External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu> on behalf of "Mora, Jocelyn S."
<jsm...@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
ATTENTION: This email originated from a sender outside of MCW. Use caution when
clicking on links or opening attachments.
________________________________
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bohorquez Montoya, Luisa
<lbohorq...@mcw.edu>
Sent: Monday, January 18, 2021 10:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all log
External Email - Use Caution
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.
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