a DOSS model and contrast [1 -1 0] to look 
for a difference between groups.
doug

On 05/16/2012 09:09 PM, ZhiLiangLong wrote:
> Hi all:
>  I'm a little confused about the DODS model and DOSS model. I have 
> two groups (patient and control) and one covariate (age), and I want 
> to compare the diffirence of thickness between the groups with age as 
> the covariate. In DODS model, is the process the analysis of variance 
> substantially (group is a factor and age is another factor)?
>Generally, if there is no interaction between age and group, then i 
> can re-run with the DOSS model to increase the statistical power.But i 
> don't know how to determine whether  there is no interaction . I 
> hope someone give me some suggestions.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] About Mapping voxels from Structural Image to Functional Image

2012-05-18 Thread Douglas N Greve

I think this scenario applies to you (just use your structural instead 
of orig.mgz).
doug

--
I have a CRS from a voxel in my functional/diffusion/ASL/rawavg/etc
"mov" volume and want to compute the CRS for the corresponding point in
the orig.mgz:

origCRS = Torig * inv(Reg) * inv(Tmov) * [movC movR movS 1]'
Torig: mri_info --vox2ras-tkr orig.mgz
Tmov: mri_info --vox2ras-tkr mov.nii
Reg: register.dat
tkregister2 --mov mov.nii --reg register.dat

Test: click on a point in tkmedit very close to the left hemi white
surface. Use the "Functional Overlay Index Coordinates" to compute
origCRS (round to the nearest integer). Compare origCRS to the "Volume
index". Note: you may need to use the "Volume RAS" from tkmedit in
the computation above to get an exact match.

--


On 05/17/2012 05:43 AM, Sinem Burcu Erdoğan wrote:
>
> Dear Freesurfer Community;
>
> I need to find the corresponding voxel in a functional image for a 
> specific structural image voxel after coregistering two images. My 
> structural image has 256*256*125 voxels and the functional image has 
> 64*64*30 voxels.
>
> I use the following command
>
>
> tkregister2 --s subjectname --targ structural.nii --mov functional.nii 
> --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat
>
>
> Where the target is structural image and movable is the functional image
>
> then click save to get MYregister.dat.
>
>
> then take the inverse of the matrix
>
> save it as invMYregister.dat, and try to use this matrix to transform 
> from
>
> anatomical to functional.
>
>
> However; as an example when I try to map voxel (169 , 62 ,35) of the 
> anatomical image to the functional space using the inverse 
> registration matrix; i get the values below
>
> - 64.3319
>
> -146.4394
>
> -157.2665
>
> as the corresponding voxels' coordinates at the functional space which 
> is far beyond the functional volume size and is negative. It is clear 
> I cannot manage to use the trasfer matrices appropriately.
>
> Your help will be greatly appreciated.
>
> Thank you;
>
> Sinem Burcu ERDOGAN
>
>
> -- 
> Sinem Burcu ERDOĞAN
> Research Assistant
> Bogazici University
> Biomedical Engineering Institute
> Kandilli Kampüs
> 34684 Çengelköy / İSTANBUL TURKEY
> Tel :+90-216-5163433
> Fax :+90-216-5163479
> e-mail: burcu.erdo...@boun.edu.tr 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses

2012-05-18 Thread Douglas N Greve

Try
asegstats2table --stats=lh.roi.stats--meas volume --skip --tablefile 
$OUTFILE

doug


On 05/17/2012 04:04 PM, Vy Dinh wrote:
> Dear Freesurfer Experts,
>
> I've created a couple of ROIs from qdec comparisons of thickness and 
> volume between two groups. We extracted the data from these ROIs for 
> each subject using mris_anatomical_stats.
>
> The stat files are located within each subjects folder:
> sub/stats/rh.roi.stats
>
> Now, we would like to combine the data from each stat file to a text 
> file using aparcstats2table and asegstats2table (for volume measures). 
> I already have batch scripts that call these functions for multiple 
> subjects. The script basically concatenates all of the subject ids and 
> inputs the concatenated string into the aparcstats2table (or 
> asegstats2table) command.
>
> EX:
> asegstats2table -s s1 -s s2 -s s3 -s s4 --hemi lh --meas volume 
> -tablefile test_stats.txt
>
> I would like to modify my script so that I can extract the data from 
> the roi.stats file. This is only a matter of entering the correct 
> inputs for aparcstats2table and asegstats2table but I have tried with 
> little success. The problems with each command are explained below.
>
> *For asegstats2table:*
> According to documentation 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table), I have 
> tried running "asegstats2table $STRING --meas volume --skip 
> --tablefile $OUTFILE " where string is "-i s1/stats/lh.roi.stats -i 
> s2/stats/lh.roi.stats ..etc" but get the error message:
>
> Building the table..
> Traceback (most recent call last):
>   File 
> "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table",
>  
> line 513, in 
> rows, columns, table = sanitize_table(options, pretable)
>   File 
> "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table",
>  
> line 412, in sanitize_table
> _specs, _id_name_map, _measl = _t[0]
> IndexError: list index out of range
>
>
> *For aparcstats2table: *
> when I run the command:
>
> aparcstats2table $STRING --hemi lh --parc roi_name --skip --tablefile 
> $OUTFILE
>
> where string is"-s s1 -s s2 -s s3 ", I get a text file with 3 columns. 
> The first column lists the subject ids, but what are the values for 
> the 2nd and 3rd columns? Also, is it possible to input more than 2 
> .stats file for the command?
>
>
> Looking forward to your responses,
>
>
> Vy
>
>
> Vy T.U. Dinh
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: vy_d...@rush.edu 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] splitting data into virtual runs

2012-05-18 Thread Douglas N Greve

try using mri_convert on the big file, something like
mri_convert f.nii --fsubsample 0 99 1 f.100.nii
This will extract the first 100 time points
doug

On 05/17/2012 04:48 PM, Guthormsen, Amy M wrote:
> Hello,
>
> I would like to use fsfast to analyze retinotopic data that I 
> collected.  I used the traditional 4 stimulus types (clockwise, 
> counterclockwise, expanding, and contracting), but rather than collect 
> each one in its own run, I took data from one long run that contained 
> all the stimuli.  Based on the logs, I can associate the pulse 
> number/dicom file number with a stimulus type.  However, when I tried 
> to just move the sets of dicom files into sub-directories, which I set 
> up as run directories, freesurfer still saw them as belonging to one 
> run (which I assume is taken from meta-data).  My question is, how can 
> I best split up these files so that I can subject them to the 
> FsFastIndividualRetinotopyAnalysis 
> 
>  process?
>
> Thank you,
>
> Amy Guthormsen
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] How to calculate Total Brain Volume from aseg.stats

2012-05-18 Thread Douglas N Greve

Hi Aaron, probably the easiest thing to do is to re-run mri_segstats for 
each of your subjects giving it the option to save this measure into the 
output stats file. To do this, you can get the basic command from the 
recon-all.log file. To this add

--brainmask mri/brainmask.mgz --brain-vol-from-seg

Below are descriptions of the values that it produces.

doug

1. BrainSegNotVent - sum of the volume of the structures
identified in the aseg.mgz volume this will include cerebellum
but not ventricles, CSF and dura. Includes partial volume
compensation with --pv. This is probably the number you want
to report.
2. BrainMask - total volume of non-zero voxels in
brainmask.mgz. This will include cerebellum, ventricles, and
possibly dura. This is probably not what you want to
report.
3. BrainSeg - sum of the volume of the structures identified
in the aseg.mgz volume. This will include cerebellum and
ventricles but should exclude dura. This does not include
partial volume compensation, so this number might be different
than the sum of the segmentation volumes.
4. IntraCranialVol (ICV) - estimate of the intracranial volume
based on the talairach transform. See
surfer.nmr.mgh.harvard.edu/fswiki/eTIV for more details. This
is the same measure as Estimated Total Intracranial Volume
(eTIV).

On 05/17/2012 04:56 PM, Goldman, Aaron (NIH/NIMH) [C] wrote:
>
> Hello,
>
> For an analysis, we’re trying to calculate a Total Brain Volume 
> covariate based on the data in aseg.stats, generated using version 
> 5.0.0. Basically, we want to include all WM and GM but not CSF.
>
> I was thinking of doing Total GM + Cortical WM + L&R Cerebellum WM. 
> Would this be the correct way to do it, or should we use some other 
> combination?
>
> Thanks,
>
> Aaron
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] How to calculate Total Brain Volume from aseg.stats

2012-05-18 Thread Douglas N Greve

ps. This will automatically be done in the next version, and you should 
be able to find this info in the wmparc.stats file already.

On 05/17/2012 04:56 PM, Goldman, Aaron (NIH/NIMH) [C] wrote:
>
> Hello,
>
> For an analysis, we’re trying to calculate a Total Brain Volume 
> covariate based on the data in aseg.stats, generated using version 
> 5.0.0. Basically, we want to include all WM and GM but not CSF.
>
> I was thinking of doing Total GM + Cortical WM + L&R Cerebellum WM. 
> Would this be the correct way to do it, or should we use some other 
> combination?
>
> Thanks,
>
> Aaron
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] make check => mris_expand FAILED

2012-05-18 Thread Akio Yamamoto

Hi Bruce

I have confirmed that all tests are passed.

