Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
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 >