You can use $SUBJECTS_DIR/fsaverage/mri/aparc+aseg.mgz (already in the
volume), then use mri_label2vol (with --seg flag) and
$FREESURFER_HOME/average/mni152.register.dat for the registration. The
problem is that the cortical labels are all very thin and won't
intersect well with your ICA volum
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 fil
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 recog
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 v
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
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 ve
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 s
