[Freesurfer] QA tools outliers, use of -gen-asegLUT

Dear freesurfers,

After reading the documentation on freesurfer web site and searching in the mail archive I wasn't able to find an answer to my question. I'm trying to perform cerebellar segmentation on 100 subjects. The recon-all step went well : every t1 image finished "without error" when I checked the recon-all log. I checked the segmentation result with tmedit and tksurfer (following the recommendation of freesurfer website). I wasn't able to find any problem. After that I use the QA tool. Again, after looking at the snapshots the result appeared correct to me. But for each t1 image, there were between 36 and 45 outliers. So I used the -gen-asegLUT option as suggested in the mail archive (Please find the result below for a t1 image called as100351_conv), but wasn't able to understand the result. The questions I would like to ask you are :

1)What should I do to correct the outliers ?

2) I don't understand this message : "ERROR: Actual file order disagrees with common file order for subject as100351_conv" and this command doesn't work "recon-all -make all -subjid as100351_conv"

3) I don't understand this message : "checking subcortical label: Left-Cerebellum-White-Matter, . +/- . as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an outlier (avg = . +/- .)..." The value that appears to be an outliers doesn't match with the value that I found in Asegstats for Left-Cerebellum-White-Matter.

Thanks a lot for your help, have a nice weekend.

Charles Laidi. (medcharleslaidi (a t) gmail.com)

----- Running recon_checker on: mercredi 16 janvier 2013, 22:47:04 (UTC+0100) ----- Most recent FreeSurfer version used to process this subject: /i2bm/local/freesurfer/bin/recon-all ----- All FreeSurfer versions used to process this subject: /i2bm/local/freesurfer/bin/recon-all ----- Checking all output files exist... Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_output_file_checker -subjid as100351_conv -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log -outputfileorderfile /home/charles/Bureau/QAtools_v1.1/default_FOF_FSv5.1 mri/rawavg.mgz last modified 2012-12-14 05:50:00.000000000 +0100 mri/orig.mgz last modified 2012-12-14 05:50:06.000000000 +0100

ERROR: Actual file order disagrees with common file order for subject as100351_conv

At least one step in the recon-all stream has been skipped or rerun out of order. Run the following command to rerun any steps which were skipped or for which the output has been modified.

recon-all -make all -subjid as100351_conv

Alternatively, examine the ReconAllTable for your version of FreeSurfer to identify the recon-all step where the discrepancy is occuring and rerun every recon-all step from that point forward. This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details.

actual order ====> common order: .......... ====> ......... mri/rawavg.mgz ====> mri/rawavg.mgz mri/orig.mgz ====> mri/orig.mgz mri/transforms/talairach.xfm ====> mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm ====> mri/transforms/talairach.xfm mri/nu.mgz ====> mri/nu.mgz mri/T1.mgz ====> mri/T1.mgz mri/brainmask.mgz ====> mri/brainmask.auto.mgz .......... ====> ......... ----- Checking status log output... Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_status_log_checker -subjid as100351_conv -details -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log Using status log: /home/charles/Bureau/QAtools_v1.1/default_status_log_FSv5.1.log

