Dear Doug, I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient? 2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview. 3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check). Thanks! > Date: Tue, 4 Mar 2014 10:37:19 -0500 > From: gr...@nmr.mgh.harvard.edu > To: andrewz...@live.com.au; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > 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
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