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/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii [1 1 2 3 4 2] mni [0 0.001 0.5 0.05 0.2] 0.0001 0.5 0.5 0.001 60 3 0 1 0 1.4 2 0.5 0 -Inf 0.5 0.5 0.5 2 0.5 0 1 optimal [1 0.3] ../derivatives/CAT12.8.1_1980 0 20 human 1070 1 1.5 12 Template_T1 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii 0.5 22 1 2 0 1 5 0 0.7 0.1 BCGWHw 2 1 1 1 0 2 10 1 1 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii 0 csf gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii 0 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii 0 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii 0 csf gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii 0 gm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii 0 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii 0 csf gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii 1 gm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii 1 gm wm [false] /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii 1 gm wm [false] Desikan /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot 0 1 Destrieux /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot 0 1 HCP /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot 0 0 Schaefer2018_100P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot 1 0 Schaefer2018_200P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot 0 0 Schaefer2018_400P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot 1 0 Schaefer2018_600P_17N /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot 1 0 0 1 3 5 7 9 11 13 13 15 17 19 21 23 25 27 0 0 0 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii 0.5 [1 0.3] 0 pbt2x /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii 0 1 1639 26 0.489371218307907 11 0.0636168569326401 0.0614614933729172 [1 1 1] [1 1 1] 1 0 [4.23799991607666 30.2461814880371 131.199234008789 230.785903930664] [0.0183633398264647 0.131057322025299 0.568488955497742 1] T1 [2.657454747905 24.4083639404401 27.9988612413306 17.3697541729206] [0.0117302108556032 0.10774040222168 0.123589135706425 0.0766714364290237] 79.7173004150391 0.345416665077209 0.151933893561363 0.299073934555054 [2 2 2] 2 0.5 [8.62399959564209 8.62400054931641 8.62400054931641 8.62400054931641] [8.624 8.624 8.624 8.624] 0.5 2.90208339691162 2.51211452484131 1.2015722990036 2.22448979591837 1.12234280457698 1.55 1.27233719825745 1.22922992706299 2.34711180035825 voxel dimensions RMS error of voxel size brain next to the image boundary mean within the tissue classes standard deviation within the tissue classes contrast between tissue classes contrast between tissue classes noise to contrast ratio inhomogeneity to contrast ratio average Euler number (characteristic) average area of topological defects average number of defects RMSE of the expected boundary intensity Ym of the IS, OS, and CS RMSE of the expected boundary position Ypp of the IS, OS, and CS Percentual area of self-intersections of the IS and OS. total intracranial volume (GM+WM+VT) relative tissue volume (CSF,GM,WM) relative WMH volume total surface area 1639 LINUX 7771 9.3 12.8.1 1980 /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m cat12 20220712-140237 1639 1639 26 0.489371218307907 11 0.0636168569326401 0.0614614933729172 26 0.489371218307907 [253.510854901961 710.736035294118 565.946611764706 0 0] 0.820152941176471 0.000535979887592994 2070.24037227973 1530.19350196078 [0.165672416316703 0.464474613428552 0.369852970254745 0 0] [2.37245388690332 0.612402860110983] [2.33881425857544 0.744630819741068 1] [1.79156057183292 0.244354177629066 0.334007410815916;2.3952109618101 0.175480171988534 0.422234869584171;3.06485114229336 0.268206468951524 0.243757719599913] [0.882159186809218 0.26785077286987 