as100351_conv COMPLETE ----- Checking asegs for outliers... Using asegLUT: test4 Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_aseg_outlier_checker -subjid as100351_conv -LookupMeansFromFile test4 -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log checking subcortical label: Left-Cerebral-Exterior, 0 +/- checking subcortical label: Left-Cerebral-White-Matter, . +/- . checking subcortical label: Left-Cerebral-Cortex, . +/- . checking subcortical label: Left-Lateral-Ventricle, . +/- . as100351_conv Left-Lateral-Ventricle value .541890500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Inf-Lat-Vent, . +/- . as100351_conv Left-Inf-Lat-Vent value .025678500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Cerebellum-Exterior, . +/- . checking subcortical label: Left-Cerebellum-White-Matter, . +/- . as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an outlier (avg = . +/- .)... checking subcortical label: Left-Cerebellum-Cortex, . +/- . as100351_conv Left-Cerebellum-Cortex value 3.768655500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Thalamus, . +/- . checking subcortical label: Left-Thalamus-Proper, . +/- . as100351_conv Left-Thalamus-Proper value .490973600 is an outlier (avg = . +/- .)... checking subcortical label: Left-Caudate, 0 +/- checking subcortical label: Left-Putamen, . +/- . as100351_conv Left-Putamen value .490533400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Pallidum, . +/- . as100351_conv Left-Pallidum value .141965600 is an outlier (avg = . +/- .)... checking subcortical label: 3rd-Ventricle, . +/- . as100351_conv 3rd-Ventricle value .083565200 is an outlier (avg = . +/- .)... checking subcortical label: 4th-Ventricle, . +/- . as100351_conv 4th-Ventricle value .152163600 is an outlier (avg = . +/- .)... checking subcortical label: Brain-Stem, . +/- . as100351_conv Brain-Stem value 1.515180400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Hippocampus, . +/- . as100351_conv Left-Hippocampus value .329418900 is an outlier (avg = . +/- .)... checking subcortical label: Left-Amygdala, . +/- . as100351_conv Left-Amygdala value .146147500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Insula, . +/- . checking subcortical label: Left-Operculum, . +/- . checking subcortical label: Line-1, . +/- . checking subcortical label: Line-2, . +/- . checking subcortical label: Line-3, . +/- . checking subcortical label: CSF, . +/- . as100351_conv CSF value .103080900 is an outlier (avg = . +/- .)... checking subcortical label: Left-Lesion, . +/- . checking subcortical label: Left-Accumbens-area, . +/- . as100351_conv Left-Accumbens-area value .060014400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Substancia-Nigra, . +/- . checking subcortical label: Left-VentralDC, . +/- . as100351_conv Left-VentralDC value .304840900 is an outlier (avg = . +/- .)... checking subcortical label: Left-undetermined, . +/- . checking subcortical label: Left-vessel, . +/- . as100351_conv Left-vessel value .008143700 is an outlier (avg = . +/- .)... checking subcortical label: Left-choroid-plexus, . +/- . as100351_conv Left-choroid-plexus value .140791700 is an outlier (avg = . +/- .)... checking subcortical label: Left-F3orb, . +/- . checking subcortical label: Left-lOg, . +/- . checking subcortical label: Left-aOg, . +/- . checking subcortical label: Left-mOg, . +/- . checking subcortical label: Left-pOg, . +/- . checking subcortical label: Left-Stellate, . +/- . checking subcortical label: Left-Porg, . +/- . checking subcortical label: Left-Aorg, . +/- . checking subcortical label: Right-Cerebral-Exterior, . +/- . checking subcortical label: Right-Cerebral-White-Matter, . +/- . checking subcortical label: Right-Cerebral-Cortex, . +/- . checking subcortical label: Right-Lateral-Ventricle, . +/- . as100351_conv Right-Lateral-Ventricle value .284664900 is an outlier (avg = . +/- .)... checking subcortical label: Right-Inf-Lat-Vent, . +/- . as100351_conv Right-Inf-Lat-Vent value .009904500 is an outlier (avg = . +/- .)... checking subcortical label: Right-Cerebellum-Exterior, . +/- . checking subcortical label: Right-Cerebellum-White-Matter, . +/- . as100351_conv Right-Cerebellum-White-Matter value 1.212467100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Cerebellum-Cortex, . +/- . as100351_conv Right-Cerebellum-Cortex value 3.943269600 is an outlier (avg = . +/- .)... checking subcortical label: Right-Thalamus, . +/- . checking subcortical label: Right-Thalamus-Proper, . +/- . as100351_conv Right-Thalamus-Proper value .520393900 is an outlier (avg = . +/- .)... checking subcortical label: Right-Caudate, 0 +/- checking subcortical label: Right-Putamen, . +/- . as100351_conv Right-Putamen value .503959600 is an outlier (avg = . +/- .)... checking subcortical label: Right-Pallidum, . +/- . as100351_conv Right-Pallidum value .119368500 is an outlier (avg = . +/- .)... checking subcortical label: Right-Hippocampus, . +/- . as100351_conv Right-Hippocampus value .360013100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Amygdala, . +/- . as100351_conv Right-Amygdala value .143212800 is an outlier (avg = . +/- .)