CORR_cat12.8.1/XHCUMS/sub-0025991/ses-2/report/cat_sub-0025991_ses-2_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   <filedata>
      <path>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2</path>
      <file>sub-0025991_ses-2_run-1_T1w</file>
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      <Fm>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/mri/msub-0025991_ses-2_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/mri/p0sub-0025991_ses-2_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0025991/ses-2/sub-0025991_ses-2_run-1_T1w</fnames>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
         </tpm>
         <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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
         </shootingT1>
         <brainmask>
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         </brainmask>
         <T1>
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         </T1>
         <cat12atlas>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
         </cat12atlas>
         <pbtres>0.5</pbtres>
         <SRP>22</SRP>
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         <thick_measure>1</thick_measure>
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         <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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               <td>[false]</td>
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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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            <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>
               <td>0</td>
               <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>
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            <tr>
               <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>
               <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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                  <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/julichbrain.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_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>
               <td>
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               <td>[false]</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/Schaefer2018_600Parcels_17Networks_order.nii</td>
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            <tr>
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                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</item>
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         <satlas>
            <tr>
               <td>Desikan</td>
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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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            <BG>5</BG>
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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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         <LASmyostr>0</LASmyostr>
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      <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
      <SurfaceDefectArea>1.0952091333067</SurfaceDefectArea>
      <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.23818528652191</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.28534579277039</SurfacePositionRMSE>
      <SIQR>2.13156577104378</SIQR>
      <IQR>2.19898194331229</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>20231031-031800</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>18</SurfaceEulerNumber>
         <SurfaceDefectArea>0.380836533226796</SurfaceDefectArea>
         <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0619092620909214</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0642672926187515</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>18</EC_abs>
      <defect_size>0.380836533226796</defect_size>
      <vol_abs_CGW>[219.281903870792 624.118023535221 507.235799505734 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.67390191844679</vol_abs_WMH>
      <vol_rel_WMH>0.000498951645524496</vol_rel_WMH>
      <surf_TSA>1862.81756316762</surf_TSA>
      <vol_TIV>1350.63572691175</vol_TIV>
      <vol_rel_CGW>[0.162354585697347 0.462092043842404 0.375553370460248 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.43407504707202 0.602637163791349]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.43556571006775 0.713623247420666 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.84885331745554 0.234864256429943 0.29950707243892;2.46628431854931 0.172155959294265 0.441357693956279;3.09627905925807 0.262143247563129 0.259135233604801]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.880179153231493 0.296889551976889 0.526947890818859;4.05375050943137 0.383825428952465 0.473052109181141]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.05783701271121</vol_TIV>
      <vol_rel_CGW>[0.765707358070169 6.14892320119261 4.59470852119699 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04989516455245</vol_rel_WMH>
      <surf_TSA>8.60646021451915</surf_TSA>
      <SQR>5.08702182133465</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.33533552 0.506382095919975]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00184661732055247 0.0013529967982322 0.310631364583969]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[770.301841802282 454.287300871411 347.396229155412 683.304600209013 789.363985702753 8918.20582403227]</SPMvols0>
      <SPMvols1>[668.334636443611 422.346181309467 226.73313869679 551.166647726195 744.995882607802 8920.7798317137]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[180.567199707031 337.036010742188 431.026000976562]</T3th>
            <Tth>
               <T3th>[-7.90376996994019 79.6885833740234 4.4101414680481 180.567199707031 337.036010742188 431.026000976562 556.25537109375 1398.47424316406]</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>[0.0208316314965487 0.0749770626425743 0.0822872892022133 0 0]</dtc>
         <ll>[0.0818998742074955 0 0.0818998742074955 0;0.189214278240593 0.00988106080750171 0.199095339048095 2107.11645507812;0.189214278240593 0.00988106080750171 0.199095339048095 2107.11645507812]</ll>
         <rmsdtc>[0.0451838150620461 0.096178263425827 0.106658063828945]</rmsdtc>
