Re: [Freesurfer] Re: Transformation of segmenation
Your answer crossed my question in cyber space. I always knew the freesurfer people were superhuman! Brian > From: Bruce Fischl <[EMAIL PROTECTED]> > Date: Sat, 25 Mar 2006 19:27:11 -0500 (EST) > To: Shahabuddin Ansari <[EMAIL PROTECTED]> > Cc: "freesurfer@nmr.mgh.harvard.edu" > Subject: [Freesurfer] Re: Transformation of segmenation > > p.s. from the subject's mri dir. > > On Sat, 25 Mar 2006, Shahabuddin Ansari > wrote: > >> Hello Bruce, >> >> Let me rephrase my question. When I pass a brain MRI >> to freesurfer, it transforms the image spatially >> before it does the segmentation. Now the segmented >> objects have >> different orientation from the original MRI. My >> question is how can I transform the segmentation back >> to original MRI? >> >> Thanks >> Shahab >> >> __ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection around >> http://mail.yahoo.com >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transformation of segmenation
Hi Folks, I have a related issue. My problem could be easy to solve if I could maintain original resolution from AFNI to Freesurfer and then back to AFNI. For instance, I would like to force no reslicing/interpolation with mri_convert. My original resolution is .938 x .938 x 1. I thought that there was a way to do this with mri_convert, but I can't seem to get it to work. There are ways to get the aseg to align with the original anat if it's moved back to AFNI, but no change in resolution would make it easier. Brian > From: Shahabuddin Ansari <[EMAIL PROTECTED]> > Date: Sat, 25 Mar 2006 16:07:24 -0800 (PST) > To: <[EMAIL PROTECTED]> > Cc: "freesurfer@nmr.mgh.harvard.edu" > Subject: [Freesurfer] Transformation of segmenation > > Hello Bruce, > > Let me rephrase my question. When I pass a brain MRI > to freesurfer, it transforms the image spatially > before it does the segmentation. Now the segmented > objects have > different orientation from the original MRI. My > question is how can I transform the segmentation back > to original MRI? > > Thanks > Shahab > > __ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coregistration?
Just in case someone hasn't mentioned it yet, try 3dWarpDrive or convert to analyze and use the AIR suite. Graham is correct. There are past posts about this on the AFNI forum that would be helpful to you. Good luck. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 > From: Graham Wideman <[EMAIL PROTECTED]> > Date: Wed, 12 Oct 2005 13:56:19 -0700 > To: "freesurfer@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] Coregistration? > > Sorry all -- my mistake. > > I thought our folks here were regularly registering functional to > anatomical scans, and I thought it was done with 3dvolreg. Just now > checking, apparently not. > > And if 3dAnatNudge can't do rotation, not so helpful (though lack of resize > should not be a problem). > > It would be interesting to see what 3dvolreg would do if the anatomy was > resampled to the same grid as that functional scans or vice versa... but > starts to look like a research topic. > > For Nate: It might be worth posting on the AFNI forum to see what other > AFNI-sters position on this topic is... doubtless it's been thought about a > lot more than by me! > > Graham > > Jeff Binder wrote: >> The AFNI program 3dvolreg does coregistration only for volumes acquired >> with the same kind of pulse sequence and consequently the same tissue >> signal values. Use it for coregistering different EPI volumes to each >> other or different T1-weighted structural scans to each other. >> >> I think what Nate was asking about was coregistering EPI data to the >> structural scans. The AFNI program 3dAnatNudge can help with this to some >> extent. It uses simple iterative translational movements to find the best >> fit between a "skull-stripped" anatomy volume and an EPI volume. No >> rotation or resizing is done. >> >> To use this program you remove the skull and other non-brain voxels from >> the anatomy volume. The AFNI programs 3dIntracranial and a newer program >> called 3dSkullStrip both do this. >> >> Jeff > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: make_average_surface
