can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails?
thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz
and I re-did it using the -rl flag as you recommended.
it did not influence anything, same problem.
I'd appreciate any trouble shooting tips.
Thanks, M
On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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?The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu