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?
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?
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
> To: andrewz...@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: gr...@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!
> > > >
> > > >
> > > >
> > > >
_______________________________________________
> > > > Freesurfer mailing list
> > > > 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
> > > 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@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
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> > > but does not contain patient information,
please contact the sender
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> > >
>
> --
> 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
> 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/
>
> _______________________________________________
> Freesurfer mailing list
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>
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