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- -----
- Running recon_checker on:
- Fri Aug 9 09:40:38 CEST 2013
- -----
- Most recent FreeSurfer version used to process this subject:
- /opt/freesurfer/5.3.0/bin/recon-all
- -----
- All FreeSurfer versions used to process this subject:
- /opt/freesurfer/5.3.0/bin/recon-all
- -----
- Checking all output files exist...
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub004 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
- -----
- Checking status log output...
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub004 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
- Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
- ERROR: Recon-all steps missing in subject sub004 status file
-
- Expected to see the following step(s):
- #@# Surf Volume rh Thu Aug 8 22:31:45 CEST 2013
- in the recon-all-status.log file before (line # 68):
- --> Parcellation Stats lh
- --> Cortical Parc 2 lh
- --> Parcellation Stats 2 lh
- --> Tessellate rh
- --> Smooth1 rh
- --> Inflation1 rh
- --> QSphere rh
- --> Fix Topology rh
- --> Make White Surf rh
- --> Smooth2 rh
- --> Inflation2 rh
- --> Curvature Stats rh
- --> Sphere rh
- --> Surf Reg rh
- --> Jacobian white rh
- --> AvgCurv rh
- --> Cortical Parc rh
- --> Make Pial Surf rh
- -----
- Checking asegs for outliers...
- Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub004 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
- checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
- checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
- checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
- checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
- checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
- checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
- checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
- checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
- checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
- checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
- checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
- checking subcortical label: Left-Putamen, 0 +/- 0
- checking subcortical label: Left-Pallidum, 0 +/- 0
- checking subcortical label: 3rd-Ventricle, 0 +/- 0
- checking subcortical label: 4th-Ventricle, 0 +/- 0
- checking subcortical label: Brain-Stem, 0 +/- 0
- checking subcortical label: Left-Hippocampus, 0 +/- 0
- checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
- checking subcortical label: Left-Insula, 0 +/- 0
- checking subcortical label: Left-Operculum, 0 +/- 0
- checking subcortical label: Line-1, 0 +/- 0
- checking subcortical label: Line-2, 0 +/- 0
- checking subcortical label: Line-3, 0 +/- 0
- checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
- checking subcortical label: Left-Lesion, 0 +/- 0
- checking subcortical label: Left-Accumbens-area, 0 +/- 0
- checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
- checking subcortical label: Left-VentralDC, 0 +/- 0
- checking subcortical label: Left-undetermined, 0 +/- 0
- checking subcortical label: Left-vessel, 0 +/- 0
- checking subcortical label: Left-choroid-plexus, 0 +/- 0
- checking subcortical label: Left-F3orb, 0 +/- 0
- checking subcortical label: Left-lOg, 0 +/- 0
- checking subcortical label: Left-aOg, 0 +/- 0
- checking subcortical label: Left-mOg, 0 +/- 0
- checking subcortical label: Left-pOg, 0 +/- 0
- checking subcortical label: Left-Stellate, 0 +/- 0
- checking subcortical label: Left-Porg, 0 +/- 0
- checking subcortical label: Left-Aorg, 0 +/- 0
- checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
- checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
- checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
- checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
- checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
- checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
- checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
- checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
- checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
- checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
- checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
- checking subcortical label: Right-Putamen, 0 +/- 0
- checking subcortical label: Right-Pallidum, 0 +/- 0
- checking subcortical label: Right-Hippocampus, 0 +/- 0
- checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
- checking subcortical label: Right-Insula, 0 +/- 0
- checking subcortical label: Right-Operculum, 0 +/- 0
- checking subcortical label: Right-Lesion, 0 +/- 0
- checking subcortical label: Right-Accumbens-area, 0 +/- 0
- checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
- checking subcortical label: Right-VentralDC, 0 +/- 0
