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- <darteltpm>
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- </shootingtpm>
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- </shootingT1>
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- </brainmask>
- <T1>
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- </T1>
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- <tr>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
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- <td>1</td>
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- <td>0</td>
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- <res_BB>0</res_BB>
- <tissue_mn>[10.6309995651245 69.4424591064453 145.213150024414 244.289154052734]</tissue_mn>
- <tissue_mnr>[0.0435180999338627 0.284263372421265 0.594431400299072 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[40.999232809349 31.873328203415 30.4587384597217 20.9791787384195]</tissue_std>
- <tissue_stdr>[0.175466731190681 0.136410087347031 0.130355983972549 0.0897857770323753]</tissue_stdr>
- <contrast>85.1418762207031</contrast>
- <contrastr>0.348529100418091</contrastr>
- <NCR>0.131684079766273</NCR>
- <ICR>0.527116119861603</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.79999515817652 1.87499996261847 1.875]</res_vx_vol>
- <res_RMS>1.85033622433673</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.85539674758911</contrastr>
- <NCR>2.22141933441162</NCR>
- <ICR>1.76715314388275</ICR>
- <SurfaceEulerNumber>4.77551020408163</SurfaceEulerNumber>
- <SurfaceDefectArea>1.39705706868424</SurfaceDefectArea>
- <SurfaceDefectNumber>3.275</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.5847430229187</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.73948705196381</SurfacePositionRMSE>
- <IQR>2.09081561024894</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_BB>brain next to the image boundary</res_BB>
- <tissue_mn>mean within the tissue classes</tissue_mn>
- <tissue_std>standard deviation within the tissue classes</tissue_std>
- <contrast>contrast between tissue classes</contrast>
- <contrastr>contrast between tissue classes</contrastr>
- <NCR>noise to contrast ratio</NCR>
- <ICR>inhomogeneity to contrast ratio</ICR>
- <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
- <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
- <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
- <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
- </qualitymeasures>
- <subjectmeasures>
- <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
- <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
- <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
- <surf_TSA>total surface area</surf_TSA>
- </subjectmeasures>
- </ratings_help>
- <software>
- <version_segment>1639</version_segment>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>1980</revision_cat>
- <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
- <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
- <qamethod>cat12</qamethod>
- <date>20220709-164735</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>76</SurfaceEulerNumber>
- <SurfaceDefectArea>1.58822827473697</SurfaceDefectArea>
- <SurfaceDefectNumber>45.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0792371481657028</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0869743525981903</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>76</EC_abs>
- <defect_size>1.58822827473697</defect_size>
- <vol_abs_CGW>[205.788538368899 697.161392563083 541.147718815164 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.13282126563568</vol_abs_WMH>
- <vol_rel_WMH>0.000784449213551476</vol_rel_WMH>
- <surf_TSA>2019.44280864179</surf_TSA>
- <vol_TIV>1444.09764974715</vol_TIV>
- <vol_rel_CGW>[0.142503201500904 0.482766101506468 0.374730696992628 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.44307582759702 0.621047306499674]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.47548222541809 0.774259205767131 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.83179013975311 0.274422108779918 0.277117041654092;2.47282819511876 0.175679270679011 0.430177197726055;3.09496570730766 0.26200069878613 0.292705760619853]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.75945402833604 0.304786025271934 0.642625536762773;4.0340877534596 0.349744892624125 0.357374463237227]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.04618967286963</vol_TIV>
