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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-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y
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-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta
reading aseg from /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_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-bas elineYear1Arm1_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-NDARINVL8EJK2V Y 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