CORR_cat12.8.1/IPCAS_7/sub-0026114/ses-1/report/cat_sub-0026114_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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         <NCstr>-Inf</NCstr>
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         <species>human</species>
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         <verb>2</verb>
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         <fontsize>10</fontsize>
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            <tr>
               <td>HCP</td>
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      <ICR>1.26948213577271</ICR>
      <SurfaceEulerNumber>2.53061224489796</SurfaceEulerNumber>
      <SurfaceDefectArea>1.20287087658592</SurfaceDefectArea>
      <SurfaceDefectNumber>2.025</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.39630579948425</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.39733016490936</SurfacePositionRMSE>
      <SIQR>2.51233318405155</SIQR>
      <IQR>2.10951981792965</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
         <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>2040</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>20231031-011125</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>32</SurfaceEulerNumber>
         <SurfaceDefectArea>0.811483506343674</SurfaceDefectArea>
         <SurfaceDefectNumber>20.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0698152929544449</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0698665082454681</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>32</EC_abs>
      <defect_size>0.811483506343674</defect_size>
      <vol_abs_CGW>[233.585765847015 724.084437656589 474.986841142509 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.582462718607405</vol_abs_WMH>
      <vol_rel_WMH>0.000406561166040461</vol_rel_WMH>
      <surf_TSA>2031.44069566935</surf_TSA>
      <vol_TIV>1432.65704464611</vol_TIV>
      <vol_rel_CGW>[0.163043742199107 0.505413658043644 0.331542599757249 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.46432883453235 0.62626729160658]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.43810701370239 0.787144560706104 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.87077893213592 0.250762372070133 0.325755281875089;2.49170710628722 0.181007885515477 0.426776743065125;3.1704327373046 0.285322117248628 0.247467975059786]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.8725110703266 0.298198310269217 0.471148297749567;4.22569280109485 0.379907975070939 0.528851702250433]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.02536665317368</vol_TIV>
      <vol_rel_CGW>[0.778084450414995 6.92696943325511 3.80428519678966 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04065611660405</vol_rel_WMH>
      <surf_TSA>8.62241514091547</surf_TSA>
      <SQR>5.67047538045543</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3348302445 0.463970093560566]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00135085312649608 0.00119586917571723 0.0405562333762646]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[891.112775158113 403.242346366261 590.860118225488 1147.86903799054 1182.57839719626 8242.5198800289]</SPMvols0>
      <SPMvols1>[726.468543430512 372.810877162061 296.308790445328 490.76390317006 1015.62513420112 8632.95857991865]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[46.608699798584 211.078506469727 395.2578125]</T3th>
            <Tth>
               <T3th>[-4.56170988082886 -4.56171035766602 2.46865153312683 46.608699798584 211.078506469727 395.2578125 569.582397460938 1149.5673828125]</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>[0.0222393255680799 0.0772906467318535 0.086200974881649 0 0]</dtc>
         <ll>[0.0881582125037515 0 0.0881582125037515 0;0.210557074392257 0.0104446491273511 0.221001723519608 2227.30053710938;0.210557074392257 0.0104446491273511 0.221001723519608 2227.30053710938]</ll>
         <rmsdtc>[0.0478153564035892 0.104645766317844 0.117113299667835]</rmsdtc>
         <rmsgdt>[0.0338456444442272 0.0484280958771706 0.0596953965723515]</rmsgdt>
         <rmsdt>0.117113299667835</rmsdt>
         <dt>0.086200974881649</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>[0.00902980845421553 0.0323671735823154 0.0426853112876415 0.0514574721455574 0.0586960576474667 0.0652315393090248]</dtc>
         <ll>[0.0848182823709085 0 0.0848182823709085 0;0.223815537240537 0.0131836538461538 0.236999191086691 6748.3828125;0.208529939753679 0.0152456476839868 0.223775587437666 10972.4755859375;0.189389829282407 0.0179454118777544 0.207335241160162 19350.03515625;0.172971503607334 0.0214255240008735 0.194397027608207 37480.8046875;0.172971503607334 0.0214255240008735 0.194397027608207 37480.8046875]</ll>
         <rmsdtc>[0.0105770910158753 0.0364041589200497 0.0545615926384926 0.0778524354100227 0.101830430328846 0.107953891158104]</rmsdtc>
         <rmsgdt>[0.00309649668633938 0.01177161000669 0.0261929593980312 0.0460980869829655 0.0647128745913506 0.0705653205513954]</rmsgdt>
         <rmsdt>0.107953891158104</rmsdt>
         <dt>0.0652315393090248</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0026114/ses-1/sub-0026114_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 31s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 4s</item>
      <item>Estimate background 4s</item>
      <item>Initial correction 4s</item>
      <item>Refine background 2s</item>
      <item>Final correction 3s</item>
      <item>Final scaling 3s</item>
      <item>24s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 6s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 47s</item>
      <item>SPM preprocessing 1 (estimate 2): 38s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 12s</item>
