ds003338_ReproVBM/sub-16/report/cat_sub-16_ses-01_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.02179266869028 0.0042654084684405 0.00904472178579558 3.87945226695029;0.0214453274958188 0.96099148276978 0.431531895101819 -20.3596133154811;-0.0154062309007837 -0.363473496299799 1.0374921771812 8.23050800229519;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[1239.79570797493 1795.62934190354 339.054405452737 735.401212099623 422.032253503857 113.952744518476 214.035498355535 1340.01309700064 2085.84781579787 1633.1979074175 902.316588071713 177.66089124166 89.6304372735295]</mn>
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      <ll>-7.11074686050415</ll>
      <Affine_translation>[3.87945226695029 -20.3596133154811 8.23050800229519]</Affine_translation>
      <Affine_rotation>[0.361569608992536 0.00667833598458916 -0.0249587900895281]</Affine_rotation>
      <Affine_scaling>[1.02213380328173 1.0270060846984 1.12309742974247]</Affine_scaling>
      <Affine_shearing>[0.0292574079970308 0.00240470076415473 0.0356131260374425]</Affine_shearing>
      <Affine0_translation>[3.87945226695029 -20.3596133154811 8.23050800229519]</Affine0_translation>
      <Affine0_rotation>[0.361569608992536 0.00667833598458916 -0.0249587900895281]</Affine0_rotation>
      <Affine0_scaling>[1.02213380328173 1.0270060846984 1.12309742974247]</Affine0_scaling>
      <Affine0_shearing>[0.0292574079970308 0.00240470076415473 0.0356131260374425]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_1497/ds/sub-16</path>
      <file>sub-16_ses-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_1497/ds/sub-16/sub-16_ses-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_1497/ds/sub-16/sub-16_ses-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_1497/ds/sub-16/mri/msub-16_ses-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_1497/ds/sub-16/mri/p0sub-16_ses-01_T1w.nii</Fp0>
      <fnames>.._1497/ds/sub-16/sub-16_ses-01_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_1980</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>32</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>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
         </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>
            <NB>0</NB>
            <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>
         <regmethod>
            <shooting>
               <shootingtpm>
                  <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
               </shootingtpm>
               <regstr>0.5</regstr>
            </shooting>
         </regmethod>
         <restypes>
            <optimal>[1 0.3]</optimal>
         </restypes>
         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
         <darteltpms>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
         </darteltpms>
         <shootingtpms>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
         </shootingtpms>
         <templates>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
         </templates>
         <inv_weighting>0</inv_weighting>
         <AMAPframing>1</AMAPframing>
      </extopts>
   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>10</SurfaceEulerNumber>
      <SurfaceDefectArea>0.157867500109961</SurfaceDefectArea>
      <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0627458691596985</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0598552450537682</SurfacePositionRMSE>
      <res_vx_vol>[1 1 1]</res_vx_vol>
      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>1</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[18.7280006408691 310.422424316406 1109.85021972656 1774.64538574219]</tissue_mn>
      <tissue_mnr>[0.0105530945584178 0.174920812249184 0.62539267539978 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[34.3190943505363 200.205607758202 199.305300066899 113.127027876078]</tissue_std>
      <tissue_stdr>[0.0195448212325573 0.1140176653862 0.113504938781261 0.0644261613488197]</tissue_stdr>
      <contrast>634.635925292969</contrast>
      <contrastr>0.357612788677216</contrastr>
      <NCR>0.12257032841444</NCR>
      <ICR>0.290474683046341</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2 2 2]</res_vx_vol>
      <res_RMS>2</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>2.71914148330688</contrastr>