- <vol_rel_CGW>[0.5 6.52022452418226 4.57993349483887 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.07844492135515</vol_rel_WMH>
- <surf_TSA>8.62209447732154</surf_TSA>
- <SQR>5.37052448970216</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.118207995096842 1 1 10970.8736788245 0.510419888397267]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0418639779090881 0.0407679677009583 0.248665198683739]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[870.543516859586 477.844429780637 365.191109303604 1422.67066722148 2016.3599800671 8011.65182237579]</SPMvols0>
- <SPMvols1>[747.355553268159 448.466282093226 210.971268013651 828.748346619957 1487.0315443844 8719.33288153132]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[73.9904022216797 164.223907470703 241.738006591797]</T3th>
- <Tth>
- <T3th>[0 0 12.8420753479004 73.9904022216797 164.223907470703 241.738006591797 325.61181640625 954.445434570312]</T3th>
- <T3thx>[0 0.02 0.05 1 2 3 4 5]</T3thx>
- </Tth>
- </gintnorm>
- </tths>
- <reginitp>
- <opt>
- <nits>16</nits>
- <vxreg>1.5</vxreg>
- <rres>3</rres>
- <stepsize>0.5</stepsize>
- <resfac>[1 1 1 1 1]</resfac>
- <ll1th>0.015</ll1th>
- <ll3th>[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]</ll3th>
- <regstr>15</regstr>
- </opt>
- <fast>0</fast>
- <clsn>2</clsn>
- <regra>1</regra>
- <testfolder>Shooting_Template_0_GS_tr1.5_rr3.0-3.0_or1.5_regstr15.0</testfolder>
- <dtc>[0.0174991358071566 0.0595840699970722 0.0652190446853638 0 0]</dtc>
- <ll>[0.083399308209612 0 0.083399308209612 0;0.197208839590524 0.0088697264031345 0.206078565993658 1891.45141601562;0.197208839590524 0.0088697264031345 0.206078565993658 1891.45141601562]</ll>
- <rmsdtc>[0.0400294326245785 0.0827822461724281 0.0937937796115875]</rmsdtc>
- <rmsgdt>[0.02918616309762 0.0442769974470139 0.0556017309427261]</rmsgdt>
- <rmsdt>0.0937937796115875</rmsdt>
- <dt>0.0652190446853638</dt>
- </reginitp>
- <reg>
- <opt>
- <nits>64</nits>
- <vxreg>1.5</vxreg>
- <rres>1.5</rres>
- <stepsize>0.25</stepsize>
- <resfac>[1.66666666666667 1.5 1.33333333333333 1.16666666666667 1]</resfac>
- <ll1th>0.051</ll1th>
- <ll3th>[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]</ll3th>
- <regstr>0.5</regstr>
- </opt>
- <fast>0</fast>
- <clsn>2</clsn>
- <regra>1</regra>
- <testfolder>Shooting_Template_0_GS_tr1.5_rr2.5-1.5_or1.5_regstr0.5</testfolder>
- <dtc>[0.00761052593588829 0.0270085781812668 0.0398514494299889 0.0497152023017406 0.0568912699818611 0.0642408281564713]</dtc>
- <ll>[0.0858894701614787 0 0.0858894701614787 0;0.222594917582418 0.0136583829365079 0.236253300518926 6991.384765625;0.204099717143802 0.0162364818431713 0.220336198986973 11685.5908203125;0.184436664056008 0.0188652629073416 0.20330192696335 20341.884765625;0.168147166409524 0.0222738621971952 0.190421028606719 38964.84765625;0.168147166409524 0.0222738621971952 0.190421028606719 38964.84765625]</ll>
- <rmsdtc>[0.0096670975908637 0.034458976238966 0.0543464906513691 0.0832862257957458 0.111789278686047 0.119933165609837]</rmsdtc>
- <rmsgdt>[0.00326430797576904 0.012642377987504 0.0277653615921736 0.049264170229435 0.0694675967097282 0.0759765431284904]</rmsgdt>
- <rmsdt>0.119933165609837</rmsdt>
- <dt>0.0642408281564713</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_5337/ds/sub-1069/sub-1069_ses-02_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 58s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 14s</item>
- <item>Refine background 4s</item>
- <item>Final correction 8s</item>
- <item>Final scaling 6s</item>
- <item>55s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 19s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 89s</item>
- <item>SPM preprocessing 1 (estimate 2): 70s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 52s</item>
- <item>Update probability maps 11s</item>
- <item>106s</item>
- <item>Global intensity correction: 21s</item>
- <item>SANLM denoising after intensity normalization (medium): 24s</item>
- <item>Fast Optimized Shooting registration 35s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.28) 17s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 48s</item>
- <item>131s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 22s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>91s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>14s</item>
