Freesurfer February 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
87 discussions

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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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

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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

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optseq2 and unique events
by Jasony Brozinsky 14 Feb '08

14 Feb '08

Hi, Can optseq2 converge on a solution when an event occurs only once? I'm having difficulty fitting a single nuisance event into a design. In each experimental block, I have 9 trials of interest, and one rare event who's HRF is unimportant to me, but which needs to be separate from the NULL condition. For the trials of interest, I'd like to keep the ITI at 2-10 seconds, but, if need be, I'd be happy to have an ITI of 60 seconds for the nuisance event if would allow this to work. Any ideas would be greatly appreciate-- the following code fails to settle on a solution: ../../optseq2 --ntp 100 --tr 2 --cost eff --tprescan 0 --psdwin 0 18 1 --ev EV1 6 3 --ev EV2 7 3 --ev EV3 8 3 --ev Nuis 11 1 --tnullmin 0 --tnullmax 12 --nsearch 1000 --focb 1000 --nkeep 100 --o output --log log --polyfit 2 P.S. The mail list's search function doesn't work for me, so please forgive me if this has been covered in a previous thread! ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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optseq2
by Julia Bender 14 Feb '08

14 Feb '08

Hi, I have a question concerning optseq2. I found that increasing the dPSD Parameter from 1/2 TR (0.92s) to 1 TR (1.84s) INCREASED the efficiency of the best schedules from about .075 to .093. I would have assumed that a more finely spaced schedule would result in better efficiency scores. Did I do (or understand) something wrong? My optseq2 command line goes as follows: /.../.../optseq2 \ --ntp 121 \ --tr 1.84 \ --tprescan 0 \ --psdwin 0 11.04 0.92 \ ## or 0 11.04 1.84 --ev trial 5.52 20 \ --ev catch 5.52 20 \ --nsearch 100 \ --nkeep 10 \ --o test \ Thank you for your support, Julia Julia Bender Humboldt Universität zu Berlin Mathematisch - Naturwissenschaftliche Fakultät II Institut für Psychologie, Abt. Klinische Psychologie Unter den Linden 6 D-10099 Berlin

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mri_convert: problem with multiple echoes in Genesis images
by Dominik Meier 13 Feb '08

13 Feb '08

Problem: mri_convert creates a NIFTI image that splits the dual echo, but pads with empty slices to the full size, e.g. a dual echo of size 256 x 256 with 108 slices will become a 4D volume with 256 x 256 x 108 x 2 instead of 256 x 256 x 54 x 2. The -nth 0 or -nth 1 option will return a volume of 54 slices, but only half of them with image data and again the lower half empty. This does not seem to happen for DICOM. Does the program look at the "echo number" tag or just de-interleave based on slice order? I noticed DICOM headers have the echo number set correctly, but Genesis headers all seem to list all slices as echo #2. If that's the source of the problem the behavior of mri_convert is not wrong (since it is getting wrong input), but unexpected. In that case: Is there an option to suppress/ignore all echo fields and read all as one volume? Environment: FREESURFER_HOME: /Programs/install/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.11.0 Power Macintosh Command: mri_convert -ot nii GE_DualEcho_PD_axial_3mm/I.001 aTestGEDual.nii Output generated $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from GE_DualEcho_PD_axial_3mm/I.001... fname_format : GE_DualEcho_PD_axial_3mm/I.%03d multi-echo genesis file detected (2 echoes)... TR=3000.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to aTestGEDual.nii... Many thanks. Dominik ______________________________________________ DOMINIK MEIER, PH.D. Center for Neurological Imaging Brigham & Women's Hospital, Harvard Medical School 221 Longwood Avenue, RF396, Boston, MA 02115 Phone: 617 278-0800 Fax: 617 264-5154

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Freesurfer February 2008