Dear Antao, Check the recent archives with the subject "make_average_subject error?" and the recent exchange with Nick. On Doug's advice, I added 'xv' to the beginning of each make_average* script So, #!/bin/tcsh -efxv Instead of #!/bin/tcsh -ef This produced the output that allowed the freesurfer developers to pinpoint the error. Also on Doug's suggestion, try adding --debug to the make_average_subject command. Nick's recommendation a few posts ago fixed the problem that I was having on a fedora core 4 machine. Based on your initial post, we seem to have similar problems, so give the above suggestions a try. If needed, comment out the offending information in make_average_subject, make_average_volume, and make_average_surface as Nick suggested (if you receive the same error message that I received). Good luck. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 > From: Antao Du <[EMAIL PROTECTED]> > Date: Fri, 7 Oct 2005 17:27:41 -0700 > To: Nick Schmansky <[EMAIL PROTECTED]> > Cc: Freesurfer Mailing List > Subject: RE: [Freesurfer] RE: make_average_surface > > There is no any output when I add --echo. > > Antao > >> -Original Message- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] Behalf Of Nick >> Schmansky >> Sent: Friday, October 07, 2005 3:04 PM >> To: Antao Du >> Cc: Freesurfer Mailing List >> Subject: Re: [Freesurfer] RE: make_average_surface >> >> >> Add --echo to the command to print its activity, and then send me the >> output. >> >> On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote: >>> Hi, When I run make_average_surface --subjects AD1293 AD1297 >> AD1299 --out >>> average_cn, it finished within 1 second without any output and any error >>> message. I don't know what is wrong. Any helps there? >>> >>> I have not updated my freesurface so I downloaded >> make_average_surface from >>> a post by Nick in July, 2005. >>> >>> Thanks, >>> >>> Antao >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: make_average_surface
/apps/freesurfer/subjects/SC013/mri/orig
Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz
after -
1.118 -0.032 -0.017 2.509;
0.032 1.031 0.204 -17.650;
0.010 -0.214 1.079 -9.587;
0.000 0.000 0.000 1.000;
-
-
INFO: Transform Matrix
1.118 -0.032 -0.017 2.509;
0.032 1.031 0.204 -17.650;
0.010 -0.214 1.079 -9.587;
0.000 0.000 0.000 1.000;
-
Reslicing using trilinear interpolation
writing to
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz...
mri_average
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz
/apps/freesurfer/subjects/test/mri/brain.mgz
Fri Oct 7 16:29:49 PDT 2005
make_average_volume done
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756
> From: Nick Schmansky <[EMAIL PROTECTED]>
> Date: Fri, 07 Oct 2005 18:52:12 -0400
> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] RE: make_average_surface
>
> This is a puzzling problem. Unfortunately I don't have access to a FC4
> system to try to recreate what you are seeing.
>
> However, can you edit your make_average_subject/surface/volume scripts
> to comment-out these lines (shown here with comment-out chars added):
>
> #set n = `echo $argv | grep -e --help | wc -l`
> #if($n != 0) then
> # set PrintHelp = 1;
> # goto usage_exit;
> #endif
>
> #set n = `echo $argv | grep -e --version | wc -l`
> #if($n != 0) then
> # echo $VERSION
> # exit 0;
> #endif
>
> This appears to be where your script is stopping, and I would like to
> see what it does if it gets beyond this point.
>
> Thanks
>
> On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
>> This sounds like a problem I am having, The same script works fine on my
>> mac, but not on my FC4 machine. Here is the output, and a message I sent to
>> before.
>>
>> I changed the flags to ³efxv² as Doug recommended, and here is the output
>> for make_average_subject, make_average_volume and make_average_surface. The
>> script doesn¹t seem to be accepting my command line arguments. I am using
>> the current dev version on a Fedora Core 4 system, if that helps.
