Dear FS experts,
I tried to run the QA Tools on a subject with the following command:
*${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF
${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT
${SUBJECTS_DIR}/AsegOutliers*
But I got all errors concerning the detection of Aseg outliers:
*Making aseg look-up table, /NAS/tupac/matthieu/FS5.3//AsegOutliers*
*parsing arguments ...*
*checking parameters ...*
*MeanFile is /NAS/tupac/matthieu/FS5.3//AsegOutliers*
*checking logs ...*
*done checking logs ...*
*done checking parameters ...*
*moving previous log files to *.bak*
*done moving previous log files*
*Processing each subcortical label ...*
*(standard_in) 1: syntax error*
*gawk: /home/matthieu/programs/QAtools_v1.1/gstd.awk:22: (FILENAME=- FNR=1)
fatal: division by zero attempted*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*-----Checking asegs for outliers...Using asegLUT:
/NAS/tupac/matthieu/FS5.3//AsegOutliersparsing arguments ...checking
parameters ...checking logs ...done checking logs ...done checking
parameters ...moving previous log files to *.bakdone moving previous log
filesProcessing each subcortical label ...(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error*
Please find attached the recon_checker summary.
Thanks in advance for any help !
Best regards,
Matthieu
----------------
Tue Jun 14 11:07:11 CEST 2016
----------------
SUBJECTS_DIR: /NAS/tupac/matthieu/FS5.3/
Generating file order list using subject 207043_M0_2010-10-07
Using file list: /NAS/tupac/matthieu/FS5.3//QA/local_default_output_order_file
checking subcortical label: Left-Cerebral-Exterior, 0 +/-
checking subcortical label: Left-Cerebral-White-Matter, 0 +/-
checking subcortical label: Left-Cerebral-Cortex, 0 +/-
checking subcortical label: Left-Lateral-Ventricle, 0 +/-
checking subcortical label: Left-Inf-Lat-Vent, 0 +/-
checking subcortical label: Left-Cerebellum-Exterior, 0 +/-
checking subcortical label: Left-Cerebellum-White-Matter, 0 +/-
checking subcortical label: Left-Cerebellum-Cortex, 0 +/-
checking subcortical label: Left-Thalamus, 0 +/-
checking subcortical label: Left-Thalamus-Proper, 0 +/-
checking subcortical label: Left-Caudate, 0 +/-
checking subcortical label: Left-Putamen, 0 +/-
checking subcortical label: Left-Pallidum, 0 +/-
checking subcortical label: 3rd-Ventricle, 0 +/-
checking subcortical label: 4th-Ventricle, 0 +/-
checking subcortical label: Brain-Stem, 0 +/-
checking subcortical label: Left-Hippocampus, 0 +/-
checking subcortical label: Left-Amygdala, 0 +/-
checking subcortical label: Left-Insula, 0 +/-
checking subcortical label: Left-Operculum, 0 +/-
checking subcortical label: Line-1, 0 +/-
checking subcortical label: Line-2, 0 +/-
checking subcortical label: Line-3, 0 +/-
checking subcortical label: CSF, 0 +/-
checking subcortical label: Left-Lesion, 0 +/-
checking subcortical label: Left-Accumbens-area, 0 +/-
checking subcortical label: Left-Substancia-Nigra, 0 +/-
checking subcortical label: Left-VentralDC, 0 +/-
checking subcortical label: Left-undetermined, 0 +/-
checking subcortical label: Left-vessel, 0 +/-
checking subcortical label: Left-choroid-plexus, 0 +/-
checking subcortical label: Left-F3orb, 0 +/-
checking subcortical label: Left-lOg, 0 +/-
checking subcortical label: Left-aOg, 0 +/-
checking subcortical label: Left-mOg, 0 +/-
checking subcortical label: Left-pOg, 0 +/-
checking subcortical label: Left-Stellate, 0 +/-
checking subcortical label: Left-Porg, 0 +/-
checking subcortical label: Left-Aorg, 0 +/-
checking subcortical label: Right-Cerebral-Exterior, 0 +/-
checking subcortical label: Right-Cerebral-White-Matter, 0 +/-
checking subcortical label: Right-Cerebral-Cortex, 0 +/-
checking subcortical label: Right-Lateral-Ventricle, 0 +/-
checking subcortical label: Right-Inf-Lat-Vent, 0 +/-
checking subcortical label: Right-Cerebellum-Exterior, 0 +/-
checking subcortical label: Right-Cerebellum-White-Matter, 0 +/-
checking subcortical label: Right-Cerebellum-Cortex, 0 +/-
checking subcortical label: Right-Thalamus, 0 +/-
checking subcortical label: Right-Thalamus-Proper, 0 +/-
checking subcortical label: Right-Caudate, 0 +/-
checking subcortical label: Right-Putamen, 0 +/-
checking subcortical label: Right-Pallidum, 0 +/-
checking subcortical label: Right-Hippocampus, 0 +/-
checking subcortical label: Right-Amygdala, 0 +/-
checking subcortical label: Right-Insula, 0 +/-
checking subcortical label: Right-Operculum, 0 +/-
checking subcortical label: Right-Lesion, 0 +/-
checking subcortical label: Right-Accumbens-area, 0 +/-
checking subcortical label: Right-Substancia-Nigra, 0 +/-
checking subcortical label: Right-VentralDC, 0 +/-
checking subcortical label: Right-undetermined, 0 +/-
checking subcortical label: Right-vessel, 0 +/-
