Freesurfer February 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
80 discussions

importing EEG coordinates in free surfer
by abel cruz vadell 23 Feb '07

23 Feb '07

Hi everyone I need to import EEG coordinates (obtained with Polhemus system in ASCII format) in the FreeSurfer workspace. My final aim is characterize small areas of the cortical surface (exactly the regions underlaying my sensors position) with typical parameters of FreeSurfer (cortical thikness,...) . I have read some papers reporting partial solutions to my needs. All of them used matlab with some exported files of FreeSurfer and registered them with the coordinates of the EEG or MEG analysis. I will like to have an opposite solution: import the file with the coordinates of the EEG into the FreeSufer workspace, maybe using the Load/overlay /registration menu of FreeSurfer or another that you can suggest me. I guess my coordinates file needs some transformations before import it to the FreeSurfer workspace thanks in advance 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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Topology fixing
by Juergen Haenggi 23 Feb '07

23 Feb '07

Dear Freesurfer users the topology fixer is running since about 18 hours on the same defect Correcting defect 100 (vertices=23181, convex hull=7929) In contrast to the other defects, the number of vertices involved in this defect is very large. Any idea? 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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Maximum number of subjects in make_average_subject?
by martijn van den heuvel 22 Feb '07

22 Feb '07

Dear Freesurfer-list, I'm trying to construct an average group surface map using 'make_average_subject'. My group consists of a rather large number of subjects, around 400 subjects. Unfortunately, running 'make_average_subject' gives an error when processing subject 253, saying it has an 'mgh reading error' on the 'T1.mgz'. I checked that the involved files are all oke. In addition, I have run 'make_average_subject' several times with different group lists, but every time it stops at subject 253. I'm using an Intel MacPro with 16 GB of system memory, and there is plenty of free memory when it runs. Is there a maximum set on the number of subjects you can use in 'make_average_subject'? Can I reset this value? Yours sincerely, Martijn van den Heuvel

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lh.thickness error
by Joongnam Yang 22 Feb '07

22 Feb '07

Hi all, I was doing mri_vol2surf to overlay functional average(FSL) onto anatomical average (Freesurfer) and got the following error message, ERROR: .................. Reading thickness /home/nam/V4RET/average/surf/lh.thickness MRISreadCurvature: could not open /home/nam/V4RET/average/surf/lh.thickness No such file or directory .................. Is "make_average_subject" supposed to produce "lh.thickness"? Please let me know what is wrong? Thanks, Nam. My command was: mri_vol2surf --src /home/nam/V4RET/FUNC/AVG/LMhori.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out /home/nam/V4RET/FUNC/AVG/LMhori.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint

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Anonymous svn checkouts?
by James Kyle 22 Feb '07

22 Feb '07

The freesurfer source is a fairly large download. I was hoping to keep our local copies up to date using an incremental update method like rsync or, ideally, a versioning system like svn. Forgive me if I've missed this information on the wiki. James A. Kyle UCLA Center for Cognitive Neuro Science David Geffen School of Medicine

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strange overlay of averages
by Joongnam Yang 21 Feb '07

21 Feb '07

Hi all, I have a functional average (using FSL group analysis) and an anatomical average (using Freesurfer make_average_subject) across 6 subjects. (The functional average shows strong activation patterns in FSL ouput, report.html) However, when I overlay the averages, the expected functional activation was almost negligible. Would someone please suggest where I start tackling the problem? Thanks. Nam.

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Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 21 Feb '07

21 Feb '07

Thanks a lot Nick. I'll try to convert the AFNI skull strip into brainmask and nu and see if I can resume the pipeline. I put in the new values for the xfm and ran recon-all again with the notalairach flag. recon-all -s Nl-TAl-001 -notalairach -all However, it still quits at the watershed step. I ran another brain where the raw images were dcm and it ran fine so the problem is definitely something specific to this brain. Nick, I know that autorecon1 ran fine for you so I really have no clue why my machine quits at the watershed step even with the transform you gave me. Any clues, suggestions? Thanks a lot, Anil. On 2/14/07, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Anil, > > Here is the transform (the contents of the talairach.xfm file) that I > generated: > > Transform_Type = Linear; > Linear_Transform = > 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 > -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 > -2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; > > Remember to use the -notalairach flag with recon-all when you create the > new talairach.xfm file, so that it doesnt get overwritten. > > 4GB is plenty to run Freesurfer, so it is strange that mri_watershed is > encountering out-of-memory errors. > > Nick > > > On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: > > Also, I ran it on a Red Hat system and I'm still getting the error so > > I don't think it is a machine specific problem. Any suggestions. > > > > Thanks. > > Anil. > > > > On 2/14/07, Anil Roy <aroy85(a)gmail.com> wrote: > > Here are the details of the acquisitions: > > > > Images acquired on a 3T Signa scanner with a standard GE head > > coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm > > thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * > > 192 matrix) > > > > The machine has 4 gigs of RAM. Also, AFNI is able to talairach > > and skull strip. Is there a way I can input the files from > > AFNI to Freesurfer to resume the recon-all pipeline. > > > > Nick, is there a way for me to see your reg so that I can be > > sure that its not my created xfm that is causing this > > problem. > > > > Thanks, > > > > Anil. > > > > > > On 2/14/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > why is the background so high? Also, what field > > strength was this at? There > > looks to be dielectric-like center brightening. The > > contrast isn't terrible > > though. > > > > On Wed, 14 Feb 2007, Nick > > Schmansky wrote: > > > > > Bruce, > > > > > > the orig.mgz can be downloaded via the filedrop, see > > link in email > > > below. > > > > > > or i have copied it to: > > > > > > > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > > > > > > N. > > > > > > > > > On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl > > wrote: > > >> put the .mgz somewhere and I'll take a look. And > > make sure it's the > > >> orig.mgz, which is un-normalized > > >> > > >> > > >> On Wed, 14 Feb 2007, Nick Schmansky wrote: > > >> > > >>> Anil, > > >>> > > >>> The image has almost no contrast. I've attached a > > TIFF of one slice. > > >>> How was this acquired? Bruce, any idea why it > > would be so white? > > >>> > > >>> Nick > > >>> > > >>> > > >>> On Wed, 2007-02-14 at 16:10 -0500, > > aroy85(a)gmail.com wrote: > > >>>> The following files have been uploaded to the > > Martinos Center FileDrop site > > >>>> by Anil Roy for you to download: > > >>>> > > >>>> (1) orig.mgz > > >>>> > > >>>> > > >>>> > > >>>> These files will expire in 30 days. > > >>>> > > >>>> To view or download these files, go in your web > > browser to: > > >>>> > > >>>> > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > > >>>> > > >>>> DO NOT SHARE this web address with anyone > > else. It is your personal access key to the files. > > >>>> > > >>>> Overall Comment about files from Anil Roy: > > >>>> > > >>>> Hi, > > >>>> > > >>>> Attached is the orig.mgz file for the subject > > that quits at the watershed step. > > >>>> > > >>>> Thanks, > > >>>> > > >>>> Anil. > > >>>> > > >>>> > > >>> > > >> > > >> > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Reprocessing the data with new FS release
by Gallo, Antonio (NIH/NINDS) [F] 21 Feb '07

21 Feb '07

Hi all, Since we have updated Freesurfer with the last (3.0.5) release, we were wondering at which point we should reprocess (i.e autorecon1, autorecon2, etc) our data in order to retain the edits we have made using the previous version. Thank you, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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question about surface-EEG fusion
by abel cruz vadell 20 Feb '07

20 Feb '07

Hello I need to import a file with the coordinates of the EEG electrodes (*.elc) obtained in the system POLHEMUS FASTRAK into the FreeSurfer system. Could I do that with the current version? Thanks in advance 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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Installing Freesurfer on Ubuntu 6.10 with AMD64 architecture
by Vincent Costa 20 Feb '07

20 Feb '07

Hi, I am attempting to install Freesurfer on a system running Ubuntu 6.10 with x86_64 architecture. On the Freesurfer Wiki it states that Debian users should install the Red Hat 9 package. I went ahead and did this, setting up and configuring Freesurfer following the directions listed on the Wiki. When I enter the tcsh shell I get the following output as expected: % tcsh -------- freesurfer-Linux-rh9-stable-pub-v3.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/vdcosta/freesurfer FSFAST_HOME /home/vdcosta/freesurfer/fsfast SUBJECTS_DIR /home/vdcosta/freesurfer/subjects MNI_DIR /home/vdcosta/freesurfer/mni GSL_DIR /home/vdcosta/freesurfer/lib/gsl FSL_DIR /home/vdcosta/freesurfer/fsl However when I attempt to test my install, all commands result in the following error: /home/vdcosta/freesurfer/bin/tkmedit.bin: Command not found. tkmedit can be replaced by other commands to generate the same error message. If I enter on the command line: recon-all --help | less : the returned ouput is what appears to be a full manual on all Freesurfer processing steps. Do I need to install the x86_64 package? The following is my .tcshrc file: setenv AFNI_PATH ~/afni set path = ($path .) set path = ($path $AFNI_PATH .) set path = ($path ~/bin) set history = 100 alias copy cp alias del rm alias dir ls alias find 'find . -name \!^ -print' alias dir/p 'ls . | more' alias type 'cat \!^ | more' alias xterm 'xterm -sb &' alias h history alias m more= setenv FREESURFER_HOME /home/vdcosta/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Any help in getting Freesurfer running would be greatly appreciated. Thanks, Vinny Costa vdcosta at ufl dot edu

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Freesurfer February 2007