CORR_cat12.8.1/XHCUMS/sub-0026003/ses-3/report/cat_sub-0026003_ses-3_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   <filedata>
      <path>/var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3</path>
      <file>sub-0026003_ses-3_run-1_T1w</file>
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      <Fp0>/var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/mri/p0sub-0026003_ses-3_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0026003/ses-3/sub-0026003_ses-3_run-1_T1w</fnames>
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   <parameter>
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         <tpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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         <ngaus>[1 1 2 3 4 2]</ngaus>
         <affreg>mni</affreg>
         <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
         <tol>0.0001</tol>
         <accstr>0.5</accstr>
         <biasstr>0.5</biasstr>
         <biasreg>0.001</biasreg>
         <biasfwhm>60</biasfwhm>
         <samp>3</samp>
         <redspmres>0</redspmres>
         <fwhm>1</fwhm>
         <biasacc>0</biasacc>
      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
         <BVCstr>0.5</BVCstr>
         <regstr>0.5</regstr>
         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
         <SLC>0</SLC>
         <mrf>1</mrf>
         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</nproc>
         <species>human</species>
         <APP>1070</APP>
         <setCOM>1</setCOM>
         <vox>1.5</vox>
         <bb>12</bb>
         <shootingsurf>Template_T1</shootingsurf>
         <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
         <darteltpm>
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         </darteltpm>
         <shootingtpm>
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         </shootingtpm>
         <shootingT1>
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         </shootingT1>
         <brainmask>
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         </brainmask>
         <T1>
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         </T1>
         <cat12atlas>
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         <pbtres>0.5</pbtres>
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         <thick_measure>1</thick_measure>
         <thick_limit>5</thick_limit>
         <close_parahipp>0</close_parahipp>
         <scale_cortex>0.7</scale_cortex>
         <add_parahipp>0.1</add_parahipp>
         <colormap>BCGWHw</colormap>
         <report/>
         <verb>2</verb>
         <ignoreErrors>1</ignoreErrors>
         <expertgui>1</expertgui>
         <subfolders>1</subfolders>
         <experimental>0</experimental>
         <print>2</print>
         <fontsize>10</fontsize>
         <send_info>1</send_info>
         <gifti_dat>1</gifti_dat>
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               <td>0</td>
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                  <item>gm</item>
                  <item>wm</item>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</td>
               <td>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
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               <td>
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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/ibsr.nii</td>
               <td>0</td>
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            <tr>
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               <td>1</td>
               <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>
               <td>1</td>
               <td>
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                  <item>wm</item>
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               <td>[false]</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>
               <td>1</td>
               <td>
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               <td>[false]</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>
               <td>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
               <td>1</td>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
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            <tr>
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                  <item>gm</item>
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                  <item>csf</item>
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               <td>[false]</td>
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         <satlas>
            <tr>
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               <td>0</td>
               <td>1</td>
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            <tr>
               <td>Destrieux</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
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            <tr>
               <td>HCP</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_100P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_200P_17N</td>
