Not sure what is happening. Does it work if you restart the long time
point from scratch (ie, remove the folder that is there)?
On 6/29/2022 5:49 PM, coope...@student.unimelb.edu.au wrote:
External Email - Use Caution
Dear FreeSurfer developers,
I’m attempting to run recon-all with the longitudinal stream, but one
subject (out of >500) fails recon-all (I’ve re-started many times).
The cross-sectional and base (i.e. steps 1 and 2 of the longitudinal
processing) have completed successfully; it’s this final step that has
the error. It appears that the error lies in mri_cc.
The final lines of the recon-all.log are below:
#--------------------------------------
#@# CC Seg Wed Jun 29 14:56:47 AEST 2022
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta
reading aseg from
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz
error: No such file or directory
error: mri_cc: volume
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz
already has CC in it.
Run with -force to reprocess (not recommended)
@#@FSTIME 2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M
21240 F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78
@#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78
Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1
SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY
exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022
Freesurfer version:
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b (I have also
attempted with version 7.1.0 with identical results)
Platform: centos7_x86_64
Recon-all.log: attached.
With thanks,
Rebecca
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