      <item>Update Segmentation 13s</item>
      <item>Update Skull-Stripping 27s</item>
      <item>Update probability maps 6s</item>
      <item>57s</item>
      <item>Global intensity correction: 10s</item>
      <item>SANLM denoising after intensity normalization (medium): 15s</item>
      <item>Fast Optimized Shooting registration 22s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 2s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 9s</item>
      <item>Estimate local tissue thresholds (WM) 12s</item>
      <item>Estimate local tissue thresholds (GM) 18s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 25s</item>
      <item>70s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 5s</item>
      <item>Major structures 2s</item>
      <item>Ventricle detection 8s</item>
      <item>Blood vessel detection 6s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.05) 13s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 2s</item>
      <item>Final corrections 3s</item>
      <item>40s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s</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) 3s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>7s</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 | 0.0848 0.0000 0.0848 | 32.0000</item>
      <item>2 | 2.50 | 0.0825 0.0011 0.0836 | 29.4886</item>
      <item>3 | 2.50 | 0.0819 0.0016 0.0835 | 26.9772</item>
      <item>4 | 2.50 | 0.0816 0.0018 0.0834 | 24.6107</item>
      <item>5 | 2.50 | 0.0813 0.0019 0.0833 | 22.6548</item>
      <item>6 | 2.50 | 0.0811 0.0020 0.0831 | 20.6989</item>
      <item>7 | 2.50 | 0.0809 0.0021 0.0829 | 18.9688</item>
      <item>8 | 2.50 | 0.0806 0.0022 0.0828 | 17.4455</item>
      <item>9 | 2.50 | 0.0804 0.0022 0.0826 | 15.9223</item>
      <item>10 | 2.50 | 0.0801 0.0023 0.0824 | 14.6627</item>
      <item>11 | 2.50 | 0.0799 0.0024 0.0822 | 13.4764</item>
      <item>12 | 2.50 | 0.0796 0.0024 0.0820 | 12.3015</item>
      <item>13 | 2.50 | 0.0793 0.0025 0.0818 | 11.3776</item>
      <item>14 | 2.50 | 0.0791 0.0025 0.0816 | 10.4537</item>
      <item>15 | 2.25 | 0.0785 0.0026 0.0811 | 9.5920</item>
      <item>16 | 2.25 | 0.0757 0.0039 0.0796 | 8.8725</item>
      <item>17 | 2.25 | 0.0746 0.0044 0.0790 | 8.1530</item>
      <item>29 | 2.00 | 0.0766 0.0020 0.0785 | 3.3283</item>
      <item>30 | 2.00 | 0.0713 0.0042 0.0755 | 3.1221</item>
      <item>31 | 2.00 | 0.0695 0.0051 0.0746 | 2.9160</item>
      <item>43 | 1.75 | 0.0688 0.0029 0.0717 | 1.5785</item>
      <item>44 | 1.75 | 0.0645 0.0052 0.0697 | 1.5194</item>
      <item>45 | 1.75 | 0.0631 0.0060 0.0691 | 1.4626</item>
      <item>57 | 1.50 | 0.0620 0.0043 0.0663 | 1.0900</item>
      <item>58 | 1.50 | 0.0587 0.0065 0.0652 | 1.0730</item>
      <item>59 | 1.50 | 0.0577 0.0071 0.0648 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 112s</item>
      <item>Prepare output 7s</item>
      <item>118s</item>
      <item>Jacobian determinant (RMS): 0.011 0.036 0.055 0.078 0.102 | 0.107954</item>
      <item>Template Matching: 0.085 0.224 0.209 0.189 0.173 | 0.172972</item>
      <item>Write result maps: 23s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 21s</item>
      <item>CSF distance: 10s</item>
      <item>PBT2x thickness: 30s</item>
      <item>64s</item>
      <item>Create initial surface 51s</item>
      <item>Topology correction: 67s</item>
      <item>Surface refinement: 63s</item>
      <item>Reduction of surface collisions with optimization: 46s</item>
      <item>Spherical mapping with areal smoothing 60s</item>
      <item>Spherical registration 174s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 19s</item>
      <item>CSF distance: 10s</item>
      <item>PBT2x thickness: 29s</item>
      <item>61s</item>
      <item>Create initial surface 49s</item>
      <item>Topology correction: 66s</item>
      <item>Surface refinement: 73s</item>
      <item>Reduction of surface collisions with optimization: 46s</item>
      <item>Spherical mapping with areal smoothing 58s</item>
      <item>Spherical registration 182s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4643 0.6262 mm</item>
      <item>Surface intensity / position RMSE: 0.0698 / 0.0699</item>
      <item>Euler number / defect number / defect size: 32.0 / 20.5 / 0.81%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/surf/lh.thickness.sub-0026114_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/surf/rh.thickness.sub-0026114_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/sub-0026114_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 6s</item>
      <item>Surface and thickness estimation takes: 1123s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 6s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 23s</item>
      <item>ROI estimation of 'lpba40' atlas 7s</item>
      <item>ROI estimation of 'hammers' atlas 16s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 6s</item>
      <item>ROI estimation of 'aal3' atlas 9s</item>
      <item>ROI estimation of 'mori' atlas 13s</item>
      <item>ROI estimation of 'anatomy3' atlas 19s</item>
      <item>ROI estimation of 'julichbrain' atlas 26s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 62s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
      <item>Write results 6s</item>
      <item>267s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/report/catreport_sub-0026114_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 33 minute(s) and 9 second(s).</item>
      <item>Image Quality Rating (IQR): 83.90% (B)</item>
      <item>GM volume (GMV): 50.54% (724.08 / 1432.66 ml)</item>
      <item>GM thickness (GMT): 2.46 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2404624/ds/IPCAS_7/sub-0026114/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>