Does the "mri" dir exist in the directory that you are running it from?

joel bruss wrote:

Hello-

I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running:

mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz

and all was running well until it exited with the following error:

Used brute-force search on 2690 voxels Writing output aseg to mri/wmparc.mgz sh: mri/wmparc.mgz: No such file or directory

I thought that the point of running this command was to create the wmparc.mgz file. Did I do something wrong with my command? Also, shouldn't recon-all create this file as well?

Thanks, Joel

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