CORR_cat12.8.1/XHCUMS/sub-0025991/ses-5/report/cat_sub-0025991_ses-5_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-5</path>
      <file>sub-0025991_ses-5_run-1_T1w</file>
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      <F>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/sub-0025991_ses-5_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/mri/msub-0025991_ses-5_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/mri/p0sub-0025991_ses-5_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0025991/ses-5/sub-0025991_ses-5_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>
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            <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>
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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>
               <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/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>
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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/ibsr.nii</td>
               <td>0</td>
               <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/aal3.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/mori.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/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>
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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>
               <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>
               </td>
               <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>
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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>
            </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>
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            <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>
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         </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>
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         <new_release>0</new_release>
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         <affmod>0</affmod>
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               <regstr>0.5</regstr>
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            <optimal>[1 0.3]</optimal>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
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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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      <ICR>1.64327132701874</ICR>
      <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
      <SurfaceDefectArea>1.09542249446462</SurfaceDefectArea>
      <SurfaceDefectNumber>1.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.26734983921051</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.30140805244446</SurfacePositionRMSE>
      <SIQR>2.15696564304458</SIQR>
      <IQR>2.22685315729129</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>20231031-021916</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>18</SurfaceEulerNumber>
         <SurfaceDefectArea>0.381689977858469</SurfaceDefectArea>
         <SurfaceDefectNumber>10</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0633674934506416</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0650704056024551</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>18</EC_abs>
      <defect_size>0.381689977858469</defect_size>
      <vol_abs_CGW>[219.59330148744 618.976118101908 511.381100804728 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.72381964506153</vol_abs_WMH>
      <vol_rel_WMH>0.000536182351965191</vol_rel_WMH>
      <surf_TSA>1868.28477601886</surf_TSA>
      <vol_TIV>1349.95052039408</vol_TIV>
      <vol_rel_CGW>[0.162667666829253 0.458517633610169 0.378814699560578 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.39862564862482 0.610070037936186]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.39826560020447 0.725974706133845 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.81930135081096 0.239807622709266 0.314342468520638;2.44414396042802 0.17498395839613 0.438307184701367;3.08571331372316 0.265523781407715 0.247350346777995]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.854739357180573 0.288607584793424 0.52959716339998;4.04685437484602 0.384951387436992 0.47040283660002]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.05944746344542</vol_TIV>
      <vol_rel_CGW>[0.771330223226528 6.08472761512516 4.65328124210808 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.05361823519652</vol_rel_WMH>
      <surf_TSA>8.607673323742</surf_TSA>
      <SQR>5.04517238468758</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3359143377 0.498061062810422]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00180114642716944 0.0013486813986674 0.309254288673401]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[759.079740992231 456.444788176012 347.985751226562 692.940749356107 776.177812459639 8922.89196469236]</SPMvols0>
      <SPMvols1>[661.852955600728 423.557366877117 230.760560885184 548.053534062952 730.46301010901 8939.66523614306]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[182.572998046875 337.689208984375 430.239898681641]</T3th>
            <Tth>
               <T3th>[-7.66816997528076 34.0351867675781 4.18803834915161 182.572998046875 337.689208984375 430.239898681641 554.073364257812 1362.89978027344]</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>[0.0202146414667368 0.0716390460729599 0.0784357339143753 0 0]</dtc>
         <ll>[0.0813570117988602 0 0.0813570117988602 0;0.191816478788781 0.00959315191225416 0.201409630701035 2045.72045898438;0.191816478788781 0.00959315191225416 0.201409630701035 2045.72045898438]</ll>
         <rmsdtc>[0.0440733656287193 0.0922185331583023 0.10260671377182]</rmsdtc>
         <rmsgdt>[0.0317777134478092 0.0422818288207054 0.0523034669458866]</rmsgdt>
         <rmsdt>0.10260671377182</rmsdt>
         <dt>0.0784357339143753</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>[0.00907905027270317 0.0330621898174286 0.0463946312665939 0.0546087734401226 0.0605569109320641 0.0673963353037834]</dtc>
