Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input: bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image? Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case? Also for --out_type, if I want an easy format to port to matlab? Thanks! > Date: Mon, 3 Mar 2014 14:20:55 -0500 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > you will need to create a registration between your volume (maps) and > the anatomical. You can do this with bbregister. Then use mri_vol2surf > to map your ICs to the surface > doug > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > Hi, > > > > I am trying to display the 20 ICA components in this nifti file > > > > http://brainmap.org/icns/maps.zip > > > > onto anatomical template they've provided here > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > My question is: > > > > How do I extract only the cortical surface from the anatomical > > template and overlay > > it with only parts of each ICA component that intersects with the surface? > > > > > > Thanks! > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. >
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