If it is really bad data, you might have to edit the brain mask by hand.
On 1/20/2021 11:56 AM, Bohorquez Montoya, Luisa wrote:
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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