      <NCR>2.0905876159668</NCR>
      <ICR>1.18024468421936</ICR>
      <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
      <SurfaceDefectArea>1.03946687502749</SurfaceDefectArea>
      <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.25491738319397</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.19710493087769</SurfacePositionRMSE>
      <IQR>2.0487878204551</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <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>1980</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>20220711-083917</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>10</SurfaceEulerNumber>
         <SurfaceDefectArea>0.157867500109961</SurfaceDefectArea>
         <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0627458691596985</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0598552450537682</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>10</EC_abs>
      <defect_size>0.157867500109961</defect_size>
      <vol_abs_CGW>[269.774168627451 737.558509803922 538.073803921569 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.04688235294118</vol_abs_WMH>
      <vol_rel_WMH>0.000677415531056436</vol_rel_WMH>
      <surf_TSA>2078.59029757332</surf_TSA>
      <vol_TIV>1545.40648235294</vol_TIV>
      <vol_rel_CGW>[0.174565185087557 0.477258584214659 0.348176230697784 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.59659206998964 0.598675191200879]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.5590877532959 0.730078203553497 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.08699778319208 0.231499138054028 0.343998393241878;2.63063305239975 0.167909266972238 0.412340389273672;3.2923997601199 0.26053494953364 0.24366121748445]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[1.01231751430478 0.392372157817691 0.54582283039251;4.20337805407725 0.329704130045171 0.45417716960749]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.48745225455241</vol_TIV>
      <vol_rel_CGW>[0.985006916083991 6.4213107797173 4.10302138465848 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06774155310564</vol_rel_WMH>
      <surf_TSA>8.6232466505456</surf_TSA>
      <SQR>5.26914733182901</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.225573973222212 1 1 8932.49 0.369224827836672]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00707208598032594 0 0.231687843799591]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[860.462745098039 483.654760784314 471.396254901961 475.734254901961 1832.51852156863 7991.49266666667]</SPMvols0>
      <SPMvols1>[762.220176470588 461.863545098039 273.865498039216 458.607058823529 1342.43783137255 8235.38246666667]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[380.464996337891 1187.61364746094 1800.56457519531]</T3th>
            <Tth>
               <T3th>[0 0 21.7932548522949 380.464996337891 1187.61364746094 1800.56457519531 2510.6142578125 4015.02954101562]</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>[0.0219052396714687 0.0767026767134666 0.0844992995262146 0 0]</dtc>
         <ll>[0.0887051842221264 0 0.0887051842221264 0;0.20367131227491 0.0114234784642617 0.215094790739172 2436.03393554688;0.20367131227491 0.0114234784642617 0.215094790739172 2436.03393554688]</ll>
         <rmsdtc>[0.0475993677973747 0.0992801561951637 0.110137097537518]</rmsdtc>
         <rmsgdt>[0.034107256680727 0.0461674332618713 0.0567116998136044]</rmsgdt>
         <rmsdt>0.110137097537518</rmsdt>
         <dt>0.0844992995262146</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>[0.0101383542641997 0.0397665947675705 0.0534209981560707 0.0619909018278122 0.0687020048499107 0.0765594244003296]</dtc>
         <ll>[0.0886676945858621 0 0.0886676945858621 0;0.223533577533578 0.0184821924603175 0.242015769993895 9460.572265625;0.204550331417289 0.0192208909388408 0.22377122235613 13833.505859375;0.184066671025493 0.0207661287284192 0.204832799753912 22391.53515625;0.166480693147695 0.0239978768221737 0.190478569969869 41980.7578125;0.166480693147695 0.0239978768221737 0.190478569969869 41980.7578125]</ll>
         <rmsdtc>[0.0117829889059067 0.0428572744131088 0.0638523399829865 0.0870504602789879 0.110117062926292 0.117010362446308]</rmsdtc>
         <rmsgdt>[0.00340206944383681 0.0132779255509377 0.0286234598606825 0.0485651455819607 0.0677759498357773 0.0729526206851006]</rmsgdt>