- checking subcortical label: Right-undetermined, 0 +/- 0
- checking subcortical label: Right-vessel, 0 +/- 0
- checking subcortical label: Right-choroid-plexus, 0 +/- 0
- checking subcortical label: Right-F3orb, 0 +/- 0
- checking subcortical label: Right-lOg, 0 +/- 0
- checking subcortical label: Right-aOg, 0 +/- 0
- checking subcortical label: Right-mOg, 0 +/- 0
- checking subcortical label: Right-pOg, 0 +/- 0
- checking subcortical label: Right-Stellate, 0 +/- 0
- checking subcortical label: Right-Porg, 0 +/- 0
- checking subcortical label: Right-Aorg, 0 +/- 0
- checking subcortical label: 5th-Ventricle, 0 +/- 0
- checking subcortical label: Left-Interior, 0 +/- 0
- checking subcortical label: Right-Interior, 0 +/- 0
- checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
- checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
- checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
- checking subcortical label: Left-WM-hypointensities, 0 +/- 0
- checking subcortical label: Right-WM-hypointensities, 0 +/- 0
- checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
- checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
- checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
- checking subcortical label: Left-F1, 0 +/- 0
- checking subcortical label: Right-F1, 0 +/- 0
- checking subcortical label: Optic-Chiasm, 0 +/- 0
- checking subcortical label: Corpus_Callosum, 0 +/- 0
- checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
- checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
- checking subcortical label: Dura, 0 +/- 0
- checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
- checking subcortical label: Epidermis, 0 +/- 0
- checking subcortical label: Conn-Tissue, 0 +/- 0
- checking subcortical label: SC-Fat/Muscle, 0 +/- 0
- checking subcortical label: CSF-SA, 0 +/- 0
- checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
- checking subcortical label: Ear, 0 +/- 0
- checking subcortical label: Adipose, 0 +/- 0
- checking subcortical label: Spinal-Cord, 0 +/- 0
- checking subcortical label: Soft-Tissue, 0 +/- 0
- checking subcortical label: Nerve, 0 +/- 0
- checking subcortical label: Bone, 0 +/- 0
- checking subcortical label: Air, 0 +/- 0
- checking subcortical label: Orbital-Fat, 0 +/- 0
- checking subcortical label: Tongue, 0 +/- 0
- checking subcortical label: Nasal-Structures, 0 +/- 0
- checking subcortical label: Globe, 0 +/- 0
- checking subcortical label: Teeth, 0 +/- 0
- checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
- checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
- checking subcortical label: Left-Claustrum, 0 +/- 0
- checking subcortical label: Right-Claustrum, 0 +/- 0
- checking subcortical label: Cornea, 0 +/- 0
- checking subcortical label: Diploe, 0 +/- 0
- checking subcortical label: Vitreous-Humor, 0 +/- 0
- checking subcortical label: Lens, 0 +/- 0
- checking subcortical label: Aqueous-Humor, 0 +/- 0
- checking subcortical label: Outer-Table, 0 +/- 0
- checking subcortical label: Inner-Table, 0 +/- 0
- checking subcortical label: Periosteum, 0 +/- 0
- checking subcortical label: Endosteum, 0 +/- 0
- sub004 has 0 outliers ...
- -----
- Checking white matter SNR measurements...
- 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
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub004 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
- wm-anat-snr results (sub004):
- SNR meanWM stdWM voxWM
- 16.91 106.97 6.33 44033
- -----
- -----
- Running recon_checker on:
- Fri Aug 9 10:06:31 CEST 2013
- -----
- Most recent FreeSurfer version used to process this subject:
- /opt/freesurfer/5.3.0/bin/recon-all
- -----
- All FreeSurfer versions used to process this subject:
- /opt/freesurfer/5.3.0/bin/recon-all
- -----
- Checking all output files exist...
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub004 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
- -----
- Checking status log output...
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub004 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
- Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
- ERROR: Recon-all steps missing in subject sub004 status file
-
- Expected to see the following step(s):
- #@# Surf Volume rh Thu Aug 8 22:31:45 CEST 2013
- in the recon-all-status.log file before (line # 68):
- --> Parcellation Stats lh
- --> Cortical Parc 2 lh
- --> Parcellation Stats 2 lh
- --> Tessellate rh
- --> Smooth1 rh
- --> Inflation1 rh
- --> QSphere rh
- --> Fix Topology rh
- --> Make White Surf rh
- --> Smooth2 rh
- --> Inflation2 rh
- --> Curvature Stats rh
- --> Sphere rh
- --> Surf Reg rh
- --> Jacobian white rh
- --> AvgCurv rh
- --> Cortical Parc rh
- --> Make Pial Surf rh
- -----
- Checking asegs for outliers...
- Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub004 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
- checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
- checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
- checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
- checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
- checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
- checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
- checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
- checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
- checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
- checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
- checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
- checking subcortical label: Left-Putamen, 0 +/- 0
- checking subcortical label: Left-Pallidum, 0 +/- 0
- checking subcortical label: 3rd-Ventricle, 0 +/- 0
- checking subcortical label: 4th-Ventricle, 0 +/- 0
- checking subcortical label: Brain-Stem, 0 +/- 0
- checking subcortical label: Left-Hippocampus, 0 +/- 0
- checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
- checking subcortical label: Left-Insula, 0 +/- 0
- checking subcortical label: Left-Operculum, 0 +/- 0
- checking subcortical label: Line-1, 0 +/- 0
- checking subcortical label: Line-2, 0 +/- 0
- checking subcortical label: Line-3, 0 +/- 0
- checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
- checking subcortical label: Left-Lesion, 0 +/- 0
- checking subcortical label: Left-Accumbens-area, 0 +/- 0
- checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
- checking subcortical label: Left-VentralDC, 0 +/- 0
- checking subcortical label: Left-undetermined, 0 +/- 0
- checking subcortical label: Left-vessel, 0 +/- 0
- checking subcortical label: Left-choroid-plexus, 0 +/- 0
- checking subcortical label: Left-F3orb, 0 +/- 0
- checking subcortical label: Left-lOg, 0 +/- 0
- checking subcortical label: Left-aOg, 0 +/- 0
- checking subcortical label: Left-mOg, 0 +/- 0
- checking subcortical label: Left-pOg, 0 +/- 0
- checking subcortical label: Left-Stellate, 0 +/- 0
- checking subcortical label: Left-Porg, 0 +/- 0
- checking subcortical label: Left-Aorg, 0 +/- 0
- checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
- checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
- checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
- checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
- checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
- checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
- checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
- checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
- checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
- checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
- checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
- checking subcortical label: Right-Putamen, 0 +/- 0
- checking subcortical label: Right-Pallidum, 0 +/- 0
- checking subcortical label: Right-Hippocampus, 0 +/- 0
- checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
- checking subcortical label: Right-Insula, 0 +/- 0
- checking subcortical label: Right-Operculum, 0 +/- 0
- checking subcortical label: Right-Lesion, 0 +/- 0
- checking subcortical label: Right-Accumbens-area, 0 +/- 0
- checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
- checking subcortical label: Right-VentralDC, 0 +/- 0
- checking subcortical label: Right-undetermined, 0 +/- 0
- checking subcortical label: Right-vessel, 0 +/- 0
- checking subcortical label: Right-choroid-plexus, 0 +/- 0
- checking subcortical label: Right-F3orb, 0 +/- 0
- checking subcortical label: Right-lOg, 0 +/- 0
- checking subcortical label: Right-aOg, 0 +/- 0
- checking subcortical label: Right-mOg, 0 +/- 0
- checking subcortical label: Right-pOg, 0 +/- 0
- checking subcortical label: Right-Stellate, 0 +/- 0
- checking subcortical label: Right-Porg, 0 +/- 0
- checking subcortical label: Right-Aorg, 0 +/- 0
- checking subcortical label: 5th-Ventricle, 0 +/- 0
- checking subcortical label: Left-Interior, 0 +/- 0
- checking subcortical label: Right-Interior, 0 +/- 0
- checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
- checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
- checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
- checking subcortical label: Left-WM-hypointensities, 0 +/- 0
- checking subcortical label: Right-WM-hypointensities, 0 +/- 0
- checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
- checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
- checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
- checking subcortical label: Left-F1, 0 +/- 0
- checking subcortical label: Right-F1, 0 +/- 0
- checking subcortical label: Optic-Chiasm, 0 +/- 0
- checking subcortical label: Corpus_Callosum, 0 +/- 0
- checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
- checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
- checking subcortical label: Dura, 0 +/- 0
- checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
- checking subcortical label: Epidermis, 0 +/- 0
- checking subcortical label: Conn-Tissue, 0 +/- 0
- checking subcortical label: SC-Fat/Muscle, 0 +/- 0
- checking subcortical label: CSF-SA, 0 +/- 0
- checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
- checking subcortical label: Ear, 0 +/- 0
- checking subcortical label: Adipose, 0 +/- 0
- checking subcortical label: Spinal-Cord, 0 +/- 0
- checking subcortical label: Soft-Tissue, 0 +/- 0
- checking subcortical label: Nerve, 0 +/- 0
- checking subcortical label: Bone, 0 +/- 0
- checking subcortical label: Air, 0 +/- 0
- checking subcortical label: Orbital-Fat, 0 +/- 0
- checking subcortical label: Tongue, 0 +/- 0
- checking subcortical label: Nasal-Structures, 0 +/- 0
- checking subcortical label: Globe, 0 +/- 0
- checking subcortical label: Teeth, 0 +/- 0
- checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
- checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
- checking subcortical label: Left-Claustrum, 0 +/- 0
- checking subcortical label: Right-Claustrum, 0 +/- 0
- checking subcortical label: Cornea, 0 +/- 0
- checking subcortical label: Diploe, 0 +/- 0
- checking subcortical label: Vitreous-Humor, 0 +/- 0
- checking subcortical label: Lens, 0 +/- 0
- checking subcortical label: Aqueous-Humor, 0 +/- 0
- checking subcortical label: Outer-Table, 0 +/- 0
- checking subcortical label: Inner-Table, 0 +/- 0
- checking subcortical label: Periosteum, 0 +/- 0
- checking subcortical label: Endosteum, 0 +/- 0
- sub004 has 0 outliers ...
