Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

Re: [Freesurfer] posting a question again
by Joongnam Yang 20 Oct '06

20 Oct '06

Thanks, Doug, I never used mri_surf2surf, the latest version I downloaded. Would you be more specific on how to convert avg_thickness to the average subject? (I tried mri_surf2surf --srcsubject SUBJECT --tfmt avg_thickness, but it's asking a whole lot more variables...) Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/20/06 12:34 PM >>> Does it work if you don't use projfrac? We have a bug in the make_average_subject code that causes the average thickness (lh.avg_thickness) to be painted on the last subject in the list instead of the averaage subject. One work-around until we get this fixed is to convert the avg_thickness to the average subject with mri_surf2surf. This will require a new version of surf2surf, which you can get from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf Run it with --tfmt curv doug Joongnam Yang wrote: >Dear all, > >I've been waiting for an answer to the following question. > >I am trying to overlay group-averaged data (FSL) on an averaged anatomical >brain (Freesurfer). >I did the following, > >mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze >--srcreg register.dat --hemi lh --projfrac 0.5 --out >AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint > >and got the following error message, > >MRISreadCurvature: could not open >/home/nam/AVERAGE/average/surf/lh.thickness >No such file or directory > >In the surf directory, I DID find "lh.avg_thickness". >I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. >Would someone please let me know how to remedy this? > > > >>Nam. >> >> >_______________________________________________ >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 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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Error running mri_ca_register in recon-all (v3.0.3)
by sliceofpy＠gmail.com 20 Oct '06

20 Oct '06

Hello, I am getting an error with mri_ca_register when running recon-all with -autorecon2 (ERROR: mri_ca_register with non-zero status), perhaps related to the one discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03626.html I'm running freesurfer-Linux-centos4-stable-pub-v3.0.3 on FC4. This is a new installation so I haven't actually successfully run through recon-all on this machine yet. Attached is the recon-log file from today's run; let me know if any other info would be helpful. Any suggestions on sources for the error or how to further troubleshoot would be much appreciated. Thanks, Jonathan

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posting a question again
by Joongnam Yang 20 Oct '06

20 Oct '06

Dear all, I've been waiting for an answer to the following question. I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint and got the following error message, MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory In the surf directory, I DID find "lh.avg_thickness". I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. Would someone please let me know how to remedy this? >Nam.

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mri_convert --unwarp_gradient_nonlinearity
by Kuijer, J.P.A. 20 Oct '06

20 Oct '06

Hello all, I'm interested in correcting the geometric distortion introduced by the non-linearity of the gradients of our Sonata MR system. I noticed that mri_convert has an option to do this: --unwarp_gradient_nonlinearity When I try to use this option, I get an error message: INFO: unwarping ... Error: couldn't open /usr/local/bin/freesurfer/data/gradientNonlinearitySonata.mff So this file seems to be missing in the freesurfer distribution. Can I request that file somewhere, or is any software available to calculate it from the spherical harmonics as provided by Siemens? cheers -- Joost

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recon-all with more than one subject
by Juergen Haenggi 19 Oct '06

19 Oct '06

Dear Freesurfer users is there any possibility to run recon-all with more than one subject? what is the option to use several subjects within one recon-all command? can one use more than one -s option in one recon-all command? thanks in advance best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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FreeSurfer Coordinates
by Doug Greve 18 Oct '06

18 Oct '06

I've created a new set of powerpoint slides with info about FreeSurfer cooridnate definitions. You can find it at: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug -- 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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tksurfer problem
by Ran Tao 18 Oct '06

18 Oct '06

Hi, I have a problem about tksurfer command. After installing the freesurfer step by step according to instruction, I followed the tutorial to do some tests. However, when I tried to use “tksurfer good_output lh inflated” command on the webpage https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData, the result is not the image on the page, the image I got is attached to this email. At the same time, The tkmedit works fine. I have downloaded the tutorial data. Is there any other demo data should be downloaded? Anyone help will be greatly appreciated. Thanks, Ran ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ The error message is as follows. surfer: current subjects dir: /home/sci/rantao/myinstalls/freesurfer/subjects/buckner_data/tutorial_subjs surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/sci/rantao Talairach transform /autofs/space/birn_045/users/BWH/buckner_data/group_study/103/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /home/sci/rantao/myinstalls/freesurfer/subjects/buckner_data/tutorial_subjs/good_output/mri/transforms/talairach.xfm surfer: Reading header info from /home/sci/rantao/myinstalls/freesurfer/subjects/buckner_data/tutorial_subjs/good_output/mri/T1.mgz surfer: vertices=125352, faces=250700 Talairach transform /autofs/space/birn_045/users/BWH/buckner_data/group_study/103/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /home/sci/rantao/myinstalls/freesurfer/subjects/buckner_data/tutorial_subjs/good_output/surf/../mri/transforms/talairach.xfm

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System requirements
by Oddbjørn Sæther 18 Oct '06

18 Oct '06

Hi, concerning system requirements for installation of FreeSurfer: System requirements says: "A 2GHz or faster processor, at least 2GB of RAM, and a 3D graphics card with accelerated OpenGL drivers, is recommended. Freesurfer is highly CPU and memory intensive (and moderately disk intensive), so concentrate on boosting those performance aspects (more memory is better). Graphics requirements are minimal." We plan to install FreeSurfer on a Linux server (probably SuSe 9), and run from Windows PCs via FreeNX/NXclient. 1. Will that work? 2. What system requirements is advisable with 3-6 users? 3. Is 3D graphics cards necessary on the Windows PCs (or how does this work)? Thanks in advance! Oddbjørn Sæther Dept. of Neuroscience Norwegian University of Science and Technology

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Rendering results of custom fMRI analyses on FreeSurfer surface
by raij＠nmr.mgh.harvard.edu 17 Oct '06

17 Oct '06

Dear FreeSurfers, We are running a FS-FAST group analysis where the individual subjects are morphed to an average brain via spherical surface. The output of that analysis (sig statistical maps, left hemisphere) is saved in $STUDY_DIR/<groupanalysisdir>/bold/<analysisname>/<smoothingdir>/<contrastname>/sig-lh_XXX.bfloat, Question 1: In the above, XXX is usually the slice number. However we have 25 slices in the input data, and our <contrastname> folder contains only bfloat numbers 000-006. I guess morphing the individual data to a sperical surface for group analysis changes the original slice structure, and hence the numbering. I guess we have seven "slices" because in the command func2sph-sess we defined -icoorder 7 (icosahedron order). Correct? Question 2: We use the above sig-lh_XXX.bfloat files as input to a custom matlab analysis. Remember we have XXX=000-006. What should the output of the matlab analysis look like so that rendering it onto a FreeSurfer surface will work? Is there any documentation related to this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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about drawing label with tksurfer
by Lei.Zhang＠uniklinik-freiburg.de 16 Oct '06

16 Oct '06

Hi, Dear FreeSurfers, >From the mailing list I got to know that the label can be drawn manually. I tried on the flatten occiptal surface with tksufer, the purpose of this is to draw the area of some functional activations for ROI analysis, -sesslabel. I loaded the flatten patch in tksufer and also the functional overlay, then around the area of the activations I make closed path -> custom fill ->save selected label. Now, I want to know: 1) Am I right to create the new label? 2) Can this label will be the structural constraint for ROI process? Thanks in advance, Lei

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