>>
>> Thanks,
>> Brian
>>
>> [EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs
>> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
>> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
>> SC036
>>
>> set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
>> $'
>> set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
>> $
>>
>> set PrintHelp = 0 ;
>> set PrintHelp = 0
>>
>> if ( $?SUBJECTS ) then
>> if ( 0 ) then
>> if ( $?SUBJECTS_DIR ) then
>> if ( 1 ) then
>> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
>> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
>> endif
>> endif
>>
>> set average_subject=average
>> set average_subject=average
>> set ddir = ${SUBJECTS_DIR}/${average_subject}
>> set ddir = /apps/freesurfer/subjects/average
>> set transform_fname=""
>> set transform_fname=
>> set XFORM_FLAG=""
>> set XFORM_FLAG=
>>
>> if ( $#argv == 0 ) then
>> if ( 27 == 0 ) then
>>
>> set n = `echo $argv | grep -e --help | wc -l`
>> set n = `echo $argv | grep -e --help | wc -l`
>> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
>> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
>> SC032 SC033 SC034 SC035 SC036
>> grep -e --help
>> wc -l
>>
>> **
>> [EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs
>> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
>> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
>> SC036
>>
>> set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
>> $' ;
>> set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $
>>
>> set PrintHelp = 0 ;
>> set PrintHelp = 0
>> set cleanup = 0 ;
>> set cleanup = 0
>> set transform_fname = talairach.xfm
>> set transform_fname = talairach.xfm
>>
Re: [Freesurfer] RE: make_average_surface
This sounds like a problem I am having, The same script works fine on my
mac, but not on my FC4 machine. Here is the output, and a message I sent to
before.
I changed the flags to ³efxv² as Doug recommended, and here is the output
for make_average_subject, make_average_volume and make_average_surface. The
script doesn¹t seem to be accepting my command line arguments. I am using
the current dev version on a Fedora Core 4 system, if that helps.
Thanks,
Brian
[EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
$'
set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
$
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=""
set transform_fname=
set XFORM_FLAG=""
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
$' ;
set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $
set PrintHelp = 0 ;
set PrintHelp = 0
set cleanup = 0 ;
set cleanup = 0
set transform_fname = talairach.xfm
set transform_fname = talairach.xfm
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject = average
set average_subject = average
set cmdargs = ( $argv ) ;
set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015
SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027
SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve
Exp $' ;
set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp
$
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=""
set transform_fname=
set XFORM_FLAG=""
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
From: Doug Greve <[EMAIL PROTECTED]>
Date: Tue, 27 Sep 2005 15:04:59 -0400
To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
Cc: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] make_average_subject error?
Try editing those scripts so that the first line is:
#!/bin/tcsh -efxv
ie, adding "xv"
This turns on all kinds of debugging
Brian Schweinsburg, Ph.D. wrote:
> Re: [Freesurfer] make_average_subject error? Hi Doug,
> The same thing happens when I try to run them separately. It exits to the
> prompt with no messages.
>
> Brian
>
> --
> Brian C. Schweinsburg, Ph.D.
> Assistant Adjunct Professor of Psychiatry
> University of California, San Diego
> Office: 858-552-8585 x6109
> Cell: 858-354-3756
&g
Re: [Freesurfer] make_average_subject error?
Title: Re: [Freesurfer] make_average_subject error?
Hi Doug,
I changed the flags to “efxv” as you recommend, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesn’t seem to be accepting my command line arguments. I am using the current dev version on a Fedora Core 4 system, if that helps.
Thanks,
Brian
[EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp $'
set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp $
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=""
set transform_fname=
set XFORM_FLAG=""
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $' ;
set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $
set PrintHelp = 0 ;
set PrintHelp = 0
set cleanup = 0 ;
set cleanup = 0
set transform_fname = talairach.xfm
set transform_fname = talairach.xfm
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject = average
set average_subject = average
set cmdargs = ( $argv ) ;
set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp $' ;
set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp $
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=""
set transform_fname=
set XFORM_FLAG=""
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
From: Doug Greve <[EMAIL PROTECTED]>
Date: Tue, 27 Sep 2005 15:04:59 -0400
To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
Cc: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] make_average_subject error?
Try editing those scripts so that the first line is:
#!/bin/tcsh -efxv
ie, adding "xv"
This turns on all kinds of debugging
Brian Schweinsburg, Ph.D. wrote:
Re: [Freesurfer] make_average_subject error? Hi Doug,
The same thing happens when I try to run them separately. It exits to the prompt with no messages.
Brian
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756
From: Doug Greve <[EMAIL PROTECTED]>
Date: Tue, 27 Sep 2005 11:16:00 -0400
To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
Cc
Re: [Freesurfer] make_average_subject error?