Thanks,
Akio

(2012/05/18 23:37), Bruce Fischl wrote:
> Hi Akio
>
> the test is wrong. Not sure how it happened, but we fixed this 
> recently in dev so you'll need to grab the new test data.
>
> cheers
> Bruce
>
>
> On Fri, 18 May 2012, Akio Yamamoto wrote:
>
>> Hi,
>>
>> When I run 'make check' after successfully completing 'make' command, I
>> get the following message:
>>
>> ..
>>
>> ./mris_expand -v 111706 -thickness lh.white 0.5 lh.midgray
>>
>> mris_expand FAILED
>> FAIL: test_mris_expand
>> =
>> 1 of 1 tests failed
>> Please report to freesurfer@nmr.mgh.harvard.edu
>> =
>>
>>
>> How can I fix this error? Any help would be appreciated.
>>
>> Thanks,
>> -- 
>> Akio Yamamoto
>> The University of Tokyo
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.
>
>
>
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Re: [Freesurfer] How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses

2012-05-18 Thread Joshua Lee

How did I miss this asegstats2table script? It looks great...and here I've
been writing my own bash scripts to get the data out.
-
J


On Fri, May 18, 2012 at 1:59 PM, Douglas N Greve
wrote:

> Try
> asegstats2table --stats=lh.roi.stats--meas volume --skip --tablefile
> $OUTFILE
>
> doug
>
>
> On 05/17/2012 04:04 PM, Vy Dinh wrote:
> > Dear Freesurfer Experts,
> >
> > I've created a couple of ROIs from qdec comparisons of thickness and
> > volume between two groups. We extracted the data from these ROIs for
> > each subject using mris_anatomical_stats.
> >
> > The stat files are located within each subjects folder:
> > sub/stats/rh.roi.stats
> >
> > Now, we would like to combine the data from each stat file to a text
> > file using aparcstats2table and asegstats2table (for volume measures).
> > I already have batch scripts that call these functions for multiple
> > subjects. The script basically concatenates all of the subject ids and
> > inputs the concatenated string into the aparcstats2table (or
> > asegstats2table) command.
> >
> > EX:
> > asegstats2table -s s1 -s s2 -s s3 -s s4 --hemi lh --meas volume
> > -tablefile test_stats.txt
> >
> > I would like to modify my script so that I can extract the data from
> > the roi.stats file. This is only a matter of entering the correct
> > inputs for aparcstats2table and asegstats2table but I have tried with
> > little success. The problems with each command are explained below.
> >
> > *For asegstats2table:*
> > According to documentation
> > (http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table), I have
> > tried running "asegstats2table $STRING --meas volume --skip
> > --tablefile $OUTFILE " where string is "-i s1/stats/lh.roi.stats -i
> > s2/stats/lh.roi.stats ..etc" but get the error message:
> >
> > Building the table..
> > Traceback (most recent call last):
> >   File
> >
> "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table",
> > line 513, in 
> > rows, columns, table = sanitize_table(options, pretable)
> >   File
> >
> "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table",
> > line 412, in sanitize_table
> > _specs, _id_name_map, _measl = _t[0]
> > IndexError: list index out of range
> >
> >
> > *For aparcstats2table: *
> > when I run the command:
> >
> > aparcstats2table $STRING --hemi lh --parc roi_name --skip --tablefile
> > $OUTFILE
> >
> > where string is"-s s1 -s s2 -s s3 ", I get a text file with 3 columns.
> > The first column lists the subject ids, but what are the values for
> > the 2nd and 3rd columns? Also, is it possible to input more than 2
> > .stats file for the command?
> >
> >
> > Looking forward to your responses,
> >
> >
> > Vy
> >
> >
> > Vy T.U. Dinh
> > Neurological Sciences
> > Rush University Medical Center
> > Phone: (312) 563-3853 
> > Fax: (312) 563-4660 
> > Email: vy_d...@rush.edu 
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Inter-hemispheric registration issue

Re: [Freesurfer] make check => mris_expand FAILED

[Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] MEMPRAGE sequence.

Re: [Freesurfer] make check => mris_expand FAILED

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] Inter-hemispheric registration issue

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] Surface Area aparc from pial surface

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

Re: [Freesurfer] surfaceRAS to Talairach

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] trac-all -path error

Re: [Freesurfer] Question about DODS model and DOSS model

Re: [Freesurfer] About Mapping voxels from Structural Image to Functional Image

Re: [Freesurfer] How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses

Re: [Freesurfer] splitting data into virtual runs

Re: [Freesurfer] How to calculate Total Brain Volume from aseg.stats

Re: [Freesurfer] How to calculate Total Brain Volume from aseg.stats

Re: [Freesurfer] make check => mris_expand FAILED

Re: [Freesurfer] How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses

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