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               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_400P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_600P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
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            <MB>13</MB>
            <BS>13</BS>
            <VT>15</VT>
            <NV>17</NV>
            <HC>19</HC>
            <HD>21</HD>
            <HI>23</HI>
            <PH>25</PH>
            <LE>27</LE>
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               <regstr>0.5</regstr>
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         <LASmyostr>0</LASmyostr>
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      <ICR>1.75074434280396</ICR>
      <SurfaceEulerNumber>2.73469387755102</SurfaceEulerNumber>
      <SurfaceDefectArea>1.31874874112784</SurfaceDefectArea>
      <SurfaceDefectNumber>2.025</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.41398167610168</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.5153214931488</SurfacePositionRMSE>
      <SIQR>2.10850879331118</SIQR>
      <IQR>2.12265276890629</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>20231031-050755</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>36</SurfaceEulerNumber>
         <SurfaceDefectArea>1.27499496451135</SurfaceDefectArea>
         <SurfaceDefectNumber>20.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0706990882754326</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0757660716772079</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>36</EC_abs>
      <defect_size>1.27499496451135</defect_size>
      <vol_abs_CGW>[313.582483666478 676.133766313298 516.244091211243 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.02476468454409</vol_abs_WMH>
      <vol_rel_WMH>0.00068047255728769</vol_rel_WMH>
      <surf_TSA>1935.81776597813</surf_TSA>
      <vol_TIV>1505.96034119102</vol_TIV>
      <vol_rel_CGW>[0.208227584146389 0.448971827358059 0.342800588495552 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.44835008498725 0.644498033724496]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.44474649429321 0.83050453075687 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.79946550843997 0.283907182529821 0.296822077388895;2.47175666617432 0.185440920572501 0.451580621985015;3.16070567811339 0.296430939111369 0.251597300626091]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.772963224551903 0.230339348558013 0.514573552425665;4.2797616430283 0.375862607796987 0.485426447574335]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.26285909202488</vol_TIV>
      <vol_rel_CGW>[1.58957586469808 5.91328712927549 4.0064760864862 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06804725572877</vol_rel_WMH>
      <surf_TSA>8.61749334361891</surf_TSA>
      <SQR>4.8620335110281</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3357639497 0.440558776373706]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00139670353382826 0.0013445948716253 0.0312225092202425]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[812.321081124584 466.157017744382 507.943063933112 439.769516333054 1146.72949769075 8631.11645557189]</SPMvols0>
      <SPMvols1>[691.508891483344 431.426002781297 339.938890960806 338.770875298853 1025.2207590444 8707.50377554993]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[152.572799682617 311.044799804688 401.137786865234]</T3th>
            <Tth>
               <T3th>[-6.95830011367798 -6.95829677581787 4.63241529464722 152.572799682617 311.044799804688 401.137786865234 525.420288085938 1359.83166503906]</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>[0.0195368733257055 0.0813934579491615 0.0908276587724686 0 0]</dtc>
         <ll>[0.0867788765896984 0 0.0867788765896984 0;0.199098621382147 0.0126335606569288 0.211732182039075 2694.08154296875;0.199098621382147 0.0126335606569288 0.211732182039075 2694.08154296875]</ll>
         <rmsdtc>[0.0460486002266407 0.109325617551804 0.122848831117153]</rmsdtc>
         <rmsgdt>[0.0336220934987068 0.0538757815957069 0.0661525726318359]</rmsgdt>
         <rmsdt>0.122848831117153</rmsdt>
         <dt>0.0908276587724686</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>[0.00897673517465591 0.0346134044229984 0.0514410994946957 0.0605588331818581 0.0672435835003853 0.0754882395267487]</dtc>
         <ll>[0.0857609731873939 0 0.0857609731873939 0;0.22360148046398 0.0150598576770452 0.238661338141026 7708.7646484375;0.199592250094482 0.0184496690928976 0.21804191918738 13278.4482421875;0.178236668832169 0.0202812727360304 0.198517941568199 21868.728515625;0.161320124497457 0.0230627275126861 0.184382852010143 40344.8515625;0.161320124497457 0.0230627275126861 0.184382852010143 40344.8515625]</ll>
         <rmsdtc>[0.010674430988729 0.0407716482877731 0.063077300786972 0.0895020440220833 0.113437794148922 0.121344238519669]</rmsdtc>
         <rmsgdt>[0.00355923571623862 0.0141216209158301 0.0299112573266029 0.05066192522645 0.0691001266241074 0.0753373131155968]</rmsgdt>
         <rmsdt>0.121344238519669</rmsdt>
         <dt>0.0754882395267487</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0026003/ses-3/sub-0026003_ses-3_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 44s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 5s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 3s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 4s</item>