Title: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. It exits to the prompt with no messages. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 From: Doug Greve <[EMAIL PROTECTED]> Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? Can you run make_average_surface and make_average_volume separately? Brian Schweinsburg, Ph.D. wrote: I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0" Brian From: Doug Greve <[EMAIL PROTECTED]> Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error?
I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0" Brian > From: Doug Greve <[EMAIL PROTECTED]> > Date: Mon, 26 Sep 2005 16:40:48 -0400 > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> > Cc: "freesurfer@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] make_average_subject error? > > > try running it with --debug and send us the output > > Brian Schweinsburg, Ph.D. wrote: > >> Hi Folks, >> >> I tried running the latest make_average_subject script (and the >> make_average_surface/volume scripts) using the expected command line syntax >> and after hitting enter it immediately exits to the csh without error, but >> does not produce anything. >> >> make_average_subject --subjects SC010 SC011 SC012 ... >> >> I am running the latested dev release with Fedora Core 4. >> >> Any ideas as to the problem? >> Brian >> >> >> >> ___ >> 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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject error?
Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon-all in background?
Is there a way to run recon-all (the new dev version) in the background, while still saving all the relevant info to the .log and .status files? I tried recon-all -subjid XXX -autorecon-all & but it still sends info to the screen. Thanks, brian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and centos4_x86_64
Hi Nick, grep -H -R "/usr/pubsw/bin/perl -w" $FREESURFER_HOME/* Produced the results below, which appear to be the only files with hard links to the "/usr/pubsw/bin/perl." grep -H -R "/usr/pubsw/bin/perl -w" $FREESURFER_HOME/* $FREESURFER_HOME/lib/mni/bin/make_template:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/nu_estimate_np_and_em:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/sharpen_volume:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/imp2field:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/nu_estimate:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/mritotal:#! /usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/autocrop:#! /usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/nu_correct:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/xfmtool:#! /usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/mritoself:#! /usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/nu_evaluate:#!/usr/pubsw/bin/perl -w $FREESURFER_HOME/lib/mni/bin/field2imp:#!/usr/pubsw/bin/perl -w My fix was simply: 1) mkdir -p /usr/pubsw/bin 2) ln -s /usr/bin/perl The recon-all -subjid XXX -autorecon-all completed successfully in 27 hours on my Fedora Core 4 (AMD sempron 2600+) with surfaces having 0 holes. No manual edits were done. The aseg.stats file is wonderful. Is there a way to overlay an individual's subcortical/cortical segmentation results on their t1.mgz volume (i.e, colorize voxels belonging to a specific structures)? Thanks for such a great program! Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 > From: Nick Schmansky <[EMAIL PROTECTED]> > Date: Tue, 06 Sep 2005 11:16:22 -0400 > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and > centos4_x86_64 > > Brian, > > I'm glad to hear that the installation is now working for you. > > The recon-all -autorecon-all command can take 24 or more hours to > complete, depending on the quality of the scan, and the difficulty of > auto-fixing any defects, and of course the machine upon which it is > running. Your machine appears to be more than adequate. > > Concerning the perl scripts which needed editing, which files (with > paths) required editing? I'd like to remove any hard-coded paths in our > installation. > > Concerning the mgz files, recon-all does expect to find each structural > scan in the mri/orig directory, with filenames 001.mgz, 002.mgz, etc.. > Given a subject having three sets of DICOMS (three runs of structural > scans), I do the following to setup a subject: > > cd $SUBJECTS_DIR > mksubjdirs > cd > cd mri/orig > mkdir 