Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

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

2 1

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) -----------------------------------------------------------

2 1

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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using freesurfer register program to register afni data
by Garrett McGrath 15 Feb '08

15 Feb '08

To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath

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bad parcellation
by Leila BH 15 Feb '08

15 Feb '08

Hello, In some brains, the parcellation into 35 gyral based parcels is bad while the white matter seems ok, do you know how to correct this? Or what could be the raison Thanks Leila

2 1

recon-all error messages
by Ryan Muetzel 15 Feb '08

15 Feb '08

Hello, I am getting some unusual error messages from recon-all. Both autorecon2 and autorecon3 are exiting with errors. The errors are showing up in all 10 data sets I am running. I've attached some of the log files located in '${SUBJECTS_DIR}/${SUBJID}/scripts/' for one subject. The error message I am noticing is: lnpi07.cmrr.lan 17> more recon-all.log | grep ERROR IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 15160.4 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 1999609.5 tol 0.000000 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 12913.8 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 1713191.2 tol 0.000000 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 15113.3 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 1982807.9 tol 0.000000 recon-all exited with ERRORS at Tue Feb 12 08:46:28 CST 2008 ERROR: cannot find /scratch1/nelsonm/18514/mri/lh.ribbon.mgz ERROR: loading /scratch1/nelsonm/18514/mri/lh.ribbon.mgz recon-all exited with ERRORS at Wed Feb 13 02:31:31 CST 2008 Any ideas? Thanks in advance for any help! -Ryan

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Qdec works for Leopard.
by zheng.hui＠singhealth.com.sg 14 Feb '08

14 Feb '08

2 1

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Freesurfer