Hi Norman
don't give it the gcs file as input - that's the atlas. Give it the
lh.aparc.annot for that subject
cheers
Bruce
On Wed, 25 Feb 2015, Norman Benbrahim wrote:
Thanks for your reply Bruce, however I get an error when try to use this
command. I'm in the directory containing the files and I ran
mri_surf2vol --surfval
lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs --hemi lh
--outvol LH.nii
and it gave me an output of
ERROR: cannot recognize the type of
lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
On Tue, Feb 24, 2015 at 4:42 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
I see. You could do what you want by sampling the ?h.aparc.annot
into the volume (mri_surf2vol), then mapping into MNI space
(mri_vol2vol). Actually, if you do surf2vol from fsaverage I
think it's already in MNI coords, but Doug can confirm. The
problem is going to be that the mapping won't be very accurate
across subjects. You would be better off doing it all on the
surface
cheers
Bruce
On Tue, 24 Feb 2015, Norman Benbrahim wrote:
No problem,
I want to take certain regions and use them as masks
in order to compute the joint
histogram between a thresholded z-score map obtained
from ICA (a resting state
network) masked in that region, and the variance of
the BOLD image. I already have
scripts set up to do this in matlab, so I would only
need the atlas in nifti format
so I can pick out which regions to use (using the
rich club paper, van den Heuvel et
al. 2011), and create masks out of those.
On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Norman
perhaps you can take a step back and tell us
what you want to use it
for?
We might be able to suggest a better analysis
strategy
Bruce
On Tue, 24 Feb 2015,
Norman Benbrahim wrote:
> Hi,
> I want to use the Desikan-Kilany atlas to
run some analysis in some
regions, however
> I am very new to freesurfer. What I would
like to accomplish is the
following:
> 1) Transform the atlas into MNI152 2mm space
> 2) Convert the atlas to a binary nifti image
(similarly to the way
FSL's atlases are
> stored)
> If anyone can help me get started that would
be awesome. Thank you!
> -Norman
>
>
_______________________________________________
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.
_______________________________________________
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.
_______________________________________________
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.
