what viewer did you check in? If not freeview, look at it in freeview On Mon, 7 Aug 2017, Michelle VanTieghem wrote:
Hi, After checking the images in the viewer, it appears that 001.mgz and brainmask.mgz are in the correct orientation, but brain.mgz (created by freesurfer) is rotated 90 degrees. The dimensions of the images don't match either.
001.mgz and brainmask.mgz are: dim1 219 dim2 268 dim3 265 dim4 1
brain.mgz is : dim1 256 dim2 256 dim3 256
On Mon, Aug 7, 2017 at 2:04 PM, Michelle VanTieghem michelle.vantieghem@gmail.com wrote: Hi Bruce,
Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command:
recon-all -all -3T -mprage -s processed/Subnum
I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask
Can you please advise?
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu