On 3/4/14 7:18 PM, Xuelong Zhao wrote:
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?
If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size)
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.
Bring up the overlay configuration window. You can control the frame/time point from there.
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).
You can just specify the output file with a .nii extension doug
Thanks!
Date: Tue, 4 Mar 2014 10:37:19 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@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: greve@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!
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