Hi, my question is strongly related to Nr. 4 and 5 below (Alex Fornito).
I am trying to run a surface-based ROI-analysis using one freesurfer-label on several subjects' imaging data which is already in standard space (fsaverage). These are resting state images from a SPM-based analysis which have been converted into surface-data. It seems that "mris_anatomical_stats" does not work on these average images, even when I try to use fsaverge as the corresponding space.
I used:
mris_anatomical_stats -l LABEL -t IMAGE -b -f DIRECTORY/LABEL.stats fsaverage lh
Any advice would be appreciated !
Thanks,
Alex Drzezga
---------------------------- Original Message ---------------------------- Subject: Freesurfer Digest, Vol 64, Issue 14 From: freesurfer-request@nmr.mgh.harvard.edu Date: Fri, June 5, 2009 3:39 pm To: freesurfer@nmr.mgh.harvard.edu --------------------------------------------------------------------------
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Today's Topics:
1. Re: RES: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu (Lucas Eggert) 2. RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu (Pedro Paulo de Magalhaes Oliveira Junior) 3. Re: RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu (Lucas Eggert) 4. Anatomical stats for fsaverage (Alex Fornito) 5. Re: Anatomical stats for fsaverage (Bruce Fischl) 6. func2roi-sess w/o analysis (Alessandro D. Gagliardi) 7. Re: func2roi-sess w/o analysis (Alessandro D. Gagliardi)
----------------------------------------------------------------------
Message: 1 Date: Fri, 05 Jun 2009 15:08:40 +0200 From: Lucas Eggert l_eggert@web.de Subject: Re: RES: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu To: ppj@netfilter.com.br Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 4A2918D8.1070500@web.de Content-Type: text/plain; charset=UTF-8; format=flowed
Sure:
Linux pc-15-301-1 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
-Lucas
Can you send the output of uname -a command
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 09:56:12 Para: ppj@netfilter.com.br Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: RES: [Freesurfer] Installing FreeSurfer on iMac running
Xubuntu
Hi,
Wow running Ubuntu on iMac and FreeSurfer I never saw.
Did you set FREESURFER_HOME
'echo $FREESURFER_HOME' gives - as it should:
'/usr/local/freesurfer'
-Lucas
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 09:20:25 Para: freesurfer@nmr.mgh.harvard.edu Assunto: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu
Dear List,
I am trying to install FreeSurfer on an iMac on which I am using Ubuntu 9.04 (jaunty).
I downloaded the CentOS 4x86_64-tar.gz file, moved it to '/usr/local/' and unpacked it there ('tar xzvf ...'). I saved the .license-file in '/usr/local/freesurfer'.
Trying for example 'mri_convert', throws the following error-message:
'bash: /usr/local/freesurfer/bin/mri_convert: cannot execute binary file'
What is my mistake?
Any help would be very much appreciated!
Thanks!
All the best, -Lucas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 2 Date: Fri, 05 Jun 2009 13:15:57 +0000 From: "Pedro Paulo de Magalhaes Oliveira Junior" ppj@netfilter.com.br Subject: RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu To: "Lucas Eggert" l_eggert@web.de Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 4a291aa0.111f5e0a.589f.fffff665@mx.google.com Content-Type: text/plain; charset="utf-8"
I think you are running a 64 bit version of FreeSurfer in a 32bit linux Kernel.
Try using FreeSurfer 32bit
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 10:08:40 Para: ppj@netfilter.com.br Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: RES: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu
Sure:
Linux pc-15-301-1 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
-Lucas
Can you send the output of uname -a command
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 09:56:12 Para: ppj@netfilter.com.br Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: RES: [Freesurfer] Installing FreeSurfer on iMac running
Xubuntu
Hi,
Wow running Ubuntu on iMac and FreeSurfer I never saw.
Did you set FREESURFER_HOME
'echo $FREESURFER_HOME' gives - as it should:
'/usr/local/freesurfer'
-Lucas
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 09:20:25 Para: freesurfer@nmr.mgh.harvard.edu Assunto: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu
Dear List,
I am trying to install FreeSurfer on an iMac on which I am using Ubuntu 9.04 (jaunty).
I downloaded the CentOS 4x86_64-tar.gz file, moved it to '/usr/local/' and unpacked it there ('tar xzvf ...'). I saved the .license-file in '/usr/local/freesurfer'.
