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.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.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