On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > 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? It should be a functional image. If the ica maps come from an individual, then use the mean functional for that subject or whatever you used for fMRI motion correction (which should be aligned with the ica maps). If it is in a group space, then use the registration target (that is exactly the same size as your maps). > > 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? For projfrac we usually use .5. You can ignore src_type. For output type, you can use nii (nifti) and then use MRIread.m doug > > 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. > >
-- 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
