It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony