----- Running recon_checker on: Fri Aug 9 09:38:18 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 status file Expected to see the following step(s): #@# Surf Volume rh Thu Aug 8 22:00:53 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 sub001 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log wm-anat-snr results (sub001): SNR meanWM stdWM voxWM 16.75 105.82 6.32 55728 ----- ----- Running recon_checker on: Fri Aug 9 10:00:26 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 status file Expected to see the following step(s): #@# Surf Volume rh Thu Aug 8 22:00:53 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 sub001 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log wm-anat-snr results (sub001): SNR meanWM stdWM voxWM 16.75 105.82 6.32 55728 ----- ----- Running recon_checker on: Mon Aug 12 12:53:24 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/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 sub001 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/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 sub001 status file Expected to see the following step(s): #@# Surf Volume rh Thu Aug 8 22:00:53 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 sub001 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/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 sub001 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log wm-anat-snr results (sub001): SNR meanWM stdWM voxWM 16.75 105.82 6.32 55728 ----- ----- Running recon_checker on: Mon Aug 12 12:59:20 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/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 sub001 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/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 sub001 status file Expected to see the following step(s): #@# Surf Volume rh Thu Aug 8 22:00:53 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 sub001 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/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 sub001 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 sub001 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub001/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log wm-anat-snr results (sub001): SNR meanWM stdWM voxWM 16.75 105.82 6.32 55728 -----