Dear surfers, Could you please help me with the following analysis workflow:
I am doing an analysis where I identify patterns on the ?h.orig surfaces. What I want to do now is to resample these patterns over vertices, such that I have vertex-wise correspondence across subjects. I believe this essentially requires the construction of and projection to a group template (although I'm aware this could be done with e.g. fsaverage). Here is where I'm at: cd(freesurfer dir) 1. Read ?h.orig surfaces; compute patterns (...some in-house stuff...) 2. Write patterns out to .mgh file Matlab save_mgh(pat,outfile,eye(4)); Python nibabel.MGHImage(pat[:,numpy.newaxis,numpy.newaxis].astype(np.float32),numpy.eye(4)).to_filename(outfile) 3. Generate group template make_average_subject --out avgsub --sd <fs dir> -subjects subj1 subj2 subj3 .... 4. Register a single example subject to the new group template mris_register -curv subj1/surf/lh.sphere avgsub/lh.reg.template.tif subj1/surf/lh.sphere.reg.avgsub 5. Project the surface patterns identified above on to the new group template, so that the vertex values correspond across subjects, and can be averaged, statistically compared. etc. mri_surf2surf --srcsubject subj1 --srcsurfreg sphere.reg.avg_sub --trgsubject avg_sub --trgsurfreg sphere.reg --hemi lh --sval <pattern mgh file> --tval /tmp/test_avgsub.mgh However this breaks down at mri_surf2surf, and I'm not particularly confident that the earlier parts are exactly right either. Could you please show me what commands I should be using for the aims as described above? Many thanks, John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