checking subcortical label: Right-choroid-plexus, 0 +/-
checking subcortical label: Right-F3orb, 0 +/-
checking subcortical label: Right-lOg, 0 +/-
checking subcortical label: Right-aOg, 0 +/-
checking subcortical label: Right-mOg, 0 +/-
checking subcortical label: Right-pOg, 0 +/-
checking subcortical label: Right-Stellate, 0 +/-
checking subcortical label: Right-Porg, 0 +/-
checking subcortical label: Right-Aorg, 0 +/-
checking subcortical label: 5th-Ventricle, 0 +/-
checking subcortical label: Left-Interior, 0 +/-
checking subcortical label: Right-Interior, 0 +/-
checking subcortical label: Left-Lateral-Ventricles, 0 +/-
checking subcortical label: Right-Lateral-Ventricles, 0 +/-
checking subcortical label: WM-hypointensities, 0 +/-
checking subcortical label: Left-WM-hypointensities, 0 +/-
checking subcortical label: Right-WM-hypointensities, 0 +/-
checking subcortical label: non-WM-hypointensities, 0 +/-
checking subcortical label: Left-non-WM-hypointensities, 0 +/-
checking subcortical label: Right-non-WM-hypointensities, 0 +/-
checking subcortical label: Left-F1, 0 +/-
checking subcortical label: Right-F1, 0 +/-
checking subcortical label: Optic-Chiasm, 0 +/-
checking subcortical label: Corpus_Callosum, 0 +/-
checking subcortical label: Left-Amygdala-Anterior, 0 +/-
checking subcortical label: Right-Amygdala-Anterior, 0 +/-
checking subcortical label: Dura, 0 +/-
checking subcortical label: Left-wm-intensity-abnormality, 0 +/-
checking subcortical label: Left-caudate-intensity-abnormality, 0 +/-
checking subcortical label: Left-putamen-intensity-abnormality, 0 +/-
checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/-
checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/-
checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/-
checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/-
checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/-
checking subcortical label: Left-VDC-intensity-abnormality, 0 +/-
checking subcortical label: Right-wm-intensity-abnormality, 0 +/-
checking subcortical label: Right-caudate-intensity-abnormality, 0 +/-
checking subcortical label: Right-putamen-intensity-abnormality, 0 +/-
checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/-
checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/-
checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/-
checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/-
checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/-
checking subcortical label: Right-VDC-intensity-abnormality, 0 +/-
checking subcortical label: Epidermis, 0 +/-
checking subcortical label: Conn-Tissue, 0 +/-
checking subcortical label: SC-Fat/Muscle, 0 +/-
checking subcortical label: CSF-SA, 0 +/-
checking subcortical label: Muscle, 0 +/-
checking subcortical label: Ear, 0 +/-
checking subcortical label: Adipose, 0 +/-
checking subcortical label: Spinal-Cord, 0 +/-
checking subcortical label: Soft-Tissue, 0 +/-
checking subcortical label: Nerve, 0 +/-
checking subcortical label: Bone, 0 +/-
checking subcortical label: Air, 0 +/-
checking subcortical label: Orbital-Fat, 0 +/-
checking subcortical label: Tongue, 0 +/-
checking subcortical label: Nasal-Structures, 0 +/-
checking subcortical label: Globe, 0 +/-
checking subcortical label: Teeth, 0 +/-
checking subcortical label: Left-Caudate/Putamen, 0 +/-
checking subcortical label: Right-Caudate/Putamen, 0 +/-
checking subcortical label: Left-Claustrum, 0 +/-
checking subcortical label: Right-Claustrum, 0 +/-
checking subcortical label: Cornea, 0 +/-
checking subcortical label: Diploe, 0 +/-
checking subcortical label: Vitreous-Humor, 0 +/-
checking subcortical label: Lens, 0 +/-
checking subcortical label: Aqueous-Humor, 0 +/-
checking subcortical label: Outer-Table, 0 +/-
checking subcortical label: Inner-Table, 0 +/-
checking subcortical label: Periosteum, 0 +/-
checking subcortical label: Endosteum, 0 +/-
207043_M0_2010-10-07 has 0 outliers ...
207043_M0_2010-10-07 has 0 outliers ...
=== Processing Subject 207043_M0_2010-10-07 ===
Writing subject QA log to:
/NAS/tupac/matthieu/FS5.3//207043_M0_2010-10-07/scripts/recon_checker.log
207043_M0_2010-10-07 has 0 outliers ...
wm-anat-snr results:
SNR: Anatomical signal-to-noise ratio in white matter
mWM: Mean white matter intensity value
stdWM: Standard deviation of white matter intensity value
voxWM: Total number of white matter voxels in eroded mask
SubjID SNR mWM stdWM voxWM
207043_M0_2010-10-07 15.84* 103.92 6.56* 42529 <------
Taking snapshots for subject 207043_M0_2010-10-07
View your snapshots by opening this file in an internet browser:
/NAS/tupac/matthieu/FS5.3///NAS/tupac/matthieu/FS5.3//QA/QA_check.html
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