         <rmsgdt>[0.0325518548488617 0.0428491160273552 0.0527891106903553]</rmsgdt>
         <rmsdt>0.106658063828945</rmsdt>
         <dt>0.0822872892022133</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>[0.00962773524224758 0.0358580052852631 0.0501970648765564 0.0582115724682808 0.0639758631587029 0.0713848322629929]</dtc>
         <ll>[0.0827133458684915 0 0.0827133458684915 0;0.215263522588523 0.0134461080586081 0.228709630647131 6882.7265625;0.194305673658352 0.0162748259025833 0.210580499560935 11713.1875;0.174009433612298 0.0183358695092704 0.192345303121569 19771.0546875;0.157281399180154 0.0211214785552144 0.178402877735368 36948.921875;0.157281399180154 0.0211214785552144 0.178402877735368 36948.921875]</ll>
         <rmsdtc>[0.0109200868755579 0.0404323935508728 0.059481855481863 0.0828447118401527 0.105038024485111 0.112570136785507]</rmsdtc>
         <rmsgdt>[0.00322450371459126 0.0125428698956966 0.0275550987571478 0.0475247912108898 0.0654380992054939 0.0712153762578964]</rmsgdt>
         <rmsdt>0.112570136785507</rmsdt>
         <dt>0.0713848322629929</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025991/ses-2/sub-0025991_ses-2_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 48s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 5s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 3s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 4s</item>
      <item>34s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 63s</item>
      <item>SPM preprocessing 1 (estimate 2): 54s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 16s</item>
      <item>Update Skull-Stripping 36s</item>
      <item>Update probability maps 8s</item>
      <item>75s</item>
      <item>Global intensity correction: 15s</item>
      <item>SANLM denoising after intensity normalization (medium): 20s</item>
      <item>Fast Optimized Shooting registration 28s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 12s</item>
      <item>Estimate local tissue thresholds (WM) 16s</item>
      <item>Estimate local tissue thresholds (GM) 22s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 38s</item>
      <item>96s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 10s</item>
      <item>Blood vessel detection 7s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.01) 19s</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 | 0.0827 0.0000 0.0827 | 32.0000</item>
      <item>2 | 2.50 | 0.0800 0.0012 0.0812 | 29.4886</item>
      <item>3 | 2.50 | 0.0792 0.0018 0.0810 | 26.9772</item>
      <item>4 | 2.50 | 0.0788 0.0020 0.0808 | 24.6107</item>
      <item>5 | 2.50 | 0.0785 0.0022 0.0807 | 22.6548</item>
      <item>6 | 2.50 | 0.0782 0.0023 0.0805 | 20.6989</item>
      <item>7 | 2.50 | 0.0779 0.0024 0.0803 | 18.9688</item>
      <item>8 | 2.50 | 0.0776 0.0025 0.0801 | 17.4455</item>
      <item>9 | 2.50 | 0.0773 0.0026 0.0798 | 15.9223</item>
      <item>10 | 2.50 | 0.0769 0.0027 0.0796 | 14.6627</item>
      <item>11 | 2.50 | 0.0766 0.0028 0.0794 | 13.4764</item>
      <item>12 | 2.50 | 0.0763 0.0028 0.0791 | 12.3015</item>
      <item>13 | 2.50 | 0.0759 0.0029 0.0789 | 11.3776</item>
      <item>14 | 2.50 | 0.0756 0.0030 0.0786 | 10.4537</item>
      <item>15 | 2.25 | 0.0747 0.0031 0.0778 | 9.5920</item>
      <item>16 | 2.25 | 0.0718 0.0045 0.0762 | 8.8725</item>
      <item>29 | 2.00 | 0.0728 0.0020 0.0749 | 3.3283</item>
      <item>30 | 2.00 | 0.0669 0.0044 0.0713 | 3.1221</item>
      <item>31 | 2.00 | 0.0648 0.0054 0.0702 | 2.9160</item>
      <item>43 | 1.75 | 0.0637 0.0031 0.0668 | 1.5785</item>
      <item>44 | 1.75 | 0.0594 0.0053 0.0648 | 1.5194</item>
      <item>45 | 1.75 | 0.0580 0.0061 0.0641 | 1.4626</item>
      <item>57 | 1.50 | 0.0565 0.0045 0.0609 | 1.0900</item>
      <item>58 | 1.50 | 0.0534 0.0064 0.0598 | 1.0730</item>
      <item>59 | 1.50 | 0.0524 0.0070 0.0595 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 137s</item>
      <item>Prepare output 8s</item>
      <item>146s</item>
      <item>Jacobian determinant (RMS): 0.011 0.040 0.059 0.083 0.105 | 0.112570</item>
      <item>Template Matching: 0.083 0.215 0.194 0.174 0.157 | 0.157281</item>
      <item>Write result maps: 28s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 30s</item>
      <item>CSF distance: 11s</item>
      <item>PBT2x thickness: 35s</item>
      <item>80s</item>
      <item>Create initial surface 70s</item>
      <item>Topology correction: 76s</item>
      <item>Surface refinement: 79s</item>
      <item>Reduction of surface collisions with optimization: 54s</item>
      <item>Spherical mapping with areal smoothing 65s</item>
      <item>Spherical registration 243s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 22s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 34s</item>
      <item>73s</item>
      <item>Create initial surface 68s</item>
      <item>Topology correction: 74s</item>
      <item>Surface refinement: 81s</item>
      <item>Reduction of surface collisions with optimization: 53s</item>
      <item>Spherical mapping with areal smoothing 62s</item>
      <item>Spherical registration 258s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4341 0.6026 mm</item>
      <item>Surface intensity / position RMSE: 0.0619 / 0.0643</item>
      <item>Euler number / defect number / defect size: 18.0 / 10.5 / 0.38%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/surf/lh.thickness.sub-0025991_ses-2_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/surf/rh.thickness.sub-0025991_ses-2_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/sub-0025991_ses-2_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1415s</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 21s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
      <item>Write results 7s</item>
      <item>307s</item>
      <item>Quality check: 9s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/report/catreport_sub-0025991_ses-2_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 41 minute(s) and 52 second(s).</item>
      <item>Image Quality Rating (IQR): 83.01% (B-)</item>
      <item>GM volume (GMV): 46.21% (624.12 / 1350.64 ml)</item>
      <item>GM thickness (GMT): 2.43 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-2/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>