- <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
- <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
- <item>1 | 2.50 | 0.0859 0.0000 0.0859 | 32.0000</item>
- <item>2 | 2.50 | 0.0824 0.0013 0.0837 | 29.4886</item>
- <item>3 | 2.50 | 0.0814 0.0020 0.0834 | 26.9772</item>
- <item>4 | 2.50 | 0.0809 0.0023 0.0832 | 24.6107</item>
- <item>5 | 2.50 | 0.0805 0.0024 0.0830 | 22.6548</item>
- <item>6 | 2.50 | 0.0802 0.0025 0.0827 | 20.6989</item>
- <item>7 | 2.50 | 0.0799 0.0026 0.0825 | 18.9688</item>
- <item>8 | 2.50 | 0.0796 0.0027 0.0823 | 17.4455</item>
- <item>9 | 2.50 | 0.0793 0.0027 0.0820 | 15.9223</item>
- <item>10 | 2.50 | 0.0790 0.0028 0.0817 | 14.6627</item>
- <item>11 | 2.50 | 0.0786 0.0028 0.0815 | 13.4764</item>
- <item>12 | 2.50 | 0.0783 0.0029 0.0812 | 12.3015</item>
- <item>13 | 2.50 | 0.0780 0.0030 0.0809 | 11.3776</item>
- <item>14 | 2.50 | 0.0776 0.0030 0.0806 | 10.4537</item>
- <item>15 | 2.25 | 0.0772 0.0031 0.0803 | 9.5920</item>
- <item>16 | 2.25 | 0.0742 0.0046 0.0788 | 8.8725</item>
- <item>29 | 2.00 | 0.0760 0.0020 0.0780 | 3.3283</item>
- <item>30 | 2.00 | 0.0700 0.0045 0.0745 | 3.1221</item>
- <item>31 | 2.00 | 0.0680 0.0054 0.0734 | 2.9160</item>
- <item>43 | 1.75 | 0.0674 0.0031 0.0705 | 1.5785</item>
- <item>44 | 1.75 | 0.0629 0.0055 0.0684 | 1.5194</item>
- <item>45 | 1.75 | 0.0615 0.0063 0.0678 | 1.4626</item>
- <item>57 | 1.50 | 0.0604 0.0046 0.0650 | 1.0900</item>
- <item>58 | 1.50 | 0.0571 0.0067 0.0638 | 1.0730</item>
- <item>59 | 1.50 | 0.0560 0.0074 0.0635 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 157s</item>
- <item>Prepare output 12s</item>
- <item>169s</item>
- <item>Jacobian determinant (RMS): 0.010 0.034 0.054 0.083 0.112 | 0.119933</item>
- <item>Template Matching: 0.086 0.223 0.204 0.184 0.168 | 0.168147</item>
- <item>Write result maps: 30s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 43s</item>
- <item>91s</item>
- <item>Create initial surface 86s</item>
- <item>Topology correction: 105s</item>
- <item>Surface refinement: 111s</item>
- <item>Reduction of surface collisions with optimization: 70s</item>
- <item>Spherical mapping with areal smoothing 82s</item>
- <item>Spherical registration 305s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 28s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 42s</item>
- <item>91s</item>
- <item>Create initial surface 80s</item>
- <item>Topology correction: 95s</item>
- <item>Surface refinement: 84s</item>
- <item>Reduction of surface collisions with optimization: 73s</item>
- <item>Spherical mapping with areal smoothing 81s</item>
- <item>Spherical registration 289s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4431 0.6206 mm</item>
- <item>Surface intensity / position RMSE: 0.0792 / 0.0870</item>
- <item>Euler number / defect number / defect size: 76.0 / 45.5 / 1.59%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_5337/ds/sub-1069/surf/lh.thickness.sub-1069_ses-02_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_5337/ds/sub-1069/surf/rh.thickness.sub-1069_ses-02_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_5337/ds/sub-1069/sub-1069_ses-02_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1747s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 39s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 27s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 10s</item>
- <item>ROI estimation of 'aal3' atlas 15s</item>
- <item>ROI estimation of 'mori' atlas 23s</item>
- <item>ROI estimation of 'anatomy3' atlas 33s</item>
- <item>ROI estimation of 'julichbrain' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 71s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s</item>
- <item>Write results 107s</item>
- <item>440s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_5337/ds/sub-1069/report/catreport_sub-1069_ses-02_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 54 minute(s) and 10 second(s).</item>
- <item>Image Quality Rating (IQR): 84.09% (B)</item>
- <item>GM volume (GMV): 48.28% (697.16 / 1444.10 ml)</item>
- <item>GM thickness (GMT): 2.44 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_5337/ds/sub-1069/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_5337/ds/sub-1069/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_5337/ds/sub-1069/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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