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.vantieg...@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
mrv2...@columbia.edu
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