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-274.51532945438] [-0.175978143148537 0.121286841668745 0.00162600335879582] [1.10724652996435 0.894505698331171 2.23588861007858] [-0.0194041557649742 -0.190256380160172 0.661231419701585] [-112.957459849856 -113.322987080212 -274.51532945438] [-0.175978143148537 0.121286841668745 0.00162600335879582] [1.10724652996435 0.894505698331171 2.23588861007858] [-0.0194041557649742 -0.190256380160172 0.661231419701585] /var/lib/condor/execute/dir_27041/ds/sub-AL034 sub-AL034_ses-1_acq-RARE_T1w /var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii /var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii /var/lib/condor/execute/dir_27041/ds/sub-AL034/mri/msub-AL034_ses-1_acq-RARE_T1w.nii /var/lib/condor/execute/dir_27041/ds/sub-AL034/mri/p0sub-AL034_ses-1_acq-RARE_T1w.nii ..41/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w /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 64 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 [true] [0.96 0.9999] /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 1 22 1.97242925460113 7 0.0630294680595398 0.10944738984108 [1.5 4.5 1.5] [1 1 1] 2.87228132326901 0 [5859.74853515625 NaN NaN 17423.400390625] [0.336314857006073 NaN NaN 1] [2897.06963634106 3392.89992547749 2742.64116260078 2416.51634753725] [0.250532418489456 0.293410748243332 0.237177759408951 0.208975180983543] NaN NaN 0 NaN [3 9 3] 5.74456264653803 0.5 [8.62400054931641 NaN NaN 8.62400054931641] [8.624 8.624 8.624 8.624] NaN NaN 0.5 NaN 2.02040816326531 1.49310731365028 1.35 1.2605893611908 2.1889476776123 5.26778717548681 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 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 20220711-215237 cat_run_job:failedBGD cat_run_job1639: Detection of background failed. 1 cat_run_job1639:nonT1contrast A non-T1 contrast was detected and the NEW EXPERIMENTAL </br>PIPELINE is used! If it is was a high-resolution T1 image, </br>the initial segmentation might have failed, probably due </br>to alignment problems (please check the image orientation). 1 [15456.60634 9232.55033 15594.24065 8108.74399 3594.694 1410.03992] cat_main:skipLAS Skip LAS due to image contrast. Use global normalization. 0 22 1.97242925460113 7 0.0630294680595398 0.10944738984108 22 1.97242925460113 [32.3583411764706 12.9342235294118 99.686462745098 0 0] 0 0 249.267491762079 144.97902745098 [0.223193255917042 0.0892144454051123 0.687592298677845 0 0] [0.7420917509033 0.420368947236289] [0.567666709423065 0.620113687500136 1] [0.532079206751011 0.0649654541017424 0.675627624295459;0.840406283702592 0.120807924795545 0.232867212225907;1.45613963060555 0.188331193925918 0.0915051634786337] [0.375746161744788 0.0499763703679095 0.175540571960009;2.17935538154097 0.291712408002683 0.824459428039991] 8.56846914481617 [1.8583558893147 0.5 10.1988559388981 0.5 0.5] 1 8.3400464690837 8.34027311965593 [0 1 0 4976.64 0.515563150136068] [false] [0.0872204813359605 0.0667394072051072 0.343850385766556] [false] [42.3634078431373 39.6758470588235 424.703976470588 1738.36661568627 1157.63332941176 1573.68630980392] 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 [0.0411871932446957 0.510926842689514 0.861334323883057 0 0] [0.249532014954419 0 0.249532014954419 0;0.137718991405156 0.0339527290408351 0.171671720445991 21721.0546875;0.253375379692893 0.151823046112976 0.405198425805869 32375.9609375] [0.0894775316119194 1.21180057525635 2.03004193305969] [0.063137948513031 0.755503714084625 1.15925705432892] 2.03004193305969

0.861334323883057

[23.0953254901961 104.303223529412 62.5117882352941 1934.05382352941 1199.35996862745 1653.366] [15456.60634 9232.55033 15594.24065] [-1.70161843299866 1052.31372070312 13559.0908203125 15868.771484375 16615.1171875 24622.69140625] [0 0.1 1 2 3 4] [0.614813089134864 0.617346147706653 0.86756636793683] [0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2] [0 1.84443926740459 1.85203844311996 2.60269910381049 4 5 6] [0.614821129482046 0.61735034418183 0.867559975803558] [0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2] [0 1.84446338844614 1.85205103254549 2.60267992741067 4 5 6] [0.308016775307319 0.301399865931127 0.939809603939654] [0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2] [0 0.90419959779338 0.924050325921957 2.81942881181896 4 5 6] [0.308017941860945 0.301405907037158 0.939806242870167] [0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2] [0 0.904217721111475 0.924053825582836 2.8194187286105 4 5 6] 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 [0.0228037312626839 0.118160769343376 0.341698855161667 0.382777482271194 0.407696515321732 1.14449417591095] [0.259390700076248 0 0.259390700076248 0;0.261658221408221 0.023425055962556 0.285083277370777 35972.1015625;0.163450854878989 0.0607845568783069 0.224235411757295 131242.125;0.219100633351325 0.2176268487914 0.436727482142725 234660.9375;0.181965293025479 0.223491985322574 0.405457278348052 390966.375;0.181965293025479 0.223491985322574 0.405457278348052 390966.375] [0.0308313313871622 0.17324087023735 0.528151214122772 1.21057617664337 2.38769769668579 2.2737410068512] [0.0125624006614089 0.0734260976314545 0.227712631225586 0.475024104118347 1.72534370422363 0.900434911251068] 2.2737410068512

1.14449417591095

------------------------------------------------------------------------ CAT12.8.1 r1980: 1/1: ./ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 2s ------------------------------------------------------------------------ WARNING 01: cat_run_job:failedBGD cat_run_job1639: Detection of background failed. ------------------------------------------------------------------------ Internal resampling (1.50x4.50x1.50mm > 1.00x1.00x1.00mm): 1s APP: Rough bias correction: Initialize 3s Estimate background 4s Initial correction 4s Refine background 2s Final correction 3s Final scaling 4s 23s Correct center-of-mass 17s Affine registration 5s SPM preprocessing 1 (estimate 1 - TPM registration): 20s Use initial fine affine registration. 44s SPM preprocessing 1 (estimate 2): 48s ---------------------------------------------------------------------------- WARNING 02: cat_run_job1639:nonT1contrast A non-T1 contrast was detected and the NEW EXPERIMENTAL PIPELINE is used! If it is was a high-resolution T1 image, the initial segmentation might have failed, probably due to alignment problems (please check the image orientation). ---------------------------------------------------------------------------- SPM preprocessing 2 (write): Write Segmentation 8s Update segmentation 9s Update skull-stripping 7s Update probability maps 5s Update registration 31s 60s Global intensity correction: SANLM denoising after intensity normalization (medium): 1s ------------------------------------------------------------------------ NOTE 01: cat_main:skipLAS Skip LAS due to image contrast. Use global normalization. ------------------------------------------------------------------------ 14s SANLM denoising after LAS (medium) 16s 18s --- Update Ym and Ymi --- ROI segmentation (partitioning): Atlas -> subject space 2s Major structures 0s Ventricle detection 2s Blood vessel detection 0s Manual stroke lesion detection 0s Closing of deep structures 0s Side alignment 1s Final corrections 2s 8s Amap using initial SPM12 segmentations (MRF filter strength 0.07): 36s AMAP peaks: [0.99 0.08,0.31 0.06,0.72 0.09] --- Update Ym and Ymi --- 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 | 0.2594 0.0000 0.2594 | 32.0000 2 | 2.50 | 0.2438 0.0051 0.2489 | 29.4886 3 | 2.50 | 0.2384 0.0086 0.2470 | 26.9772 4 | 2.50 | 0.2354 0.0104 0.2458 | 24.6107 5 | 2.50 | 0.2330 0.0117 0.2447 | 22.6548 6 | 2.50 | 0.2308 0.0127 0.2435 | 20.6989 7 | 2.50 | 0.2281 0.0137 0.2418 | 18.9688 8 | 2.50 | 0.2257 0.0148 0.2405 | 17.4455 9 | 2.50 | 0.2232 0.0157 0.2389 | 15.9223 10 | 2.50 | 0.2204 0.0170 0.2374 | 14.6627 11 | 2.50 | 0.2175 0.0182 0.2357 | 13.4764 12 | 2.50 | 0.2146 0.0192 0.2338 | 12.3015 13 | 2.50 | 0.2113 0.0208 0.2320 | 11.3776 14 | 2.50 | 0.2081 0.0220 0.2300 | 10.4537 15 | 2.25 | 0.2617 0.0234 0.2851 | 9.5920 16 | 2.25 | 0.2445 0.0339 0.2785 | 8.8725 17 | 2.25 | 0.2355 0.0387 0.2742 | 8.1530 18 | 2.25 | 0.2282 0.0419 0.2701 | 7.5234 19 | 2.25 | 0.2216 0.0444 0.2660 | 6.9630 20 | 2.25 | 0.2153 0.0463 0.2616 | 6.4027 