Trying for example 'mri_convert', throws the following error-message:
'bash: /usr/local/freesurfer/bin/mri_convert: cannot execute binary file'
What is my mistake?
Any help would be very much appreciated!
Thanks!
All the best, -Lucas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 3 Date: Fri, 05 Jun 2009 17:24:46 +0200 From: Lucas Eggert l_eggert@web.de Subject: Re: RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu To: ppj@netfilter.com.br Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 4A2938BE.40306@web.de Content-Type: text/plain; charset=UTF-8; format=flowed
Hi,
Try using FreeSurfer 32bit
That's it!
Thank you very much for your quick help! -Lucas
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 10:08:40 Para: ppj@netfilter.com.br Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: RES: Re: [Freesurfer] Installing FreeSurfer on iMac
running Xubuntu
Sure:
Linux pc-15-301-1 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
-Lucas
Can you send the output of uname -a command
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 09:56:12 Para: ppj@netfilter.com.br Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: RES: [Freesurfer] Installing FreeSurfer on iMac running
Xubuntu
Hi,
Wow running Ubuntu on iMac and FreeSurfer I never saw.
Did you set FREESURFER_HOME
'echo $FREESURFER_HOME' gives - as it should:
'/usr/local/freesurfer'
-Lucas
Enviado do meu celular Nokia -----Msg original----- De: Lucas Eggert Enviada: 05/06/2009 09:20:25 Para: freesurfer@nmr.mgh.harvard.edu Assunto: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu
Dear List,
I am trying to install FreeSurfer on an iMac on which I am using Ubuntu 9.04 (jaunty).
I downloaded the CentOS 4x86_64-tar.gz file, moved it to '/usr/local/' and unpacked it there ('tar xzvf ...'). I saved the .license-file in '/usr/local/freesurfer'.
Trying for example 'mri_convert', throws the following error-message:
'bash: /usr/local/freesurfer/bin/mri_convert: cannot execute binary file'
What is my mistake?
Any help would be very much appreciated!
Thanks!
All the best, -Lucas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4 Date: Fri, 05 Jun 2009 16:46:31 +0100 From: Alex Fornito fornitoa@unimelb.edu.au Subject: [Freesurfer] Anatomical stats for fsaverage To: freesurfer@nmr.mgh.harvard.edu Message-ID: C64EFC67.DB44%fornitoa@unimelb.edu.au Content-Type: text/plain; charset=US-ASCII
Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file.
Thanks for your help, Alex
mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory
------------------------------
Message: 5 Date: Fri, 5 Jun 2009 12:15:38 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Anatomical stats for fsaverage To: Alex Fornito fornitoa@unimelb.edu.au Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: Pine.LNX.4.62.0906051214320.3041@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi Alex,
if all you care about is surface area you can probably just copy the wm.mgz from any subject into the fsaverage/mri dir. Other stats will of course then be incorrect. You also have to be careful as the fsaverage surfaces contain less surface area (due to averaging) than individual subjects. There is a correction factor stored in the fsaverage surface files you can use if you want, I think mris_info will print it out.
cheers Bruce
On Fri, 5 Jun 2009, Alex Fornito wrote:
Hi, I'm playing around with different ways of generating custom annotation
files
using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file.
Thanks for your help, Alex
mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 6 Date: Fri, 5 Jun 2009 14:29:00 -0400 From: "Alessandro D. Gagliardi" eklypse@psychology.rutgers.edu Subject: [Freesurfer] func2roi-sess w/o analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: af2c8600906051129v3b30349dha3858bf51c919b91@mail.gmail.com Content-Type: text/plain; charset="utf-8"
I'd like to extract a BOLD series for a given anatomical region. It seems like this should be possible with func2roi-sess (with the -anatlabel option) but it appears to need an analysis for some reason. I'm using continuous data, no event-related or block design paradigm, so I don't have an FS-FAST analysis. I just want the time series for a given ROI, so I don't see why I should need an analysis, but I can't figure out how to tell func2roi-sess not to use one. Perhaps I'm misunderstanding func2roi-sess or maybe there's a better function for me to use for this. What is the best way to extract the time series from a given ROI (e.g. rh.medialorbitofrontal) using FreeSurfer?
Thanks,-- Alessandro D. Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis