it is in the 'vol' field
On 03/12/2014 08:54 PM, Xuelong Zhao wrote:
> Hmm, it seems I may have misinterpreted the fields in the matlab
> structure after using MRIRead
>
> rsn20_surf = MRIread('rsn20_surf.nii')
>
> I thought perhaps the data would be in the 'volsize' field?
>
> rsn20_surf =
>
> srcbext: ''
> analyzehdr: []
> bhdr: []
> vol: [4-D double]
> niftihdr: [1x1 struct]
> fspec: 'rsn20_surf.nii'
> pwd: '~/rsn_smith09'
> flip_angle: 0
> tr: 1000
> te: 0
> ti: 0
> vox2ras0: [4x4 double]
> volsize: [1 139732 1]
> height: 1
> width: 139732
> depth: 1
> nframes: 20
> vox2ras: [4x4 double]
> nvoxels: 139732
> xsize: 1
> ysize: 1
> zsize: 1
> x_r: -1
> x_a: 0
> x_s: 0
> y_r: 0
> y_a: 1
> y_s: 0
> z_r: 0
> z_a: 0
> z_s: 1
> c_r: -1
> c_a: -17
> c_s: 19
> vox2ras1: [4x4 double]
> Mdc: [3x3 double]
> volres: [1 1 1]
> tkrvox2ras: [4x4 double]
>
> ------------------------------------------------------------------------
> Date: Wed, 12 Mar 2014 10:55:23 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: andrewz...@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> 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: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> To: andrewz...@live.com.au <mailto:andrewz...@live.com.au>
> CC: freesurfer@nmr.mgh.harvard.edu
> <mailto: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: andrewz...@live.com.au <mailto:andrewz...@live.com.au>
> To: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Date: Tue, 11 Mar 2014 11:54:10 +1100
> CC: freesurfer@nmr.mgh.harvard.edu
> <mailto: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: gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> > To: andrewz...@live.com.au <mailto:andrewz...@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 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: gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> > > To: andrewz...@live.com.au <mailto:andrewz...@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 3/6/14 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: gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu>
> > > To: andrewz...@live.com.au <mailto:andrewz...@live.com.au>
> <mailto:andrewz...@live.com.au> <mailto:andrewz...@live.com.au>
> > > CC: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto: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: gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu>
> > > > To: andrewz...@live.com.au
> <mailto:andrewz...@live.com.au>
> <mailto:andrewz...@live.com.au> <mailto:andrewz...@live.com.au>;
> > > freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto: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: gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu>
> > > > > > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto: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>
> > > <mailto: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
> > > > > > gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto: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
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > >
> <http://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
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> > > > > >
> 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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> > > >
> > > > --
> > > > Douglas N. Greve, Ph.D.
> > > > MGH-NMR Center
> > > > gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto: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
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > >
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > > Outgoing:
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> > > >
> > > > _______________________________________________
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> > >
> > >
> > >
> > > _______________________________________________ Freesurfer
> mailing
> > > list Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > <mailto: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
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> > > the Partners Compliance HelpLine at
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> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto: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
> <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
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> The information in this e-mail is intended only for the person
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>
>
> _______________________________________________ Freesurfer mailing
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> information in this e-mail is intended only for the person to whom
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> 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
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