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Thank you for the reply. For some reason, when I change the DCM file to nii and look at them, in majority of our subjects, the cerebellum and lower brain stem has been cut off, but in this specific subject, I don't think the CST is truncated or out of field more than any other subjects that the TRACULA steps have been run for without any errors. I have taken a few screenshots of both this subject and another one whom -prep and -bedp have been run for without any errors and uploaded them to google drive. Please find the link here:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF/view?usp=sharing

Moreover, it is worth mentioning that this specific subject had profound global atrophy with diagnosis of Alzheimer's.

As always, I appreciate your time and help.

Kind regards,

Ela

Yendiki, Anastasia Wed, 29 Jun 2022 08:41:26 -0700

Any chance that part of the left CST is truncated in this one subject? E.g., if 
the top part of the brain was outside the field of view?

Anastasia.
___________

From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Wednesday, June 29, 2022 11:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: trac-all -prep -c ERROR

Dear experts,

I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I get the following error in -prep step:

((INFO: Distances between consecutive points in test subject's space are 10 13 12 13 13 12

WARN: Could not find satisfactory control point fit - try 17034

Writing output files to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_*

Writing spline volume to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz

Segmentation fault (core dumped)

Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022))

I am attaching the log file as well: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy/view?usp=sharing

On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible?

Thank you,

Ela