Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

extracting bval and bvecs from Siemens trio DWI
by raka maitra 08 Jun '09

08 Jun '09

Hello Doug The Siemen's Trio gives us Diffusion weighted images in the form of MR.10284.746.There are no extensions such as .dcm or .ima I can convert the dicom to nifti .nii format using SPM or FSL.But neither program extracts the bval or bvec information. I am working on Mac OsX 10.5 and am using FS v4.3.1 I tried using mri_convert subject/MR* dwi.nii -it siemens_dicom I am trying to ckeck the quality of the DWI and hence would like to perform eddy current correction and preprocess the images to generate FA maps. Thanks in advanceRaka

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Disentangling age effects
by mmoayedi＠uhnres.utoronto.ca 08 Jun '09

08 Jun '09

Hi, I am studying two groups and have found that age is a confound (or is a covariate with an interaction between the two groups). Simply, when I correlate age between the two groups, there is an interaction (i.e., the slopes are different). My questions are: 1) is it appropriate to proceed with a map-wise t-test (with or without age as a nuisance covariate)? 2) is there a way to pull out age effects on each group specifically, i.e., use age as a covariate of interest? If neither of these methods is statistically sound, is there a method that can be used to describe age effects in each group, or characterize the findings? Thanks, Massih Moayedi

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Color scale for the probability maps
by Eylem Kirlangic 08 Jun '09

08 Jun '09

Hi, When I plot the probability maps, the color scale bar takes negative values too (e.g., setting the threshold min 0 max 0.5, you get a scale bar between -0.5 and +0.5). How can I change the color scale bar so that it shows percentages? Thanks! Eylem ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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Temporal lobe segmentation
by Seyed Shahab Sharifi 08 Jun '09

08 Jun '09

Subject: Temporal lobe segmentation Date: Tue, 2 Jun 2009 17:40:21 +0100 Hi all, I am interested in automated segmentation of temporal lobe using freesurfer. I understand that it is possible to add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. But I am not sure about the practicality of this approach for two reasons; first if all the regions of a temporal lobe can be labeled by Free Surfer, second because I am thinking that the most medial border of the superior temporal lobe could be my arbitrary cut off point of segmenting the temporal lobe, what anatomical/imaging feature has been defined for Free Surfer that distinguishes the white matter of the superior temporal lobe from the stem of temporal lobe (or say putamen) . I would appreciate it if one can guide me through this process if possible. cheers Shahab View your Twitter and Flickr updates from one place - Learn more! _________________________________________________________________ Share your photos with Windows Live Photos – Free. http://clk.atdmt.com/UKM/go/134665338/direct/01/

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how to?
by Hoptman, Matthew 06 Jun '09

06 Jun '09

Hi all, How do I apply a Talairach registration to a segmentation? I can apply the transformation to the main volume and auxiliary volume in tkmedit, but I am not sure how to apply it to a segmentation volume. It looks like I can't load an aseg.mgz file as a main or auxiliary volume. --Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Re: Fw: [Freesurfer] Anatomical stats for fsaverage
by Rudolph Pienaar 06 Jun '09

06 Jun '09

> -----Original Message----- > From: Alex Fornito <fornitoa(a)unimelb.edu.au> > > Thanks, > I did as you suggested, but got a different error telling me that > mris_anatomical_stats cannot be used with fsaverage as it is an average > subject. > You can try the following "hack": convert the annotation to a series of labels, and then use 'mris_curvature_stats' on these label files. It will dump a bunch of curvature-related measures, but you can ignore these and just extract the surface area measures that it also generates. $>mri_annotation2label --subject <SUBJ> --hemi lh --annotation lh.test.aparc.annot --labelbase base This will create a series of label files, base-XXX.label in the <SUBJ>/label directory. You can use 'mris_curvature_stats' on each of these label files. Pass it any curvature file, and just grep for "ROI": $>mris_curvature_stats -l base-000.label <SUBJ> <hemi> curv | grep ROI ... Raw Mean Vertex Separation (ROI Surface): 0.83274 +- 0.24399 mm Raw ROI Surface Area: 4349.99756 mm^2 Raw ROI Number of Vertices: 07370 Raw ROI Surface Area Percentage: 5.52% Raw Average Vertex Area (ROI Surface): 0.59023 mm^2 ... -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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ROI analysis in average space
by adrzezga＠nmr.mgh.harvard.edu 05 Jun '09

05 Jun '09

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(a)nmr.mgh.harvard.edu Date: Fri, June 5, 2009 3:39 pm To: freesurfer(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." 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(a)web.de> Subject: Re: RES: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu To: ppj(a)netfilter.com.br Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4A2918D8.1070500(a)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(a)netfilter.com.br > Cc: freesurfer(a)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(a)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(a)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(a)netfilter.com.br> Subject: RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu To: "Lucas Eggert" <l_eggert(a)web.de> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4a291aa0.111f5e0a.589f.fffff665(a)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(a)netfilter.com.br Cc: freesurfer(a)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(a)netfilter.com.br > Cc: freesurfer(a)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(a)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(a)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(a)web.de> Subject: Re: RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu To: ppj(a)netfilter.com.br Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4A2938BE.40306(a)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(a)netfilter.com.br > Cc: freesurfer(a)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(a)netfilter.com.br >> Cc: freesurfer(a)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(a)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(a)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(a)unimelb.edu.au> Subject: [Freesurfer] Anatomical stats for fsaverage To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <C64EFC67.DB44%fornitoa(a)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(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Anatomical stats for fsaverage To: Alex Fornito <fornitoa(a)unimelb.edu.au> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <Pine.LNX.4.62.0906051214320.3041(a)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(a)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(a)psychology.rutgers.edu> Subject: [Freesurfer] func2roi-sess w/o analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <af2c8600906051129v3b30349dha3858bf51c919b91(a)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

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func2roi-sess w/o analysis
by Alessandro D. Gagliardi 05 Jun '09

05 Jun '09

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

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RES: Re: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu
by Pedro Paulo de Magalhaes Oliveira Junior 05 Jun '09

05 Jun '09

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(a)netfilter.com.br Cc: freesurfer(a)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(a)netfilter.com.br > Cc: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > > >

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RES: Re: [Freesurfer] Installing FreeSurfer on iMac running Xubuntu
by Pedro Paulo de Magalhaes Oliveira Junior 05 Jun '09

05 Jun '09

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(a)netfilter.com.br Cc: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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