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Hello,

I had a question about re-running recon-all with a precalculated brainmask. I have a brain mask that was created outside of FreeSurfer that I would like to use instead of the brainmask that is created in recon-all. I tried the following command (also with the mask in its original .nii form) and I get an error that the brainmask doesn't exist and thus does not continue throughout the pipeline (attached).

recon-all -subjid test -i sub-HV3WJK_ses-MRI_rec-t1_N4norm.nii -xmask tweakedFSBrainMask2.mgz -all -noskullstrip

error: mghRead(/home/acrawford/ATP_calibration_data/sub-HV3WJK/ses-MRI/run-001/fsNormPipeline_1/FStweakedMask/mri/brainmask.mgz, -1): could not open file\00 error: mri_em_register: could not open mask volume brainmask.mgz. \00

I have also tried running the full recon-all as is, then substituting in my brainmask and the skull-stripped T1 (brain.mgz) using the -autorecon2 -autorecon3 flags, but continue to run into errors. Additionally, I tried just using the skull-stripped T1 as the input file to recon-all -all which also did not work.

Is there a way to run recon-all with an 'outside' mask?

Thank you, Anna _________________________ Anna Crawford Senior Image Analyst Phone: +1 (475) 318-8228

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