0.471828358208955;4.08902703018754 0.391501260467205 0.528171641791045] 1.39333269205519 [0.825294833274121 6.19171360324267 4.49233064394298 0.5 0.5] 1.0535979887593 8.62313863702237 5.11041103548612 [0.329663276672363 1 1 7731.889 0.453612665576795] [false] [0.0125599633902311 0 0.100677229464054] [false] [875.490670588235 499.245435294118 510.473019607843 415.012490196078 2686.80408627451 7205.51943921569] [744.249454901961 472.8386 271.041133333333 411.919439215686 1518.65053333333 8115.69435686274] [39.1174011230469 142.860397338867 238.711196899414] [0 0 4.02223300933838 39.1174011230469 142.860397338867 238.711196899414 338.508087158203 709.642822265625] [0 0.02 0.05 1 2 3 4 5] 16 1.5 3 0.5 [1 1 1 1 1] 0.015 [0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03] 15 0 2 1 Shooting_Template_0_GS_tr1.5_rr3.0-3.0_or1.5_regstr15.0 [0.0215902496129274 0.071717232465744 0.0784871280193329 0 0] [0.0848151577525541 0 0.0848151577525541 0;0.202390434933739 0.0091668932664008 0.21155732820014 1954.82165527344;0.202390434933739 0.0091668932664008 0.21155732820014 1954.82165527344] [0.0454086288809776 0.0923995226621628 0.101841196417809] [0.0323111712932587 0.0412918440997601 0.0511767901480198] 0.101841196417809
0.0784871280193329
64 1.5 1.5 0.25 [1.66666666666667 1.5 1.33333333333333 1.16666666666667 1] 0.051 [0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501] 0.5 0 2 1 Shooting_Template_0_GS_tr1.5_rr2.5-1.5_or1.5_regstr0.5 [0.00982104893773794 0.0343051515519619 0.0472993068397045 0.0545479990541935 0.0602859295904636 0.0675658732652664] [0.084650181473412 0 0.084650181473412 0;0.222396672771673 0.0130128653464591 0.235409538118132 6660.96044921875;0.203562436259226 0.0156656846766484 0.219228120935874 11274.78125;0.183635092189169 0.0181862105671157 0.201821302756285 19609.681640625;0.166831751510416 0.0214579801968213 0.188289731707237 37537.58203125;0.166831751510416 0.0214579801968213 0.188289731707237 37537.58203125] [0.0113842962309718 0.039673425257206 0.0576891154050827 0.080867312848568 0.103891953825951 0.111298024654388] [0.00316602503880858 0.0119087863713503 0.026316249743104 0.0463715009391308 0.0651938319206238 0.0712189972400665] 0.111298024654388
0.0675658732652664
------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./sub-NC233_ses-20190512_acq-highres_run-01_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 53s APP: Rough bias correction: Initialize 8s Estimate background 8s Initial correction 7s Refine background 4s Final correction 6s Final scaling 7s 49s Correct center-of-mass 6s Affine registration 12s SPM preprocessing 1 (estimate 1 - TPM registration): 87s SPM preprocessing 1 (estimate 2): 86s SPM preprocessing 2 (write): Write Segmentation 22s Update Segmentation 25s Update Skull-Stripping 53s Update probability maps 11s 110s Global intensity correction: 21s SANLM denoising after intensity normalization (medium): 12s Fast Optimized Shooting registration 44s Local adaptive segmentation (LASstr=0.50): Prepare maps 5s Prepare partitions 3s Prepare segments (LASmod = 1.06) 19s Estimate local tissue thresholds (WM) 21s Estimate local tissue thresholds (GM) 28s Intensity transformation 0s SANLM denoising after LAS (medium) 26s 106s ROI segmentation (partitioning): Atlas -> subject space 10s Major structures 4s Ventricle detection 18s Blood vessel detection 11s WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 28s Manual stroke lesion detection 0s Closing of deep structures 2s Side alignment 5s Final corrections 5s 84s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 5s Level 1 cleanup (brain masking) 4s Level 2 cleanup (CSF correction) 2s Level 3 cleanup (CSF/WM PVE) 3s 14s Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50): Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii" 