what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
cheers
Bruce
On Mon,
7 Aug 2017, Michelle VanTieghem 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?
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