21 | 2.25 | 0.2089 0.0486 0.2576 | 5.9447 22 | 2.25 | 0.2028 0.0505 0.2533 | 5.5083 23 | 2.25 | 0.1966 0.0520 0.2486 | 5.0803 24 | 2.25 | 0.1891 0.0542 0.2433 | 4.7404 25 | 2.25 | 0.1832 0.0554 0.2386 | 4.4005 26 | 2.25 | 0.1772 0.0568 0.2339 | 4.0868 27 | 2.25 | 0.1711 0.0585 0.2295 | 3.8221 28 | 2.25 | 0.1652 0.0595 0.2247 | 3.5574 29 | 2.00 | 0.1635 0.0608 0.2242 | 3.3283 30 | 2.00 | 0.1561 0.0621 0.2181 | 3.1221 31 | 2.00 | 0.1507 0.0625 0.2132 | 2.9160 32 | 2.00 | 0.1441 0.0637 0.2078 | 2.7495 33 | 2.00 | 0.1390 0.0643 0.2034 | 2.5890 34 | 2.00 | 0.1339 0.0649 0.1988 | 2.4330 35 | 2.00 | 0.1289 0.0660 0.1949 | 2.3080 36 | 2.00 | 0.1241 0.0667 0.1907 | 2.1830 37 | 2.00 | 0.1193 0.0673 0.1867 | 2.0688 38 | 2.00 | 0.1148 0.0682 0.1830 | 1.9714 39 | 2.00 | 0.1104 0.0686 0.1791 | 1.8740 40 | 2.00 | 0.1051 0.0693 0.1744 | 1.7907 41 | 2.00 | 0.1013 0.0697 0.1710 | 1.7148 42 | 2.00 | 0.0976 0.0698 0.1675 | 1.6390 43 | 1.75 | 0.0939 0.0707 0.1646 | 1.5785 44 | 1.75 | 0.0896 0.0718 0.1614 | 1.5194 45 | 1.75 | 0.0864 0.0721 0.1585 | 1.4626 46 | 1.75 | 0.0835 0.0724 0.1560 | 1.4166 47 | 1.75 | 0.0809 0.0725 0.1534 | 1.3706 48 | 1.75 | 0.0784 0.0726 0.1509 | 1.3290 49 | 1.75 | 0.0751 0.0728 0.1478 | 1.2932 50 | 1.75 | 0.0730 0.0725 0.1456 | 1.2574 57 | 1.50 | 0.0742 0.0661 0.1403 | 1.0900 Problem with Shooting (dets: 0.00337295 .. 2.14688) 58 | 1.50 | 0.0667 0.0713 0.1380 | 1.0730 59 | 1.50 | 0.0631 0.0733 0.1363 | 1.0579 60 | 1.50 | 0.0607 0.0745 0.1352 | 1.0447 Shooting registration with 2.50:-0.25:1.50 mm takes: 320s Prepare output 7s 327s Jacobian determinant (RMS): 0.031 0.173 0.528 1.211 2.388 | 2.273741 Template Matching: 0.259 0.262 0.163 0.219 0.182 | 0.181965 Write result maps: 16s Surface and thickness estimation: lh: Thickness estimation (0.50 mm ): WM distance: 3s CSF distance: 2s PBT2x thickness: 4s 10s Create initial surface 14s Topology correction: 17s Surface refinement: 37s Reduction of surface collisions with optimization: 17s Spherical mapping with areal smoothing 31s Spherical registration 335s rh: Thickness estimation (0.50 mm ): WM distance: 3s CSF distance: 2s PBT2x thickness: 4s 10s Create initial surface 12s Topology correction: 16s Surface refinement: 37s Reduction of surface collisions with optimization: 18s Spherical mapping with areal smoothing 31s Spherical registration 326s Final surface processing results: Average thickness (FS): 0.7421 0.4194 mm Surface intensity / position RMSE: 0.0630 / 0.1094 Euler number / defect number / defect size: 22.0 / 7.0 / 1.97% Display thickness: /var/lib/condor/execute/dir_27041/ds/sub-AL034/surf/lh.thickness.sub-AL034_ses-1_acq-RARE_T1w Display thickness: /var/lib/condor/execute/dir_27041/ds/sub-AL034/surf/rh.thickness.sub-AL034_ses-1_acq-RARE_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii Surface ROI estimation: 1368s Surface and thickness estimation takes: 1336s ROI estimation in native space: ROI estimation of 'cobra' atlas 3s ROI estimation of 'neuromorphometrics' atlas 12s ROI estimation of 'lpba40' atlas 3s ROI estimation of 'hammers' atlas 8s ROI estimation of 'thalamus' atlas 1s ROI estimation of 'ibsr' atlas 3s ROI estimation of 'aal3' atlas 5s ROI estimation of 'mori' atlas 7s ROI estimation of 'anatomy3' atlas 10s ROI estimation of 'julichbrain' atlas 14s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 6s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 10s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 22s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 33s Write results 34s 138s Quality check: 1s Print 'Graphics' figure to: /var/lib/condor/execute/dir_27041/ds/sub-AL034/report/catreport_sub-AL034_ses-1_acq-RARE_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 29 minute(s) and 36 second(s). Image Quality Rating (IQR): 52.32% (E-) GM volume (GMV): 8.92% (12.93 / 144.98 ml) GM thickness (GMT): 0.74 0.42 mm Segmentations are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/mri Reports are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/report Labels are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/label ------------------------------------------------------------------------