External Email - Use Caution
Hi All,
I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated.
I then tried recon-all with the -notal-check flag, which exited “without errors” although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white).
I’m including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks!
The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all
And for the second run, -notal-check was added after -all
For tkregister2: tkregister2 --s subj# --fstal --surf orig
Bryna Goeckner (she/her) Graduate Student Meier Labhttps://secure-web.cisco.com/1pur5M1FnQYnB8iXyrOEPR6TC3h-zcLEgSRygNp0xNHDNFaXD1i9-hPhj4Oaq7TDIvti413rNC9uMY0VMqc0BLx51pq_PXmRoypSPWBkRpLmqFydLNzaEPHOdJXWdRLTEUYo5NRJEfXTSdVU7iLzTCc1UQ23ZLxfHhu6BBI7xeykqdgLkfnskuLA9cBN5rareF2ZVEm7EJ1-5SRGPa-Yy-cKtYsSsDZ1ZLu0FpmRYrSft1XWegfp9_r3MB99se6slt5EKoA83CdtSQQYyNW8MwoTzjhQRkYLE2ACGBCiRt8T_cqUCCQN5BsVfpILRu1Pal_d5Y5I6dCqc7jNcZ3PtOQ/https%3A%2F%2Fwww.mcw.edu%2Fdepartments%2Fneurosurgery%2Fresearch%2Fmeier-laboratory Medical College of Wisconsin Neuroscience Doctoral Program
Hi Bryna,
In this tutorial, it talks about how to fix bad output from the talairach registration:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Goeckner, Bryna Sent: Friday, February 10, 2023 3:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all exited with errors
External Email - Use Caution Hi All,
I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated.
I then tried recon-all with the -notal-check flag, which exited "without errors" although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white).
I'm including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks!
The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all
And for the second run, -notal-check was added after -all
For tkregister2: tkregister2 --s subj# --fstal --surf orig
Bryna Goeckner (she/her) Graduate Student Meier Labhttps://secure-web.cisco.com/1pur5M1FnQYnB8iXyrOEPR6TC3h-zcLEgSRygNp0xNHDNFaXD1i9-hPhj4Oaq7TDIvti413rNC9uMY0VMqc0BLx51pq_PXmRoypSPWBkRpLmqFydLNzaEPHOdJXWdRLTEUYo5NRJEfXTSdVU7iLzTCc1UQ23ZLxfHhu6BBI7xeykqdgLkfnskuLA9cBN5rareF2ZVEm7EJ1-5SRGPa-Yy-cKtYsSsDZ1ZLu0FpmRYrSft1XWegfp9_r3MB99se6slt5EKoA83CdtSQQYyNW8MwoTzjhQRkYLE2ACGBCiRt8T_cqUCCQN5BsVfpILRu1Pal_d5Y5I6dCqc7jNcZ3PtOQ/https%3A%2F%2Fwww.mcw.edu%2Fdepartments%2Fneurosurgery%2Fresearch%2Fmeier-laboratory Medical College of Wisconsin Neuroscience Doctoral Program
freesurfer@nmr.mgh.harvard.edu
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Goeckner, Bryna -
Huang, Yujing