1 | 2.50 | 0.0847 0.0000 0.0847 | 32.0000 2 | 2.50 | 0.0819 0.0012 0.0831 | 29.4886 3 | 2.50 | 0.0810 0.0018 0.0829 | 26.9772 4 | 2.50 | 0.0807 0.0021 0.0827 | 24.6107 5 | 2.50 | 0.0803 0.0022 0.0826 | 22.6548 6 | 2.50 | 0.0801 0.0023 0.0824 | 20.6989 7 | 2.50 | 0.0798 0.0024 0.0822 | 18.9688 8 | 2.50 | 0.0795 0.0025 0.0820 | 17.4455 9 | 2.50 | 0.0792 0.0025 0.0818 | 15.9223 10 | 2.50 | 0.0789 0.0026 0.0815 | 14.6627 11 | 2.50 | 0.0786 0.0027 0.0813 | 13.4764 12 | 2.50 | 0.0783 0.0028 0.0811 | 12.3015 13 | 2.50 | 0.0780 0.0029 0.0808 | 11.3776 14 | 2.50 | 0.0777 0.0029 0.0806 | 10.4537 15 | 2.25 | 0.0770 0.0030 0.0800 | 9.5920 16 | 2.25 | 0.0741 0.0043 0.0785 | 8.8725 29 | 2.00 | 0.0756 0.0019 0.0775 | 3.3283 30 | 2.00 | 0.0698 0.0042 0.0741 | 3.1221 31 | 2.00 | 0.0679 0.0052 0.0731 | 2.9160 43 | 1.75 | 0.0669 0.0030 0.0699 | 1.5785 44 | 1.75 | 0.0627 0.0052 0.0679 | 1.5194 45 | 1.75 | 0.0612 0.0061 0.0673 | 1.4626 57 | 1.50 | 0.0599 0.0044 0.0643 | 1.0900 58 | 1.50 | 0.0567 0.0065 0.0632 | 1.0730 59 | 1.50 | 0.0556 0.0072 0.0628 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 226s Prepare output 11s 237s Jacobian determinant (RMS): 0.011 0.040 0.058 0.081 0.104 | 0.111298 Template Matching: 0.085 0.222 0.204 0.184 0.167 | 0.166832 Write result maps: 39s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 52s CSF distance: 19s PBT2x thickness: 60s 140s Create initial surface 109s Topology correction: 150s Surface refinement: 93s Reduction of surface collisions with optimization: 97s Spherical mapping with areal smoothing 105s Spherical registration 278s rh: Thickness estimation (0.50 mm ): WM distance: 52s CSF distance: 19s PBT2x thickness: 60s 139s Create initial surface 110s Topology correction: 121s Surface refinement: 115s Reduction of surface collisions with optimization: 100s Spherical mapping with areal smoothing 107s Spherical registration 280s Final surface processing results: Average thickness (FS): 2.3725 0.6124 mm Surface intensity / position RMSE: 0.0636 / 0.0615 Euler number / defect number / defect size: 26.0 / 11.0 / 0.49% Display thickness: /var/lib/condor/execute/dir_11697/ds/sub-NC233/surf/lh.thickness.sub-NC233_ses-20190512_acq-highres_run-01_T1w Display thickness: /var/lib/condor/execute/dir_11697/ds/sub-NC233/surf/rh.thickness.sub-NC233_ses-20190512_acq-highres_run-01_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_11697/ds/sub-NC233/sub-NC233_ses-20190512_acq-highres_run-01_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 2059s ROI estimation in native space: ROI estimation of 'cobra' atlas 16s ROI estimation of 'neuromorphometrics' atlas 59s ROI estimation of 'lpba40' atlas 15s ROI estimation of 'hammers' atlas 38s ROI estimation of 'thalamus' atlas 3s ROI estimation of 'ibsr' atlas 13s ROI estimation of 'aal3' atlas 21s ROI estimation of 'mori' atlas 31s ROI estimation of 'anatomy3' atlas 46s ROI estimation of 'julichbrain' atlas 60s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 98s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 159s Write results 161s 615s Quality check: 6s Print 'Graphics' figure to: /var/lib/condor/execute/dir_11697/ds/sub-NC233/report/catreport_sub-NC233_ses-20190512_acq-highres_run-01_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 63 minute(s) and 27 second(s). Image Quality Rating (IQR): 81.53% (B-) GM volume (GMV): 46.45% (710.74 / 1530.19 ml) GM thickness (GMT): 2.37 0.61 mm Segmentations are saved in /var/lib/condor/execute/dir_11697/ds/sub-NC233/mri Reports are saved in /var/lib/condor/execute/dir_11697/ds/sub-NC233/report Labels are saved in /var/lib/condor/execute/dir_11697/ds/sub-NC233/label ------------------------------------------------------------------------