I don't know of anything that will do this (or what a single object would mean in this case). If you have the overlay in a volume format (eg, mgz), you can use MRIread.m. This gives you a value for each vertex, not face, so you'd have to write something to assign the value to a face.
doug
On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks.
From: andrewzhao@live.com.au To: greve@nmr.mgh.harvard.edu Date: Tue, 11 Mar 2014 11:54:10 +1100 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks.
Date: Mon, 10 Mar 2014 11:25:23 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
Hi Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the mov, whereas the target comparison looks very pristine. I was just wondering if this is expected. The mov, as I scroll through the
layers
seem to be also slightly offset in certain regions, I guess this
again
may be due to the fuzziness of the mov fmri data.
Yes this is somewhat expected. The target is the data the surface was generated from, so it should look perfect.
Regarding my second q:
I've got this working now- the segfault was due to me naively loading the surface image as a surface, instead of using it as an overlay, I can now successfully scroll through the various frames. However, I noticed that in the documentation to load into matlab, say the left pial surface (with the ICA components on it), I have to save it as a mgz file and then use MRI_read. However, freeview doesn't seem to offer this option once I load the pial surface and the the ICA
components?
Sorry, what has to be mgz? What matlab command? What instructions? doug
Date: Thu, 6 Mar 2014 10:19:25 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug,
A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?
I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?
Can you be more specific? What are your vol2surf and fv command
lines?
Have you tried it in tksurfer?
Thanks again.
Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
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
mailto:greve@nmr.mgh.harvard.edu
To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au;
freesurfer@nmr.mgh.harvard.edu mailto: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
mailto:greve@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu
>
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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/
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