Hello, no it wasn’t a T1. I am trying to process a super old data with a bad T1 (the contrast is not the best). I think the recon-all is failing in the skullstrip part. Do you have any advices on how to deal with this? I already tried changing the watershed and I don’t have success. If I change this I got same T1.mgz error.

I am also trying to skull strip before the recon all.

“you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz” what does it means to make a link from brainmask.auto.mgz to brainmask.mgz?? just a copy?

Thanks for your help!!

Luisa Bohorquez, PhD.

Department of Psychiatry,

Medical College of Wisconsin.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mora, Jocelyn S." <JSMORA@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 19, 2021 at 12:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all log

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Hi Luisa,

There seems to be an error opening the T1.mgz file. Is there a T1.mgz file in your mri folder?

Best,

Jocelyn

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bohorquez Montoya, Luisa <lbohorquez@mcw.edu>
Sent: Monday, January 18, 2021 10:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all log

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Good morning freesurfer, I am new using recon all. Would you mind to help me with this error I am getting? What should I do?

Attached is the log and here is my command.

recon-all \

-subject ${ANATDIR} \

-i ${ANATDIR}/${subject}/*Ax_FSPGR_3D_GR.nii.gz \

-T2 ${ANATDIR}/${subject}/*Ax_T2_FLAIR_SE_IR.nii.gz \

-T2pial \

-parallel -openmp 12 \

Thank you so much for your time

Luisa Bohorquez, PhD.

Department of Psychiatry,

Medical College of Wisconsin.