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.