Hi Rakshathi

I don’t think this is the right recon-all.log. It seems to have finished with no error:

Started at Sun Jan 15 04:38:40 IST 2023 Ended at Sun Jan 15 06:00:56 IST 2023 #@#%# recon-all-run-time-hours 1.371

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Rakshathi Basavaraju Sent: Saturday, January 28, 2023 4:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] What if FS fails

External Email - Use Caution To, Yujing Huang

Here they are. Thanks for your answer. Waiting for your response.

Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

On Fri, Jan 27, 2023 at 4:10 PM Rakshathi Basavaraju <rakshathi.b@gmail.commailto:rakshathi.b@gmail.com> wrote: What is to be done if we get such an error message for recon-all: (copied from recon-allstatus log)

status file for recon-all Tue Jan 3 22:43:36 IST 2023 #@# MotionCor Tue Jan 3 22:43:41 IST 2023 #@# Talairach Tue Jan 3 22:43:53 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:47:14 IST 2023 #@# Talairach Tue Jan 3 22:47:15 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:50:31 IST 2023 #@# Talairach Tue Jan 3 22:50:32 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:53:29 IST 2023 Darwin JAGADISHAs-Mac-mini.local 21.2.0 Darwin Kernel Version 21.2.0: Sun Nov 28 20:29:10 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T8101 x86_64

recon-all -s subj39_anat exited with ERRORS at Tue Jan 3 22:53:30 IST 2023

Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

I see talairach check failed. Can you try the steps that are suggested in recon-all.log?

“ #@# Talairach Failure Detection Wed Jan 4 15:13:30 IST 2023 /Volumes/Rakshathi/Freesurfer/subj55_anat/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0027, pval=0.0000 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://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 Rakshathi Basavaraju Sent: Monday, January 30, 2023 2:18 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] What if FS fails

External Email - Use Caution Dear Bruce,

Sorry for the error. Here are the correct files.

Thanks, Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

On Sat, Jan 28, 2023 at 2:47 PM Rakshathi Basavaraju <rakshathi.b@gmail.commailto:rakshathi.b@gmail.com> wrote: To, Yujing Huang

Here they are. Thanks for your answer. Waiting for your response.

Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

On Fri, Jan 27, 2023 at 4:10 PM Rakshathi Basavaraju <rakshathi.b@gmail.commailto:rakshathi.b@gmail.com> wrote: What is to be done if we get such an error message for recon-all: (copied from recon-allstatus log)

status file for recon-all Tue Jan 3 22:43:36 IST 2023 #@# MotionCor Tue Jan 3 22:43:41 IST 2023 #@# Talairach Tue Jan 3 22:43:53 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:47:14 IST 2023 #@# Talairach Tue Jan 3 22:47:15 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:50:31 IST 2023 #@# Talairach Tue Jan 3 22:50:32 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:53:29 IST 2023 Darwin JAGADISHAs-Mac-mini.local 21.2.0 Darwin Kernel Version 21.2.0: Sun Nov 28 20:29:10 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T8101 x86_64

recon-all -s subj39_anat exited with ERRORS at Tue Jan 3 22:53:30 IST 2023

Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320