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