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@partners.org ckeller@nmr.mgh.harvard.edu
If you've made a label from a group surface, then you should use mri_label2label with the --regmethod surface option to map to the individuals.
As for isxavg-re-sess, there is a problem with it reading in non-bfloat files. Use roisummary-sess to create a summary file, then read the spread sheet into a stats program and do the RE analysis there.
doug
On Fri, 15 Feb 2008, Keller, Corey J. wrote:
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@partners.org ckeller@nmr.mgh.harvard.edu
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Doug Greve -
Keller, Corey J.