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 <fis...@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?





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Michelle VanTieghem
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mrv2...@columbia.edu

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