001 > mkdir 002 > mkdir 003 > cp -r /9-2-*.dcm 001/ > cp -r /9-3-*.dcm 002/ > cp -r /9-7-*.dcm 003/ > mri_convert -it dicom -ot mgz 001/ 001.mgz > mri_convert -it dicom -ot mgz 002/ 002.mgz > mri_convert -it dicom -ot mgz 003/ 003.mgz > > Now you will have three .mgz files in mri/orig, and recon-all will > automatically take these three structural scans and average/motion- > correct them. > > The reason that we now encourage .mgz files over the COR format is > because the COR format is limited to storage of volume data in unsigned > char format only, and does not allow int, float, double or long formats. > Also, the COR format historically assumes a slice size of 256 by 256 > voxels. For these reasons, the COR format is deprecated in favor of the > newer mgh (and mgz) format. > > Concerning csurf, we no longer actively maintain csurf, in favor of > recon-all. csurf is essentially an older copy of the recon-all script, > and is not kept in-line with recon-all. We encourage using the recon- > all script because it is easier to see what is going on, and to > maintain. But we'll look into the possibility of at least csurf > supporting the opening of .mgz files. > > Nick > > > On Mon, 2005-09-05 at 21:58 -0700, Brian Schweinsburg, Ph.D. wrote: >> Hi Nick, >> >> I downloaded freesurfer-Linux-rh9-dev20050905-full.tar.gz and installed it >> on the following system: >> Fedora Core 4; AMD Sempron 2600+ on an ECS KT600-A board; Nvidia GeForce 2; >> 1 GB DDR 400 RAM. >> >> 'recon-all -subjid XXX -autorecon-all' would not run at first because it >> could not find some of the mni tools. The ones that it was having difficulty >> with were the perl scripts (not the binary MNI files). I noticed the first >> line in each of the scripts points to what looks like the MGH specific perl >> installation (i.e., /usr/
Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and centos4_x86_64
Hi Nick, I downloaded freesurfer-Linux-rh9-dev20050905-full.tar.gz and installed it on the following system: Fedora Core 4; AMD Sempron 2600+ on an ECS KT600-A board; Nvidia GeForce 2; 1 GB DDR 400 RAM. 'recon-all -subjid XXX -autorecon-all' would not run at first because it could not find some of the mni tools. The ones that it was having difficulty with were the perl scripts (not the binary MNI files). I noticed the first line in each of the scripts points to what looks like the MGH specific perl installation (i.e., /usr/pubsw/bin/perl), which does not exist on my system. I tested two different solutions 1) change the first line of each file and 2) mkdir -p /usr/pubsw/bin and then add a symbolic link to my perl binary. Both methods appear to work, and 'recon-all -subjid XXX -autorecon-all' has been running successfully for about 12 hours. I assume it is working! I also noticed that recon-all expected the mgz files for each separate anatomical to both be located in $FREESURFER_HOME/subjects/XXX/mri/orig. This is opposed to what I recall for the old COR method of placing separate anats in 001 002 etc (for obvious overwriting reasons). I believe this is documented in the recon-all help file, but could be confusing for some users at first. Csurf, tkmedit, and tksurfer gui's loaded without a problem on my FC4 machine. Csurf loads surfaces fine, but I cannot get it to load mgz files. It seems to expect COR files. Out of habit, I did all of my volume edits using 'Edit Segmentation' in csurf, but may have to switch tkmedit/tksurfer. No problem there. In sum, the current dev version for Redhat 9 appears to be running fine on a basic Fedora Core 4 machine. Thanks, Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 > From: Nick Schmansky <[EMAIL PROTECTED]> > Date: Mon, 05 Sep 2005 16:32:33 -0400 > To: Freesurfer Mailing List > Subject: [Freesurfer] new 'dev' release for Linux rh9, centos4 and > centos4_x86_64 > > Freesurfer community, > > For those who wish to install a 'development' release > of Freesurfer on Linux RedHat 9, CentOS 4 or CentOS 4 x86_64 > platforms, distribution files are now posted at: > > http://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D > > On this distribution site, a README is available: > > freesurfer-Linux-platform-dev20050905-full.README.txt > > The new distributions include: > > freesurfer-Linux-rh9-dev20050905-full.tar.gz > > freesurfer-Linux-centos4-dev20050905-full.tar.gz > > freesurfer-Linux-centos4_x86_64-dev20050905-full.tar.gz > > The 'dev' release contains all the functionality of > the upcoming 'stable' release, but has not been fully > tested, particularly in regards to installation issues. > > This 'dev' release is intended for those who wish to > attempt an installation on their Linux platform, and are > willing to give feedback on possible installation problems. > > This 'dev' release contains most of the libraries that > Freesurfer requires: the MINC toolkit, Tcl/Tk/Tix and BLT > libraries, GSL and Qt, as well as sample MRI data. > > The release may be installed in any directory. > > A Mac OS X 'dev' build is not available just yet. > > Please direct comments or questions to this mailing list. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Binary locations--new linux distro
Thanks Kevin. I will do that. Brian > From: Kevin Teich <[EMAIL PROTECTED]> > Date: Mon, 25 Apr 2005 15:20:34 -0400 (EDT) > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> > Cc: "freesurfer@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] Binary locations--new linux distro > > Thanks; this is a leftover fixed path name in the csurf script. I'll fix > it to be relative to the FREESURFER_HOME variable. If you'd like, you can > fix your own version by editing the line in csurf that starts with 'set > bindir', around line number 118, to be this: > > set bindir $env(FREESURFER_HOME)/bin > > > > On Mon, 25 Apr 2005, Brian Schweinsburg, Ph.D. wrote: > >> Hi, >> >> After installing the freesurfer-Linux-rh9-20050415.tar.gz and setting up the >> SetUpFreeSurfer and FreesurferEnv, I get an error message when csurf loads. >> It states that it cannot find numerous binaries in >> /usr/local/freesurfer/beta/bin. This issue seemed to resolve by >> symbollically linking the my $FREESURFER_HOME/bin directory to previously >> mentioned one. >> >> Is there a place to change where csurf expects to find the binaries? Did I >> miss it in the FreesurferEnv setup? >> >> Thanks for your time, >> Brian >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Kevin Teich > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Binary locations--new linux distro
Hi, After installing the freesurfer-Linux-rh9-20050415.tar.gz and setting up the SetUpFreeSurfer and FreesurferEnv, I get an error message when csurf loads. It states that it cannot find numerous binaries in /usr/local/freesurfer/beta/bin. This issue seemed to resolve by symbollically linking the my $FREESURFER_HOME/bin directory to previously mentioned one. Is there a place to change where csurf expects to find the binaries? Did I miss it in the FreesurferEnv setup? Thanks for your time, Brian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Stats and viewing parcellation problem
Hi Tosa,
Is it true that tksurfer must have tcl/tk 8.3? I get an error message
stating that there is a package conflict because I have version 8.4. I
didn't receive this message with the old tksurfer version, so I must have
something set up wrong. The new tksurfer also couldn't find the following
shared libaries: libBLT.2, libtix8.1.8.4, libtk8.4, and libglut.3.
Once I specified these, I got the error message below on my powerbook G4.
Thanks for the help.
Brian
##error log###
surfer: current subjects dir:
/unix-apps/freesurfer-20040218/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3
surfer:
/unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/T1/COR-.info
INFO: Volume /tmp/mritotal_2018/orig_8_dxyz.mnc cannot be found.
INFO: Volume /tmp/mritotal_2018/orig_8_dxyz.mnc cannot be found.
INFO: found the orig volume (mri/orig) to get c_(ras) information for src
INFO: added info to the surface.
surfer: vertices=151063, faces=302122
Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3
/usr/local/fsl/lib/tcl8.4
/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl: version
conflict for package "Tcl": have 8.4, need 8.3
version conflict for package "Tcl": have 8.4, need 8.3
while executing
"package require -exact Tcl 8.3"
(file
"/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl" line
19)
invoked from within
"source /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $tclfile]"
This probably means that Tcl wasn't installed properly.
Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following
directories:
./library
./tix8.1
./library
./tix8.1
/usr/local/fsl/lib/tix8.1
/unix-apps/freesurfer-20040218/freesurfer/local/lib/Darwin/tix4.1
This probably means that Tix wasn't installed properly.
surfer: using interface
/unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tksurfer.tcl
Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tkm_common.tcl
Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/fsgdfPlot.tcl
surfer: couldn't dis/enable menu set 0: can't read
"glMenuGroups(mg_InflatedVSetLoaded)": no such variable
surfer: couldn't dis/enable menu set 1: can't read
"glMenuGroups(mg_WhiteVSetLoaded)": no such variable
surfer: couldn't dis/enable menu set 2: can't read
"glMenuGroups(mg_PialVSetLoaded)": no such variable
surfer: couldn't dis/enable menu set 4: can't read
"glMenuGroups(mg_TimeCourseLoaded)": no such variable
surfer: couldn't dis/enable menu set 5: can't read
"glMenuGroups(mg_OverlayLoaded)": no such variable
surfer: couldn't dis/enable menu set 6: can't read
"glMenuGroups(mg_CurvatureLoaded)": no such variable
surfer: couldn't dis/enable menu set 7: can't read
"glMenuGroups(mg_LabelLoaded)": no such variable
surfer: couldn't dis/enable menu set 8: can't read
"glMenuGroups(mg_FieldSignLoaded)": no such variable
surfer: couldn't dis/enable menu set 9: can't read
"glMenuGroups(mg_FieldMaskLoaded)": no such variable
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
San Diego State University/University of California, San Diego
Joint Doctoral Program in Clinical Psychology
VA San Diego Healthcare System
Mailcode 151C
3350 La Jolla Village Drive
San Diego, CA 92161
Office: 858-552-8585 x6109
> From: Yasunari Tosa <[EMAIL PROTECTED]>
> Date: Tue, 07 Dec 2004 13:14:14 -0500
> To: Xander Meadow <[EMAIL PROTECTED]>
> Cc: <[EMAIL PROTECTED]>
> Subject: Re: [Freesurfer] Stats and viewing parcellation problem
>
> This is just a bug fix for tksurfer, reading annotation file.
> Nothing related to afni script.
>
> Tosa
>
> Xander Meadow wrote:
>
>> Just a quick question, will this update be incorporated if I use the
>> UPDATER script from the afni website? I don't necessarily mean right
>> now, but upon the next upgrade. Thanks.
>>
>>
>>
>>> Xander
>>>
>>>
>>
>> On Tue, 2004-12-07 at 11:44, Yasunari Tosa wrote:
>>
>>
>>> Fixed MacOSX version of tksurfer is available on our ftp page.
>>>
>>> $ ftp surfer.nmr.mgh.harvard.edu
>&g
Re: [Freesurfer] Stats and viewing parcellation problem
Sounds good. Thanks. Brian > From: Bruce Fischl <[EMAIL PROTECTED]> > Date: Tue, 7 Dec 2004 11:50:50 -0500 (EST) > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> > Cc: <[EMAIL PROTECTED]> > Subject: Re: [Freesurfer] Stats and viewing parcellation problem > > Hi Brian, > > this is a bug that Tosa has fixed. He has a new Mac version of tksurfer > that he'll send you shortly. > > cheers, > Bruce > > > On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote: > >> Hi All, >> >> I am having problems computing stats using the parcellation file. In >> addition, when I try to display the parcellation results in tksurfer (File >> -> Label -> Import Annotation -> rh.aparc.annot), which were completed >> without an error message using parcellate_subject-rh, I get an error >> message. I am not sure how to procede. Any hints? >> >> In both error logs, there is a reference to an older location of the >> Simple_surface_labels2002.txt file, which never existed on my machine. Is >> that related to the problem? >> >> My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218. >> >> I appreciate any assistance. >> Brian >> >> >> >> ### >> mris_anatomical_stats error message >> ### >> mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 >> rh >> computing statistics for each annotation in >> /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno >> t. >> reading volume >> /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... >> reading input surface >> /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... >> Computing inter-vertex distance >> >> computing second fundamental form...reading colortable from annotation >> file... >> colortable with 85 entries read (originally >> /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) >> reading colortable from annotation file... >> *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 >> CTABreadFrom: could not allocate -1073747536 bin table >> Cannot allocate memory >> Bus error >> >> ### >> Tksurfer error message >> ### >> reading colortable from annotation file... >> colortable with 85 entries read (originally >> /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) >> *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 >> CTABreadFrom: could not allocate -1073756992 bin table >> Cannot allocate memory >> >> Command Finished >> >> >> ___ >> Freesurfer mailing list >> [EMAIL PROTECTED] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Stats and viewing parcellation problem
Hi All, I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints? In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem? My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218. I appreciate any assistance. Brian ### mris_anatomical_stats error message ### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error ### Tksurfer error message ### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory Command Finished ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