... checking subcortical label: Right-Insula, . +/- . checking subcortical label: Right-Operculum, . +/- . checking subcortical label: Right-Lesion, . +/- . checking subcortical label: Right-Accumbens-area, . +/- . as100351_conv Right-Accumbens-area value .065150100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Substancia-Nigra, . +/- . checking subcortical label: Right-VentralDC, . +/- . as100351_conv Right-VentralDC value .298237800 is an outlier (avg = . +/- .)... checking subcortical label: Right-undetermined, . +/- . checking subcortical label: Right-vessel, . +/- . as100351_conv Right-vessel value .005575900 is an outlier (avg = . +/- .)... checking subcortical label: Right-choroid-plexus, . +/- . as100351_conv Right-choroid-plexus value .143066100 is an outlier (avg = . +/- .)... checking subcortical label: Right-F3orb, . +/- . checking subcortical label: Right-lOg, . +/- . checking subcortical label: Right-aOg, . +/- . checking subcortical label: Right-mOg, . +/- . checking subcortical label: Right-pOg, . +/- . checking subcortical label: Right-Stellate, . +/- . checking subcortical label: Right-Porg, . +/- . checking subcortical label: Right-Aorg, . +/- . checking subcortical label: 5th-Ventricle, . +/- . as100351_conv 5th-Ventricle value .000293400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Interior, . +/- . checking subcortical label: Right-Interior, . +/- . checking subcortical label: Left-Lateral-Ventricles, . +/- . checking subcortical label: Right-Lateral-Ventricles, . +/- . checking subcortical label: WM-hypointensities, . +/- . as100351_conv WM-hypointensities value .098165300 is an outlier (avg = . +/- .)... checking subcortical label: Left-WM-hypointensities, . +/- . checking subcortical label: Right-WM-hypointensities, . +/- . checking subcortical label: non-WM-hypointensities, . +/- . as100351_conv non-WM-hypointensities value .001393900 is an outlier (avg = . +/- .)... checking subcortical label: Left-non-WM-hypointensities, . +/- . checking subcortical label: Right-non-WM-hypointensities, . +/- . checking subcortical label: Left-F1, . +/- . checking subcortical label: Right-F1, . +/- . checking subcortical label: Optic-Chiasm, . +/- . as100351_conv Optic-Chiasm value .018635200 is an outlier (avg = . +/- .)... checking subcortical label: Corpus_Callosum, . +/- . checking subcortical label: Left-Amygdala-Anterior, . +/- . checking subcortical label: Right-Amygdala-Anterior, . +/- . checking subcortical label: Dura, . +/- . checking subcortical label: Left-wm-intensity-abnormality, . +/- . checking subcortical label: Left-caudate-intensity-abnormality, . +/- . checking subcortical label: Left-putamen-intensity-abnormality, . +/- . checking subcortical label: Left-accumbens-intensity-abnormality, . +/- . checking subcortical label: Left-pallidum-intensity-abnormality, . +/- . checking subcortical label: Left-amygdala-intensity-abnormality, . +/- . checking subcortical label: Left-hippocampus-intensity-abnormality, . +/- . checking subcortical label: Left-thalamus-intensity-abnormality, . +/- . checking subcortical label: Left-VDC-intensity-abnormality, . +/- . checking subcortical label: Right-wm-intensity-abnormality, . +/- . checking subcortical label: Right-caudate-intensity-abnormality, . +/- . checking subcortical label: Right-putamen-intensity-abnormality, . +/- . checking subcortical label: Right-accumbens-intensity-abnormality, . +/- . checking subcortical label: Right-pallidum-intensity-abnormality, . +/- . checking subcortical label: Right-amygdala-intensity-abnormality, . +/- . checking subcortical label: Right-hippocampus-intensity-abnormality, . +/- . checking subcortical label: Right-thalamus-intensity-abnormality, . +/- . checking subcortical label: Right-VDC-intensity-abnormality, . +/- . checking subcortical label: Epidermis, . +/- . checking subcortical label: Conn-Tissue, . +/- . checking subcortical label: SC-Fat/Muscle, . +/- . checking subcortical label: CSF-SA, . +/- . checking subcortical label: Muscle, . +/- . checking subcortical label: Ear, . +/- . checking subcortical label: Adipose, . +/- . checking subcortical label: Spinal-Cord, . +/- . checking subcortical label: Soft-Tissue, . +/- . checking subcortical label: Nerve, . +/- . checking subcortical label: Bone, . +/- . checking subcortical label: Air, . +/- . checking subcortical label: Orbital-Fat, . +/- . checking subcortical label: Tongue, . +/- . checking subcortical label: Nasal-Structures, . +/- . checking subcortical label: Globe, . +/- . checking subcortical label: Teeth, . +/- . checking subcortical label: Left-Caudate/Putamen, . +/- . checking subcortical label: Right-Caudate/Putamen, . +/- . checking subcortical label: Left-Claustrum, . +/- . checking subcortical label: Right-Claustrum, . +/- . checking subcortical label: Cornea, . +/- . checking subcortical label: Diploe, . +/- . checking subcortical label: Vitreous-Humor, . +/- . checking subcortical label: Lens, . +/- . checking subcortical label: Aqueous-Humor, . +/- . checking subcortical label: Outer-Table, . +/- . checking subcortical label: Inner-Table, . +/- . checking subcortical label: Periosteum, . +/- . checking subcortical label: Endosteum, . +/- . as100351_conv has 34 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/charles/Bureau/QAtools_v1.1/recon_all_wm-anat-snr_checker -subjid as100351_conv -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log wm-anat-snr results (as100351_conv): SNR meanWM stdWM voxWM 21,16 108,11 5,11 44847 -----