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

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine0_shearing>[0.0222266218120969 0.0031629055900908 0.0258149585301443]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1</path>
      <file>sub-0025991_ses-1_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/mri/msub-0025991_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/mri/p0sub-0025991_ses-1_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
            <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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
         </darteltpm>
         <shootingtpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
         </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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
         </brainmask>
         <T1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
         </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>
         <reduce_mesh>1</reduce_mesh>
         <vdist>2</vdist>
         <pbtlas>0</pbtlas>
         <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>
         <atlas>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <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>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</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/hammers.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
               <td>0</td>
               <td>
                  <item>gm</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/suit.nii</td>
               <td>0</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/ibsr.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <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/aal3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</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/mori.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_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_600Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
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               <td>[false]</td>
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            <tr>
               <td>/var/lib/condor/execute/dir_359023/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</item>
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               <td>[false]</td>
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         </atlas>
         <satlas>
            <tr>
               <td>Desikan</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <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>
            </tr>
            <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>
            </tr>
            <tr>
               <td>Schaefer2018_100P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_200P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_400P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <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>
            </tr>
         </satlas>
         <LAB>
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            <CT>1</CT>
            <CB>3</CB>
            <BG>5</BG>
            <BV>7</BV>
            <TH>9</TH>
            <ON>11</ON>
            <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>
         </LAB>
         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
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               <shootingtpm>
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               <regstr>0.5</regstr>
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         <restypes>
            <optimal>[1 0.3]</optimal>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
         <darteltpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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         <shootingtpms>
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         <templates>
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      <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
      <SurfaceDefectArea>1.06798591180038</SurfaceDefectArea>
      <SurfaceDefectNumber>1.35</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.2168140411377</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.2669712305069</SurfacePositionRMSE>
      <SIQR>2.20533691287534</SIQR>
      <IQR>2.28051915544889</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>20231031-041101</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>12</SurfaceEulerNumber>
         <SurfaceDefectArea>0.271943647201505</SurfaceDefectArea>
         <SurfaceDefectNumber>7</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0608407035470009</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0633485615253448</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>12</EC_abs>
      <defect_size>0.271943647201505</defect_size>
      <vol_abs_CGW>[229.443462521623 613.121969511493 508.940822034605 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.642760871574464</vol_abs_WMH>
      <vol_rel_WMH>0.000475588529198369</vol_rel_WMH>
      <surf_TSA>1866.12319721863</surf_TSA>
      <vol_TIV>1351.50625406772</vol_TIV>
      <vol_rel_CGW>[0.169768702017509 0.453658255495406 0.376573042487085 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.39731064542035 0.602022591616326]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.39408683776855 0.711272024517254 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.81161448915119 0.238640030615825 0.29893853202961;2.42597983892495 0.171749301664317 0.447456323258497;3.06503412653724 0.265077064820163 0.253605144711892]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.861636691239277 0.28233966921891 0.522082018927445;4.01960219211704 0.377585405184507 0.477917981072555]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.05582253592992</vol_TIV>
      <vol_rel_CGW>[0.898863182785728 5.99745430128243 4.61302159639161 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04755885291984</vol_rel_WMH>
      <surf_TSA>8.60720321657809</surf_TSA>
      <SQR>4.97587165725744</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3368864552 0.494021941655461]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00174072524532676 0.00143107760231942 0.0257366932928562]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[753.323415996118 456.95044242741 352.443090984667 679.72497071033 817.313177624497 8900.99854564786]</SPMvols0>
      <SPMvols1>[657.485904946073 424.539653713619 236.135443822278 545.690046631495 768.633276898103 8901.87078106039]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[179.297897338867 335.695098876953 428.923187255859]</T3th>
            <Tth>
               <T3th>[-7.43140983581543 27.0798034667969 4.33699464797974 179.297897338867 335.695098876953 428.923187255859 553.73583984375 1393.29211425781]</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>[0.0214407220482826 0.0777897164225578 0.0856336802244186 0 0]</dtc>
