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-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
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-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
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.
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-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
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-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
* 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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Bohorquez Montoya, Luisa -
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