Freesurfer May 2007

freesurfer@nmr.mgh.harvard.edu

53 participants
97 discussions

problem of group analysis
by Wang, Xin 04 May '07

04 May '07

Hello, Group I have a question about mri_glmfit. I can not run this commend on my data. An error "MatrixReadTxT: could not scan value [1] [2] file exists ERROR: loading C age.mat" appeared. I do not know what is wrong. The only warning I saw is "ERROR: cound not find volume $SUBJECTS_DIR/average/surf/../mri/orig. Does it exist?" when I ran mri_surf2surf. I am doing group comparison of cortical thickness on 2X2 data. The following is my fsgd.txt and *.mat. GroupDescriptorFile 1 Title thick vs group Class group1 Class group2 Variables age Input APL02R700 group1 48 Input APN02G650 group1 35 Input APN02G700 group2 35 Input APN03L700 group2 30 DefaultVariable age age.mat: -1, 1, 0 If anyone know what is wrong in my analysis, please help. Thank you in advance, Xin

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Re: [Freesurfer] symbolic links
by skloeppe＠uke.uni-hamburg.de 04 May '07

04 May '07

Thanks Doug, I checked all the limits. This shouldn't be the problem. The descriptor limit is indeed 1024. I am using freesurfer-Linux-centos4-stable-pub-v3.0.3 It would be great if you could make the fix available for this version. Regards, Stefan > Stephan, > > You can find out how many open files are allowed by a process by typing: > > limit > > and look for the 'descriptors' setting. If that is less than 102, then > that is likely your problem, and you could try changing the line to: > > limit descriptors 128 > > If your current descriptors default is some number much greater (like > 1024), then the problem is something else. > > Which freesurfer distribution are you using? If the problem is indeed > the 'too many open descriptors' problem, there was a bug that was fixed > to address this (but hasnt yet made to the public distribution), and I > could post the binaries for your platform. > > Nick > > > > On Thu, 2007-05-03 at 17:26 +0000, skloeppe(a)uke.uni-hamburg.de wrote: > > 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 > > > > > > > > > > > > > _______________________________________________ > 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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RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 03 May '07

03 May '07

Hi Xin, Within the *h.aparc.annot files for each subject, there should be individual label files for *h.precentral.label and *h.postcentral.label. If you take a look at your *h.aparc.stats, there should be a value for the thickness and volume. You can, of course, take this *h.aparc.stats file and upload it into matlab, spss or any other stats package and do statistics on these values. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Dear Rahul > The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. > Thank you, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 3:52 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > What exactly do SI and MI cortices refer to? > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> Hello, group >> I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly tell me the tools I could use for my study? >> Thank you in advance. >> Xin Wang >> > > -- > > > > > > > > > > --

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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

2 1

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

1 0

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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Freesurfer May 2007