         <ll>[0.0818820242842939 0 0.0818820242842939 0;0.216402304639805 0.0122594990079365 0.228661803647741 6275.3310546875;0.19681514098695 0.0155341392741993 0.21234928026115 11180.1064453125;0.176535741329646 0.0180447262350084 0.194580467564654 19457.123046875;0.159766657301299 0.0210151267354273 0.180781784036727 36762.875;0.159766657301299 0.0210151267354273 0.180781784036727 36762.875]</ll>
         <rmsdtc>[0.0103258742019534 0.0375512428581715 0.0553572624921799 0.0786236971616745 0.101487457752228 0.109085150063038]</rmsdtc>
         <rmsgdt>[0.00311546283774078 0.012080330401659 0.0270036142319441 0.0471484214067459 0.0655862763524055 0.0713841244578362]</rmsgdt>
         <rmsdt>0.109085150063038</rmsdt>
         <dt>0.0673963353037834</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025991/ses-5/sub-0025991_ses-5_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 4s</item>
      <item>Final scaling 5s</item>
      <item>34s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 65s</item>
      <item>SPM preprocessing 1 (estimate 2): 54s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 16s</item>
      <item>Update Segmentation 17s</item>
      <item>Update Skull-Stripping 39s</item>
      <item>Update probability maps 8s</item>
      <item>81s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 22s</item>
      <item>Fast Optimized Shooting registration 31s</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) 13s</item>
      <item>Estimate local tissue thresholds (WM) 17s</item>
      <item>Estimate local tissue thresholds (GM) 24s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 42s</item>
      <item>105s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 12s</item>
      <item>Blood vessel detection 8s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.03) 23s</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>62s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 33s</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) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</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 | 0.0819 0.0000 0.0819 | 32.0000</item>
      <item>2 | 2.50 | 0.0797 0.0010 0.0807 | 29.4886</item>
      <item>3 | 2.50 | 0.0790 0.0016 0.0805 | 26.9772</item>
      <item>4 | 2.50 | 0.0786 0.0018 0.0804 | 24.6107</item>
      <item>5 | 2.50 | 0.0783 0.0020 0.0803 | 22.6548</item>
      <item>6 | 2.50 | 0.0781 0.0020 0.0801 | 20.6989</item>
      <item>7 | 2.50 | 0.0778 0.0021 0.0799 | 18.9688</item>
      <item>8 | 2.50 | 0.0776 0.0022 0.0798 | 17.4455</item>
      <item>9 | 2.50 | 0.0773 0.0023 0.0796 | 15.9223</item>
      <item>10 | 2.50 | 0.0770 0.0024 0.0794 | 14.6627</item>
      <item>11 | 2.50 | 0.0767 0.0025 0.0792 | 13.4764</item>
      <item>12 | 2.50 | 0.0764 0.0025 0.0790 | 12.3015</item>
      <item>13 | 2.50 | 0.0761 0.0026 0.0788 | 11.3776</item>
      <item>14 | 2.50 | 0.0758 0.0027 0.0785 | 10.4537</item>
      <item>15 | 2.25 | 0.0749 0.0027 0.0777 | 9.5920</item>
      <item>16 | 2.25 | 0.0721 0.0041 0.0762 | 8.8725</item>
      <item>29 | 2.00 | 0.0735 0.0019 0.0754 | 3.3283</item>
      <item>30 | 2.00 | 0.0677 0.0042 0.0719 | 3.1221</item>
      <item>31 | 2.00 | 0.0656 0.0052 0.0708 | 2.9160</item>
      <item>43 | 1.75 | 0.0645 0.0030 0.0675 | 1.5785</item>
      <item>44 | 1.75 | 0.0603 0.0052 0.0655 | 1.5194</item>
      <item>45 | 1.75 | 0.0588 0.0060 0.0649 | 1.4626</item>
      <item>57 | 1.50 | 0.0573 0.0044 0.0617 | 1.0900</item>
      <item>58 | 1.50 | 0.0543 0.0064 0.0607 | 1.0730</item>
      <item>59 | 1.50 | 0.0533 0.0070 0.0603 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 166s</item>
      <item>Prepare output 10s</item>
      <item>176s</item>
      <item>Jacobian determinant (RMS): 0.010 0.038 0.055 0.079 0.101 | 0.109085</item>
      <item>Template Matching: 0.082 0.216 0.197 0.177 0.160 | 0.159767</item>
      <item>Write result maps: 32s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 37s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 40s</item>
      <item>96s</item>
      <item>Create initial surface 81s</item>
      <item>Topology correction: 89s</item>
      <item>Surface refinement: 76s</item>
      <item>Reduction of surface collisions with optimization: 64s</item>
      <item>Spherical mapping with areal smoothing 82s</item>
      <item>Spherical registration 291s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 24s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 38s</item>
      <item>80s</item>
      <item>Create initial surface 78s</item>
      <item>Topology correction: 85s</item>
      <item>Surface refinement: 94s</item>
      <item>Reduction of surface collisions with optimization: 59s</item>
      <item>Spherical mapping with areal smoothing 76s</item>
      <item>Spherical registration 304s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3988 0.6098 mm</item>
      <item>Surface intensity / position RMSE: 0.0634 / 0.0651</item>
      <item>Euler number / defect number / defect size: 18.0 / 10.0 / 0.38%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/surf/lh.thickness.sub-0025991_ses-5_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/surf/rh.thickness.sub-0025991_ses-5_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/sub-0025991_ses-5_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1644s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 8s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 29s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 21s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 12s</item>
      <item>ROI estimation of 'mori' atlas 18s</item>
      <item>ROI estimation of 'anatomy3' atlas 26s</item>
      <item>ROI estimation of 'julichbrain' atlas 34s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
      <item>Write results 8s</item>
      <item>353s</item>
      <item>Quality check: 11s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/report/catreport_sub-0025991_ses-5_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 48 minute(s) and 1 second(s).</item>
      <item>Image Quality Rating (IQR): 82.73% (B-)</item>
      <item>GM volume (GMV): 45.85% (618.98 / 1349.95 ml)</item>
      <item>GM thickness (GMT): 2.40 0.61 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_359023/ds/XHCUMS/sub-0025991/ses-5/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>