         <ll>[0.0830985165062119 0 0.0830985165062119 0;0.190506988928384 0.0103539229870415 0.200860911915425 2207.95336914062;0.190506988928384 0.0103539229870415 0.200860911915425 2207.95336914062]</ll>
         <rmsdtc>[0.0462930873036385 0.0999212190508842 0.110840171575546]</rmsdtc>
         <rmsgdt>[0.03328637778759 0.044433057308197 0.0547024868428707]</rmsgdt>
         <rmsdt>0.110840171575546</rmsdt>
         <dt>0.0856336802244186</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>[0.0100035071372986 0.0374669879674911 0.0525382198393345 0.0606902092695236 0.0663011968135834 0.0741088390350342]</dtc>
         <ll>[0.083658569411769 0 0.083658569411769 0;0.217255448717949 0.0139874313186813 0.23124288003663 7159.81640625;0.195593905965164 0.0166737946263575 0.212267700591521 12000.330078125;0.174911643931216 0.0186082128106359 0.193519856741852 20064.71484375;0.158166958727027 0.0212932518836964 0.179460210610723 37249.4140625;0.158166958727027 0.0212932518836964 0.179460210610723 37249.4140625]</ll>
         <rmsdtc>[0.0113383773714304 0.0421354174613953 0.0619737394154072 0.0857337564229965 0.107657372951508 0.11521939188242]</rmsdtc>
         <rmsgdt>[0.00329647655598819 0.0128694083541632 0.0278799962252378 0.0479375459253788 0.0654673725366592 0.0712466537952423]</rmsgdt>
         <rmsdt>0.11521939188242</rmsdt>
         <dt>0.0741088390350342</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 42s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 5s</item>
      <item>Initial correction 4s</item>
      <item>Refine background 2s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 4s</item>
      <item>29s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 7s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 53s</item>
      <item>SPM preprocessing 1 (estimate 2): 49s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 13s</item>
      <item>Update Segmentation 15s</item>
      <item>Update Skull-Stripping 34s</item>
      <item>Update probability maps 7s</item>
      <item>69s</item>
      <item>Global intensity correction: 14s</item>
      <item>SANLM denoising after intensity normalization (medium): 19s</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 = 1.00) 11s</item>
      <item>Estimate local tissue thresholds (WM) 15s</item>
      <item>Estimate local tissue thresholds (GM) 20s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 36s</item>
      <item>90s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 9s</item>
      <item>Blood vessel detection 7s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.04) 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>50s</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 | 0.0837 0.0000 0.0837 | 32.0000</item>
      <item>2 | 2.50 | 0.0809 0.0012 0.0821 | 29.4886</item>
      <item>3 | 2.50 | 0.0800 0.0019 0.0818 | 26.9772</item>
      <item>4 | 2.50 | 0.0796 0.0021 0.0817 | 24.6107</item>
      <item>5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548</item>
      <item>6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989</item>
      <item>7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688</item>
      <item>8 | 2.50 | 0.0783 0.0026 0.0809 | 17.4455</item>
      <item>9 | 2.50 | 0.0780 0.0027 0.0806 | 15.9223</item>
      <item>10 | 2.50 | 0.0776 0.0028 0.0804 | 14.6627</item>
      <item>11 | 2.50 | 0.0773 0.0029 0.0802 | 13.4764</item>
      <item>12 | 2.50 | 0.0769 0.0029 0.0799 | 12.3015</item>
      <item>13 | 2.50 | 0.0766 0.0030 0.0796 | 11.3776</item>
      <item>14 | 2.50 | 0.0762 0.0031 0.0793 | 10.4537</item>
      <item>15 | 2.25 | 0.0754 0.0032 0.0786 | 9.5920</item>
      <item>16 | 2.25 | 0.0724 0.0047 0.0771 | 8.8725</item>
      <item>29 | 2.00 | 0.0734 0.0021 0.0755 | 3.3283</item>
      <item>30 | 2.00 | 0.0673 0.0046 0.0719 | 3.1221</item>
      <item>31 | 2.00 | 0.0652 0.0056 0.0708 | 2.9160</item>
      <item>43 | 1.75 | 0.0640 0.0032 0.0672 | 1.5785</item>
      <item>44 | 1.75 | 0.0597 0.0054 0.0652 | 1.5194</item>
      <item>45 | 1.75 | 0.0583 0.0062 0.0645 | 1.4626</item>
      <item>57 | 1.50 | 0.0567 0.0045 0.0612 | 1.0900</item>
      <item>58 | 1.50 | 0.0537 0.0065 0.0602 | 1.0730</item>
      <item>59 | 1.50 | 0.0527 0.0071 0.0598 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 133s</item>
      <item>Prepare output 8s</item>
      <item>142s</item>
      <item>Jacobian determinant (RMS): 0.011 0.042 0.062 0.086 0.108 | 0.115219</item>
      <item>Template Matching: 0.084 0.217 0.196 0.175 0.158 | 0.158167</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: 28s</item>
      <item>CSF distance: 11s</item>
      <item>PBT2x thickness: 33s</item>
      <item>77s</item>
      <item>Create initial surface 66s</item>
      <item>Topology correction: 74s</item>
      <item>Surface refinement: 51s</item>
      <item>Reduction of surface collisions with optimization: 53s</item>
      <item>Spherical mapping with areal smoothing 62s</item>
      <item>Spherical registration 248s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 21s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 33s</item>
      <item>70s</item>
      <item>Create initial surface 64s</item>
      <item>Topology correction: 73s</item>
      <item>Surface refinement: 80s</item>
      <item>Reduction of surface collisions with optimization: 52s</item>
      <item>Spherical mapping with areal smoothing 61s</item>
      <item>Spherical registration 252s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3973 0.6019 mm</item>
      <item>Surface intensity / position RMSE: 0.0608 / 0.0633</item>
      <item>Euler number / defect number / defect size: 12.0 / 7.0 / 0.27%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/surf/lh.thickness.sub-0025991_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/surf/rh.thickness.sub-0025991_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/sub-0025991_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1357s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 26s</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 10s</item>
      <item>ROI estimation of 'mori' atlas 15s</item>
      <item>ROI estimation of 'anatomy3' atlas 21s</item>
      <item>ROI estimation of 'julichbrain' atlas 28s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 67s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
      <item>Write results 7s</item>
      <item>294s</item>
      <item>Quality check: 9s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/report/catreport_sub-0025991_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 39 minute(s) and 47 second(s).</item>
      <item>Image Quality Rating (IQR): 82.19% (B-)</item>
      <item>GM volume (GMV): 45.37% (613.12 / 1351.51 ml)</item>
      <item>GM thickness (GMT): 2.40 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>