Freesurfer

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30080 discussions

mri_label2vol
by bell0368＠umn.edu 19 Feb '08

19 Feb '08

Freesurfers, I wish to use a concatenated .mat file created using FSL tools within the mri_label2vol tool. Is this possible? Is it possible to convert a .mat file to a register.dat file, which seems to be the format that mri_label2vol expects? Also, what interpolation method does mri_label2vol use, out of curiousity. Chris Bell

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Problem make_average_subject
by Juergen Haenggi 19 Feb '08

19 Feb '08

Dear FS experts I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error: [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% I set the descriptor limit to 4096, but the make_average_subject command will not start anymore. Any idea what is wrong here? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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'.license' file
by Henrique Fernandes 19 Feb '08

19 Feb '08

The installation was successful! I have created the file in 'pico', as Nick Schmansky told me to do, and fortunately the file '.license' was successfully created. Thank you all for your kind attention, Regards, Henrique Fernandes

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".license" file
by Henrique Fernandes 19 Feb '08

19 Feb '08

Thanks for the suggestions, I'm now having another problem. I created a .license file with the information about my license. Although, to keep the file stored I must have a name for it other else the system won't allow me to create that file. So, after giving a random name to the file, during the test for installation I received an error message like the one above: -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- How should I create the file .license? Any suggestions? Thanks in advance fot he help, Regards Henrique Fernandes

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Problem: 'source'
by Henrique Fernandes 19 Feb '08

19 Feb '08

Dear collegues, I had a problem during the installation of Freesurfer on my computer. I have a Mac Intel, and since the shell I'm using is the bash, I've entered those two lines written in the installation instructions: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh The problem is that when I wrote the second line I received an error message like the one above: bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh bash: /Applications/freesurfer/SetUpFreeSurfer.sh: No such file or directory What would you recommend me to do? I would prefer to continue the installation only after solving this problem, since it is recommended by you to "perform the setup described at this point in the time". Hope you can solve my problem, and I'll be able to use your program very soon, Best regards, Henrique Fernandes _________________________ Researcher in Medical Imaging

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FS download
by Gallo, Antonio (NIH/NINDS) [F] 18 Feb '08

18 Feb '08

Hi All, Just a couple of questions: 1) are there any differences between Linux-CentOS4 and Linux-CentOS5 as platforms for FS4.0.2.? 2) which version of FS should be downloaded for a 64bit machine with Linux-CentOS5 ? Thanks a lot for your help, Antonio

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mri_ca_register error
by Alan Anticevic 16 Feb '08

16 Feb '08

Hi, I was hoping someone can help me with this issue. We are running the recon-all command on a bunch of subjects and most of them (16/21) process just fine (no errors and nice surfaces), however some (5/21) subjects encounter an error like this: Segmentation fault ERROR: mri_ca_register with non-zero status Darwin ccpmac1.wustl.edu 9.1.0 Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jan 16 19:56:59 CST 2008 All the subjects were collected using the same pulse sequence (MPRAGE) and are of good quality. I attached an example log file. Any suggestions how fix this error? Any advice would be much appreciated. Thank you. Best, alan Alan Anticevic -------------------------------------------------------------------- Deptartment of Psychology - CCP Lab Washington University in St. Louis One Brookings Dr. Campus Box 1125 Tel: 314-935-8547 St. Louis, MO 63110 Email: aanticev(a)wustl.edu --------------------------------------------------------------------

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intersubject averaging error across ROIs
by Keller, Corey J. 15 Feb '08

15 Feb '08

Hi Freesurfers, I have created ROI masks for each subject by saving a patch from my averaged brain using tksurfer. I am assuming that the way to average ROIs across subjects is to use talairch space to create one patch and use that patch for each subject with func2roi. I used the command below for this: multnomah:ckeller[96] func2roi-sess -roidef ROI_simple_v_complex_tan -analysis simple_v_complex/ -labelfile r_tan.label -labelspace tal -maskcontrast simple_v_complex/ -maskthresh 2 -masktail pos -maskmap minsig -s PROZ06002 PROZ06003 PROZ06004 PROZ06006 PROZ06009 PROZ06010 PROZ06011 -d . Now in each subject file there is a bold/simple_v_complex/ROI_simple_v_complex_tan subfolder. But when I go to do the intersubject averaging it gives me the following error: multnomah:ckeller[95] isxavg-re-sess -analysis simple_v_complex -contrast simple_v_complex -group average_for_roi_tan -space ROI_simple_v_complex_tan -sf sessid Log file is /autofs/space/multnomah_003/users/gow/PROZ06/fMRI/log/isxavg-re-sess-simple_v_co mplex-simple_v_complex.log Fri Feb 15 10:25:01 EST 2008 ERROR: cannot find /autofs/space/multnomah_003/users/gow/PROZ06/fMRI/PROZ06002/bold/simple_v_comple x/ROI_simple_v_complex_tan/h However, there is h-offset.txt, h.tbl, h-offset.nii, h.txt, and h.nii in each of those subfolders. Is there a reason it is not recognizing these h files? Thanks so much. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital VBK 830, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

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Make_average_subject problem
by Juergen Haenggi 15 Feb '08

15 Feb '08

Dear FS experts, Dear Doug We are still trying to do an average of 92 subjects, but failed due to the known problem with make_average_subject. Is there any work around for that problem or is it possible to do several averages (e.g., 3 times with 30 subjects) and average these three averages again? Does this problem is Mac specific and should we try to run it on a Linux OS? Although I have 8 GB of RAM I cannot average more than about 50 subjects. Thanks a lot for your help Best regards Juergen PS: sorry for your inconvenience ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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checking accuracy of talairach_with_skull.lta transform
by Michael Harms 15 Feb '08

15 Feb '08

Hello, Since the ICV ("eTIV") value is derived from the determinant of "talairach_with_skull.lta", we were wondering if there is a way to check the accuracy of this transform? (e.g., as there is for talairach.xfm using tkregister2) Using 'mri_convert', we were able to convert "RB_all_withskull_2007-08-08.gca" to a conformed (1 x 1 x 1 mm) mgz file for visualization of the RB_all_withskull space. However, despite trying a bunch of different syntaxes with 'tkregister2', we couldn't subsequently figure out how to actually view/confirm the accuracy of the talairach_with_skull.lta transform. In your experience, is the the talairach_with_skull.lta transform always reasonable, or does it sometimes fail (and if the latter, is the failure rate version dependent?) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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