- -----
- Checking white matter SNR measurements...
- 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
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub004 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
- wm-anat-snr results (sub004):
- SNR meanWM stdWM voxWM
- 16.91 106.97 6.33 44033
- -----
- -----
- Running recon_checker on:
- Mon Aug 12 13:03:37 CEST 2013
- -----
- Most recent FreeSurfer version used to process this subject:
- /opt/freesurfer/5.3.0/bin/recon-all
- -----
- All FreeSurfer versions used to process this subject:
- /opt/freesurfer/5.3.0/bin/recon-all
- -----
- Checking all output files exist...
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub004 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
- -----
- Checking status log output...
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub004 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
- Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
- ERROR: Recon-all steps missing in subject sub004 status file
-
- Expected to see the following step(s):
- #@# Surf Volume rh Thu Aug 8 22:31:45 CEST 2013
- in the recon-all-status.log file before (line # 68):
- --> Parcellation Stats lh
- --> Cortical Parc 2 lh
- --> Parcellation Stats 2 lh
- --> Tessellate rh
- --> Smooth1 rh
- --> Inflation1 rh
- --> QSphere rh
- --> Fix Topology rh
- --> Make White Surf rh
- --> Smooth2 rh
- --> Inflation2 rh
- --> Curvature Stats rh
- --> Sphere rh
- --> Surf Reg rh
- --> Jacobian white rh
- --> AvgCurv rh
- --> Cortical Parc rh
- --> Make Pial Surf rh
- -----
- Checking asegs for outliers...
- Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub004 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
- checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
- checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
- checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
- checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
- checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
- checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
- checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
- checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
- checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
- checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
- checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
- checking subcortical label: Left-Putamen, 0 +/- 0
- checking subcortical label: Left-Pallidum, 0 +/- 0
- checking subcortical label: 3rd-Ventricle, 0 +/- 0
- checking subcortical label: 4th-Ventricle, 0 +/- 0
- checking subcortical label: Brain-Stem, 0 +/- 0
- checking subcortical label: Left-Hippocampus, 0 +/- 0
- checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
- checking subcortical label: Left-Insula, 0 +/- 0
- checking subcortical label: Left-Operculum, 0 +/- 0
- checking subcortical label: Line-1, 0 +/- 0
- checking subcortical label: Line-2, 0 +/- 0
- checking subcortical label: Line-3, 0 +/- 0
- checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
- checking subcortical label: Left-Lesion, 0 +/- 0
- checking subcortical label: Left-Accumbens-area, 0 +/- 0
- checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
- checking subcortical label: Left-VentralDC, 0 +/- 0
- checking subcortical label: Left-undetermined, 0 +/- 0
- checking subcortical label: Left-vessel, 0 +/- 0
- checking subcortical label: Left-choroid-plexus, 0 +/- 0
- checking subcortical label: Left-F3orb, 0 +/- 0
- checking subcortical label: Left-lOg, 0 +/- 0
- checking subcortical label: Left-aOg, 0 +/- 0
- checking subcortical label: Left-mOg, 0 +/- 0
- checking subcortical label: Left-pOg, 0 +/- 0
- checking subcortical label: Left-Stellate, 0 +/- 0
- checking subcortical label: Left-Porg, 0 +/- 0
- checking subcortical label: Left-Aorg, 0 +/- 0
- checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
- checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
- checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
- checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
- checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
- checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
- checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
- checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
- checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
- checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
- checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
- checking subcortical label: Right-Putamen, 0 +/- 0
- checking subcortical label: Right-Pallidum, 0 +/- 0
- checking subcortical label: Right-Hippocampus, 0 +/- 0
- checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
- checking subcortical label: Right-Insula, 0 +/- 0
- checking subcortical label: Right-Operculum, 0 +/- 0
- checking subcortical label: Right-Lesion, 0 +/- 0
- checking subcortical label: Right-Accumbens-area, 0 +/- 0
- checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
- checking subcortical label: Right-VentralDC, 0 +/- 0
- checking subcortical label: Right-undetermined, 0 +/- 0
- checking subcortical label: Right-vessel, 0 +/- 0
- checking subcortical label: Right-choroid-plexus, 0 +/- 0
- checking subcortical label: Right-F3orb, 0 +/- 0
- checking subcortical label: Right-lOg, 0 +/- 0
- checking subcortical label: Right-aOg, 0 +/- 0
- checking subcortical label: Right-mOg, 0 +/- 0
- checking subcortical label: Right-pOg, 0 +/- 0
- checking subcortical label: Right-Stellate, 0 +/- 0
- checking subcortical label: Right-Porg, 0 +/- 0
- checking subcortical label: Right-Aorg, 0 +/- 0
- checking subcortical label: 5th-Ventricle, 0 +/- 0
- checking subcortical label: Left-Interior, 0 +/- 0
- checking subcortical label: Right-Interior, 0 +/- 0
- checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
- checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
- checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
- checking subcortical label: Left-WM-hypointensities, 0 +/- 0
- checking subcortical label: Right-WM-hypointensities, 0 +/- 0
- checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
- checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
- checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
- checking subcortical label: Left-F1, 0 +/- 0
- checking subcortical label: Right-F1, 0 +/- 0
- checking subcortical label: Optic-Chiasm, 0 +/- 0
- checking subcortical label: Corpus_Callosum, 0 +/- 0
- checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
- checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
- checking subcortical label: Dura, 0 +/- 0
- checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
- checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
- checking subcortical label: Epidermis, 0 +/- 0
- checking subcortical label: Conn-Tissue, 0 +/- 0
- checking subcortical label: SC-Fat/Muscle, 0 +/- 0
- checking subcortical label: CSF-SA, 0 +/- 0
- checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
- checking subcortical label: Ear, 0 +/- 0
- checking subcortical label: Adipose, 0 +/- 0
- checking subcortical label: Spinal-Cord, 0 +/- 0
- checking subcortical label: Soft-Tissue, 0 +/- 0
- checking subcortical label: Nerve, 0 +/- 0
- checking subcortical label: Bone, 0 +/- 0
- checking subcortical label: Air, 0 +/- 0
- checking subcortical label: Orbital-Fat, 0 +/- 0
- checking subcortical label: Tongue, 0 +/- 0
- checking subcortical label: Nasal-Structures, 0 +/- 0
- checking subcortical label: Globe, 0 +/- 0
- checking subcortical label: Teeth, 0 +/- 0
- checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
- checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
- checking subcortical label: Left-Claustrum, 0 +/- 0
- checking subcortical label: Right-Claustrum, 0 +/- 0
- checking subcortical label: Cornea, 0 +/- 0
- checking subcortical label: Diploe, 0 +/- 0
- checking subcortical label: Vitreous-Humor, 0 +/- 0
- checking subcortical label: Lens, 0 +/- 0
- checking subcortical label: Aqueous-Humor, 0 +/- 0
- checking subcortical label: Outer-Table, 0 +/- 0
- checking subcortical label: Inner-Table, 0 +/- 0
- checking subcortical label: Periosteum, 0 +/- 0
- checking subcortical label: Endosteum, 0 +/- 0
- sub004 has 0 outliers ...
- -----
- Checking white matter SNR measurements...
- 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
- Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub004 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub004/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
- wm-anat-snr results (sub004):
- SNR meanWM stdWM voxWM
- 16.91 106.97 6.33 44033
- -----
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