Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

functional overlay values
by abel cruz vadell 03 May '07

03 May '07

Hi everyone Could I divide the values of a functional overlay volume by a known constant in tkmedit or using any other function of freeSurfer? thanks abel ____________________________________________________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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Re: [Freesurfer] symbolic links
by skloeppe＠uke.uni-hamburg.de 03 May '07

03 May '07

Hi Doug, Thanks for your swift reply. When I run your version I always received the error: "limit: descriptors: Can't remove limit" I then deleted the following line in your code: "limit descriptors unlimited " That helped but after 88 subjects I always get on error message now: "88 of 102: reading /mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz... mghRead: encountered error executing: 'zcat /mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797. mgz',frame -1 mri_average: MRIread(/mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz) failed" I am wondering if it might be related to the line I deleted as the one above the deleted one reads # increase number of allowable open files to maximum: Many thanks, Stefan > > Copy these into your freesurfer bin > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > > then run with --no-link > > doug > > skloeppe(a)uke.uni-hamburg.de wrote: > > >Hi Doug, > > > >I am also running FS on a virtual machine and encoutered the same problem > >with the symbolic links that is described below. When I run the > >make_average_subject script only data for the right hemisphere is created. > >Then it seems to stop with the message: > > > >ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not > >supported > > > >I was wondering if you have modified the script to allow a copy instead of > >a link. Will symbolic links be used later in the group analysis steps as well? > > > >Many thanks, > > > >Stefan > > > > > > > >Re: [Freesurfer] symbolic links > > > >Doug Greve > >Fri, 01 Dec 2006 09:25:04 -0800 > >I don't think recon-all uses any sym links. I can mod the average subj > >script to copy instead of link. > > > >[EMAIL PROTECTED] wrote: > > > > > >Hi Doug, > > > > > > while trying to expand the volume of my virtual machine to be able to > >create symbolic links I started wondering if the way I preprocessed my > >data with recon_all might be affected somehow by the fact symbolic links > >were not supported (the data was located on a mounted drive). The only > >error message regarding this came during the make_average_subject part... > > > > Is there any way to use freesurfer avoiding the creation of symbolic > >links? > > > >many thanks > >bogdan > > > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer(a)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 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus

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scan res
by Kirk, Gregory 02 May '07

02 May '07

Hi, If I did a good job looking through the maillist archive the use of scans with resolution less than 1mm is not handled automatically yet, i.e. have to manually normalize ( divide ) quantities so the numbers are correct. Since we can only get a tiny bit less than 1mm ( 0.9mm ) for patient scans it seems best ( for me ) to just do 1mm is my reading correct ? Is there a fix in near future that would make it worth to wait a month or two to start processing a new study ? thank you Greg.

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setting up freesurfer on supercomputer
by Paul Greenberg 02 May '07

02 May '07

Hi all, I've installed freesurfer 3.0.5 SuSE linux version, on a supercomputer, modified the setup .csh file and am getting the following errors. mri_convert: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I've included the following information in case it helps. Typing: which mri_convert /gpfs/pagreenb/SuSEfreesurfer5_Apr8/bin//mri_convert Typing: ldd mri_convert mri_convert: ./mri_convert: /lib/libc.so.6: version `GLIBC_2.3' not found (required by ./mri_convert) libgsl.so.0 => /gpfs/pagreenb/SuSEfreesurfer5_Apr8/lib/gsl/lib/libgsl.so.0 (0x40018000) libgslcblas.so.0 => /gpfs/pagreenb/SuSEfreesurfer5_Apr8/lib/gsl/lib/libgslcblas.so.0 (0x40174000) libjpeg.so.62 => not found libtiff.so.3 => not found libz.so.1 => /lib/libz.so.1 (0x401a8000) libm.so.6 => /lib/libm.so.6 (0x401b8000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x401e0000) libc.so.6 => /lib/libc.so.6 (0x40214000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) Thanks in advance, Paul

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nature of mris_anatomical_stats problem in v3.0.5
by Michael Harms 02 May '07

02 May '07

Hello, The FS release notes for v3.0.5 state: "mris_anatomical_stats produces incorrect results. There is no work- around. A replacement for Linux is here. This fix will appear in the next release." Is the entire output of 'mris_anatomical_stats' incorrect, or just one part of it? And, does the problem, whatever it is, apply to any previous stable versions (e.g., v3.0.4)? thanks, Mike Harms

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Re: [Freesurfer] symbolic links
by Doug Greve 02 May '07

02 May '07

Copy these into your freesurfer bin ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… then run with --no-link doug skloeppe(a)uke.uni-hamburg.de wrote: >Hi Doug, > >I am also running FS on a virtual machine and encoutered the same problem >with the symbolic links that is described below. When I run the >make_average_subject script only data for the right hemisphere is created. >Then it seems to stop with the message: > >ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not >supported > >I was wondering if you have modified the script to allow a copy instead of >a link. Will symbolic links be used later in the group analysis steps as well? > >Many thanks, > >Stefan > > > >Re: [Freesurfer] symbolic links > >Doug Greve >Fri, 01 Dec 2006 09:25:04 -0800 >I don't think recon-all uses any sym links. I can mod the average subj >script to copy instead of link. > >[EMAIL PROTECTED] wrote: > > >Hi Doug, > > > while trying to expand the volume of my virtual machine to be able to >create symbolic links I started wondering if the way I preprocessed my >data with recon_all might be affected somehow by the fact symbolic links >were not supported (the data was located on a mounted drive). The only >error message regarding this came during the make_average_subject part... > > Is there any way to use freesurfer avoiding the creation of symbolic >links? > >many thanks >bogdan > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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 > >In order to help us help you, please follow the steps in: >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Numerical values of cortical thickness in average subject
by Inês Souta 02 May '07

02 May '07

Hi, I'm new to freesurfer and I'd like to know how I can have access to the numerical values of the cortical thickness of an average subject. Thanks. Inês

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mris_anatomical_stats
by deepa preeti 02 May '07

02 May '07

Hi all, I am a Freesurfer beginner and trying to do cortical surface analysis. I wanted to have whitematter, gray volume and avg.thickness for each hemisphere. So when I run mris_anatomical_stats -t thickness <subject> lh I get the following data: total white matter volume = 729800 mm^3 total surface area = 90850 mm^2 total gray matter volume = 181205 mm^3 average cortical thickness = 1.971 mm +- 0.739 mm average integrated rectified mean curvature = 0.129 average integrated rectified Gaussian curvature = 0.039 folding index = 1574.464 intrinsic curvature index = 204.376 Please correct me if I have this wrong. > total whitematter volume ---> is of the total brain > total surface area ---------> what does it represent ? I am bit confused here. Thanks, Deepa Ramasamy.

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Re: [Freesurfer] symbolic links
by skloeppe＠uke.uni-hamburg.de 02 May '07

02 May '07

Hi Doug, I am also running FS on a virtual machine and encoutered the same problem with the symbolic links that is described below. When I run the make_average_subject script only data for the right hemisphere is created. Then it seems to stop with the message: ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not supported I was wondering if you have modified the script to allow a copy instead of a link. Will symbolic links be used later in the group analysis steps as well? Many thanks, Stefan Re: [Freesurfer] symbolic links Doug Greve Fri, 01 Dec 2006 09:25:04 -0800 I don't think recon-all uses any sym links. I can mod the average subj script to copy instead of link. [EMAIL PROTECTED] wrote: Hi Doug, while trying to expand the volume of my virtual machine to be able to create symbolic links I started wondering if the way I preprocessed my data with recon_all might be affected somehow by the fact symbolic links were not supported (the data was located on a mounted drive). The only error message regarding this came during the make_average_subject part... Is there any way to use freesurfer avoiding the creation of symbolic links? many thanks bogdan _______________________________________________ Freesurfer mailing list Freesurfer(a)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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus

1 0

about the Gray matter volume
by hankee 01 May '07

01 May '07

hi, Now I use the parahippocampal gyrus gray matter volume to divide the total gray matter volume,after that I use the ratio to do the statistics. I think though this procedure can adjust the head size for individual subjects. Am I riht? or I can do like this way? Bests hankee hankee，duhanjian(a)sohu.com 2007-04-29

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