Freesurfer

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4 participants
30076 discussions

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

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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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tkregister2
by Reschke, Cole 01 May '07

01 May '07

Is it possible to spatially align PET data to an MRI using tkregister2? Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

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Talairach transform
by Chuan.Chih.Yang＠rwth-aachen.de 01 May '07

01 May '07

Dear list, After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct). I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ? Thanks. Jackie

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FOV in freesurfer
by Trina Kok 01 May '07

01 May '07

Hi All, I have a few scans that were done with a field of view of 200. I was wondering how freesurfer extrapolates that to a 256 by 256 by 256 matrix. Thanks, Trina

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Help with FS
by Lusineh Gharapetian 30 Apr '07

30 Apr '07

Hello, I don't know how to edit a problem that I have run into on several slices in both hemispheres of multiple brains. The problem is that the pial surface line crosses into white matter. I have attached a couple of instances of this occurring. It happens on multiple slices in a row or as a single slice problem. I would greatly appreciate any advice on how to deal with this. Let me know if you need any further information. Thanks! Sincerely, Lusineh Gharapetian Staff Research Associate Multi Modal Imaging Lab (MMIL) UC San Diego office. 858. 822.1818 email. lgharapetian(a)gmail.com

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