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
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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