      <item>31s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 7s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 55s</item>
      <item>SPM preprocessing 1 (estimate 2): 49s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 14s</item>
      <item>Update Segmentation 16s</item>
      <item>Update Skull-Stripping 34s</item>
      <item>Update probability maps 7s</item>
      <item>70s</item>
      <item>Global intensity correction: 14s</item>
      <item>SANLM denoising after intensity normalization (medium): 20s</item>
      <item>Fast Optimized Shooting registration 26s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.04) 12s</item>
      <item>Estimate local tissue thresholds (WM) 15s</item>
      <item>Estimate local tissue thresholds (GM) 22s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 38s</item>
      <item>94s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 11s</item>
      <item>Blood vessel detection 8s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.17) 18s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>53s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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>9s</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 | 0.0858 0.0000 0.0858 | 32.0000</item>
      <item>2 | 2.50 | 0.0829 0.0013 0.0841 | 29.4886</item>
      <item>3 | 2.50 | 0.0820 0.0020 0.0839 | 26.9772</item>
      <item>4 | 2.50 | 0.0815 0.0022 0.0837 | 24.6107</item>
      <item>5 | 2.50 | 0.0811 0.0024 0.0835 | 22.6548</item>
      <item>6 | 2.50 | 0.0808 0.0025 0.0833 | 20.6989</item>
      <item>7 | 2.50 | 0.0805 0.0026 0.0831 | 18.9688</item>
      <item>8 | 2.50 | 0.0801 0.0028 0.0829 | 17.4455</item>
      <item>9 | 2.50 | 0.0798 0.0029 0.0826 | 15.9223</item>
      <item>10 | 2.50 | 0.0794 0.0030 0.0824 | 14.6627</item>
      <item>11 | 2.50 | 0.0790 0.0031 0.0821 | 13.4764</item>
      <item>12 | 2.50 | 0.0787 0.0032 0.0818 | 12.3015</item>
      <item>13 | 2.50 | 0.0783 0.0033 0.0816 | 11.3776</item>
      <item>14 | 2.50 | 0.0779 0.0034 0.0813 | 10.4537</item>
      <item>15 | 2.25 | 0.0776 0.0035 0.0811 | 9.5920</item>
      <item>16 | 2.25 | 0.0745 0.0050 0.0796 | 8.8725</item>
      <item>29 | 2.00 | 0.0757 0.0023 0.0780 | 3.3283</item>
      <item>30 | 2.00 | 0.0689 0.0050 0.0739 | 3.1221</item>
      <item>31 | 2.00 | 0.0665 0.0061 0.0727 | 2.9160</item>
      <item>43 | 1.75 | 0.0654 0.0036 0.0689 | 1.5785</item>
      <item>44 | 1.75 | 0.0609 0.0059 0.0668 | 1.5194</item>
      <item>45 | 1.75 | 0.0594 0.0068 0.0662 | 1.4626</item>
      <item>57 | 1.50 | 0.0580 0.0049 0.0630 | 1.0900</item>
      <item>58 | 1.50 | 0.0548 0.0070 0.0618 | 1.0730</item>
      <item>59 | 1.50 | 0.0538 0.0077 0.0615 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 131s</item>
      <item>Prepare output 8s</item>
      <item>140s</item>
      <item>Jacobian determinant (RMS): 0.011 0.041 0.063 0.090 0.113 | 0.121344</item>
      <item>Template Matching: 0.086 0.224 0.200 0.178 0.161 | 0.161320</item>
      <item>Write result maps: 27s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 46s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 36s</item>
      <item>99s</item>
      <item>Create initial surface 67s</item>
      <item>Topology correction: 79s</item>
      <item>Surface refinement: 86s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 65s</item>
      <item>Spherical registration 237s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 40s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 37s</item>
      <item>94s</item>
      <item>Create initial surface 67s</item>
      <item>Topology correction: 77s</item>
      <item>Surface refinement: 58s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 64s</item>
      <item>Spherical registration 247s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4485 0.6439 mm</item>
      <item>Surface intensity / position RMSE: 0.0707 / 0.0758</item>
      <item>Euler number / defect number / defect size: 36.0 / 20.5 / 1.27%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/surf/lh.thickness.sub-0026003_ses-3_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/surf/rh.thickness.sub-0026003_ses-3_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/sub-0026003_ses-3_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1432s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 11s</item>
      <item>ROI estimation of 'mori' atlas 16s</item>
      <item>ROI estimation of 'anatomy3' atlas 23s</item>
      <item>ROI estimation of 'julichbrain' atlas 30s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
      <item>Write results 7s</item>
      <item>312s</item>
      <item>Quality check: 9s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/report/catreport_sub-0026003_ses-3_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 41 minute(s) and 40 second(s).</item>
      <item>Image Quality Rating (IQR): 83.77% (B)</item>
      <item>GM volume (GMV): 44.90% (676.13 / 1505.96 ml)</item>
      <item>GM thickness (GMT): 2.45 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3011310/ds/XHCUMS/sub-0026003/ses-3/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>