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
To: andrewz...@live.com.au
CC: 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>
> To: andrewz...@live.com.au <mailto:andrewz...@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: gr...@nmr.mgh.harvard.edu
<mailto:gr...@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
> > > 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
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<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 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/
>
> _______________________________________________
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