QA_tools test

(base) jameshartzell@Jamess-MacBook-Pro subjects % $QA_TOOLS/recon_checker -s S6_HU0936_05_04_12

Parsing flags:
     -s

ERROR: No HTML file specified for snapshots
Using default HTML file name for snapshots: /Users/jameshartzell/freesurfer/subjects/QA/QA_check.html
Writing QA summary log to:
/Users/jameshartzell/freesurfer/subjects/QA/recon_checker.ALL.summary.log


SUBJECTS_DIR: /Users/jameshartzell/freesurfer/subjects 

Checking if output file order file specified...NO
     File order list was not specified.
     Using default order based on FreeSurfer v5.1 output
     Using file list: /Users/jameshartzell/freesurfer/QAtools_v1.2/default_FOF_FSv5.1


=== Processing Subject S6_HU0936_05_04_12 ===

Writing subject QA log to:
/Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/scripts/recon_checker.log
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Running recon_checker on:
Tue Sep 15 11:35:59 CEST 2020
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Most recent FreeSurfer version used to process this subject:
/Users/jameshartzell/freesurfer/bin/recon-all -s S6_HU0936_05_04_12 -autorecon3
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All FreeSurfer versions used to process this subject:
xargs: illegal option -- i
usage: xargs [-0opt] [-E eofstr] [-I replstr [-R replacements]] [-J replstr]
             [-L number] [-n number [-x]] [-P maxprocs] [-s size]
             [utility [argument ...]]
xargs: illegal option -- i
usage: xargs [-0opt] [-E eofstr] [-I replstr [-R replacements]] [-J replstr]
             [-L number] [-n number [-x]] [-P maxprocs] [-s size]
             [utility [argument ...]]
-----
Checking all output files exist...


     Checking if all files exist...FAILED
     (read ../S6_HU0936_05_04_12/scripts/recon_checker.log)
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/transforms/talairach.m3z.inv.x.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/transforms/talairach.m3z.inv.y.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/transforms/talairach.m3z.inv.z.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/nu_noneck.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/aseg.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.white
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.curv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.area
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.K.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.H.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.K1.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.K2.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.S.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.C.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.BE.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.smoothwm.FI.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/lh.curv.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.pial
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.curv.pial
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.area.pial
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.thickness
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.area.mid
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/lh.volume
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/lh.aparc.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.aparc.a2009s.annot
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/lh.aparc.a2009s.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.white
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.curv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.area
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.K.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.H.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.K1.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.K2.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.S.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.C.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.BE.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.smoothwm.FI.crv
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/rh.curv.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.pial
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.curv.pial
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.area.pial
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.thickness
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.area.mid
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../surf/rh.volume
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/aparc.annot.ctab
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/rh.aparc.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.aparc.a2009s.annot
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/aparc.annot.a2009s.ctab
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/rh.aparc.a2009s.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/ribbon.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/lh.ribbon.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/rh.ribbon.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/aseg.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/aparc+aseg.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/aparc.a2009s+aseg.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../mri/wmparc.mgz
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/wmparc.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA1.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA2.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA3a.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA3b.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA4a.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA4p.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA6.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA44.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA45.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.V1.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.V2.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.MT.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.BA.annot
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/lh.BA.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA1.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA2.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA3a.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA3b.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA4a.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA4p.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA6.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA44.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA45.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.V1.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.V2.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.MT.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.BA.annot
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/BA.ctab
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/rh.BA.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/lh.entorhinal_exvivo.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/lh.entorhinal_exvivo.stats
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../label/rh.entorhinal_exvivo.label
     ERROR: Subject S6_HU0936_05_04_12 missing output file ../stats/rh.entorhinal_exvivo.stats

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Checking status log output...


Using status log: /Users/jameshartzell/freesurfer/QAtools_v1.2/default_status_log_FSv5.1.log

ERROR: Recon-all steps missing in subject S6_HU0936_05_04_12 status file
\n \nExpected to see the following step(s): \n#@# SubCort Seg Mon Sep 14 19:03:29 CEST 2020 \nin the recon-all-status.log file before (line # 18): \n--> CA Reg Inv \n--> Remove Neck \n--> SkullLTA

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Checking asegs for outliers...
Using asegLUT: /Users/jameshartzell/freesurfer/QAtools_v1.2/DefaultAsegMeans.txt


parsing arguments ...
checking parameters ...
checking logs ...
done checking logs ...
done checking parameters ...
moving previous log files to *.bak
done moving previous log files
Processing each subcortical label ...
log: Undefined variable.
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Checking white matter SNR measurements...




ERROR: cannot find /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/aparc+aseg.mgz
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Taking snapshots...

====================
Snapshots are about to be collected.  Your screen saver should
be disabled and no windows should be overlapping the tkmedit and
tksurfer screens that will open.  Ctrl+C now if you are not ready!
====================


     Taking snapshots for subject S6_HU0936_05_04_12
tkmedit: Command not found.
tksurfer: Command not found.
tksurfer: Command not found.

     Converting snapshots to tiff and making html page...

View your snapshots by opening this file in an internet browser:
/Users/jameshartzell/freesurfer/subjects//Users/jameshartzell/freesurfer/subjects/QA/QA_check.html

Summary files for individual subjects:
/Users/jameshartzell/freesurfer/subjects/[SUBJECT_ID]/scripts/recon_checker.log
 
Summary file for ALL subjects:
/Users/jameshartzell/freesurfer/subjects/QA/recon_checker.ALL.summary.log
 
recon_checker FINISHED
(base) jameshartzell@Jamess-MacBook-Pro subjects % 
