I'm doing this on the mgh connectome scanner data. There didn't appear to be any freesurfer data in that release.
Ok so sounds like you think making a custom subject average is overkill, and I should just use fsaverage? If so then would you mind just checking that I've got steps 2 and 5 right; saving to .mgh from matlab/python and projecting to the common space? At present the resulting files make freeview crash, so something's not right. 2. Write patterns out to .mgh file matlab: save_mgh(pattern,outfile,eye(4)); ...and/or python: nibabel.MGHImage(pattern[:,numpy.newaxis,numpy.newaxis].astype(np.float32),numpy.eye(4)).to_filename(outfile) 5. Project the resultant files on to the group template 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 Much appreciated! John On 6 February 2016 at 15:58, Glasser, Matthew <[email protected]> wrote: > Indeed why use the orig surfaces? They are missing a lot of corrections > and improvements. > > Peace, > > Matt. > > From: <[email protected]> on behalf of "Harms, > Michael" <[email protected]> > Date: Saturday, February 6, 2016 at 2:56 PM > To: John Griffiths <[email protected]>, " > [email protected]" <[email protected]> > Subject: Re: [HCP-Users] vertex-wise correspondences across subjects > > > Hi John, > Why not just use the surfaces from HCP that already have vertex-wise > correspondence? Or, why can’t you use the usual FS machinery (i.e., > through ‘fsaverage’)? > > If you indeed need to start from the FS ?h.orig surfaces, then this is > indeed more appropriate for the FS list. Note that I think that FS’s > ‘make_average_subject’ just creates average surfaces for your particular > group of subjects. I don’t think what you are attempting actually changes > the registration, since you are not changing the sphere.reg files. (To do > that is much more complicated). > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: <[email protected]> on behalf of John Griffiths > <[email protected]> > Date: Saturday, February 6, 2016 at 11:33 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] vertex-wise correspondences across subjects > > Dear hcp peeps, > > Could you please help me with the following analysis workflow: > > > I am doing an analysis with HCP data 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(pattern,outfile,eye(4)); > > ...and/or python: > nibabel.MGHImage(pattern[:,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... > > Then for each subject: > > > 4. Register 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 in 1. and 2. 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 > > > > > (p.s. yes this is a cross-post from freesurfer list; but got no response from > there, and it is regarding analysis of HCP data, so didn't seem to heinous) > > > > > -- > > Dr. John Griffiths > > Post-Doctoral Research Fellow > > Rotman Research Institute, Baycrest > > Toronto, Canada > > and > > Honorary Associate > > School of Physics > > University of Sydney > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
