You would apply it to the column, row, and slice of a voxel. Note that the volume structure is volume(row,col,slice). But I'm not sure why you need to do this. If you read in the ICA maps after running mri_vol2surf, there will be a value for each vertex, no need to do any mapping

doug



On 3/11/14 7:00 PM, Xuelong Zhao wrote:
Okay, I think I'm getting close to what I want in the matlab object. I've successfully imported both the pial surface (using read_surf.m) and the ICA components on the surface in mgh format using MRIread.m

I've had a look at the MRIread.m script and it says I can use vox2ras1 to convert column, row, and slice to XYZ coordinates. Which field of the matlab structure should I apply this to? I"m guessing its voxels but wanted to make sure, and also I'd have to do this for each individual frame? Thanks.

Date: Mon, 10 Mar 2014 23:54:18 -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


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>
> > > > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > >
> > > > > --
> > > > > Douglas N. Greve, Ph.D.
> > > > > MGH-NMR Center
> > > > > greve@nmr.mgh.harvard.edu <mailto:greve@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
> > <http://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
> > <mailto: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
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> > > > HelpLine at
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> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu <mailto:greve@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
> > <http://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
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > _______________________________________________ Freesurfer mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> > <mailto: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
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> > 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
> greve@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/
>

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_______________________________________________ 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.