         <rmsdt>0.117010362446308</rmsdt>
         <dt>0.0765594244003296</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_1497/ds/sub-16/sub-16_ses-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 79s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 6s</item>
      <item>Refine background 3s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 6s</item>
      <item>38s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 9s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 70s</item>
      <item>SPM preprocessing 1 (estimate 2): 64s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 17s</item>
      <item>Update Segmentation 19s</item>
      <item>Update Skull-Stripping 42s</item>
      <item>Update probability maps 8s</item>
      <item>86s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 23s</item>
      <item>Fast Optimized Shooting registration 32s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 14s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 26s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 31s</item>
      <item>99s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 15s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.07) 26s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 4s</item>
      <item>71s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.99 0.04]</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 | 0.0887 0.0000 0.0887 | 32.0000</item>
      <item>2 | 2.50 | 0.0848 0.0015 0.0863 | 29.4886</item>
      <item>3 | 2.50 | 0.0837 0.0023 0.0860 | 26.9772</item>
      <item>4 | 2.50 | 0.0831 0.0026 0.0857 | 24.6107</item>
      <item>5 | 2.50 | 0.0827 0.0028 0.0855 | 22.6548</item>
      <item>6 | 2.50 | 0.0823 0.0029 0.0852 | 20.6989</item>
      <item>7 | 2.50 | 0.0819 0.0031 0.0850 | 18.9688</item>
      <item>8 | 2.50 | 0.0815 0.0032 0.0847 | 17.4455</item>
      <item>9 | 2.50 | 0.0811 0.0033 0.0844 | 15.9223</item>
      <item>10 | 2.50 | 0.0807 0.0034 0.0841 | 14.6627</item>
      <item>11 | 2.50 | 0.0803 0.0035 0.0838 | 13.4764</item>
      <item>12 | 2.50 | 0.0799 0.0036 0.0834 | 12.3015</item>
      <item>13 | 2.50 | 0.0795 0.0037 0.0831 | 11.3776</item>
      <item>14 | 2.50 | 0.0790 0.0037 0.0828 | 10.4537</item>
      <item>15 | 2.25 | 0.0794 0.0039 0.0833 | 9.5920</item>
      <item>16 | 2.25 | 0.0759 0.0056 0.0815 | 8.8725</item>
      <item>17 | 2.25 | 0.0745 0.0062 0.0807 | 8.1530</item>
      <item>29 | 2.00 | 0.0765 0.0028 0.0793 | 3.3283</item>
      <item>30 | 2.00 | 0.0703 0.0054 0.0757 | 3.1221</item>
      <item>31 | 2.00 | 0.0682 0.0064 0.0746 | 2.9160</item>
      <item>43 | 1.75 | 0.0674 0.0037 0.0711 | 1.5785</item>
      <item>44 | 1.75 | 0.0629 0.0061 0.0690 | 1.5194</item>
      <item>45 | 1.75 | 0.0614 0.0069 0.0683 | 1.4626</item>
      <item>57 | 1.50 | 0.0601 0.0051 0.0651 | 1.0900</item>
      <item>58 | 1.50 | 0.0567 0.0073 0.0639 | 1.0730</item>
      <item>59 | 1.50 | 0.0555 0.0080 0.0635 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 157s</item>
      <item>Prepare output 10s</item>
      <item>167s</item>
      <item>Jacobian determinant (RMS): 0.012 0.043 0.064 0.087 0.110 | 0.117010</item>
      <item>Template Matching: 0.089 0.224 0.205 0.184 0.166 | 0.166481</item>
      <item>Write result maps: 25s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 31s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 51s</item>
      <item>106s</item>
      <item>Create initial surface 97s</item>
      <item>Topology correction: 102s</item>
      <item>Surface refinement: 86s</item>
      <item>Reduction of surface collisions with optimization: 77s</item>
      <item>Spherical mapping with areal smoothing 98s</item>
      <item>Spherical registration 279s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 36s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 48s</item>
      <item>106s</item>
      <item>Create initial surface 88s</item>
      <item>Topology correction: 98s</item>
      <item>Surface refinement: 118s</item>
      <item>Reduction of surface collisions with optimization: 76s</item>
      <item>Spherical mapping with areal smoothing 89s</item>
      <item>Spherical registration 289s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5965 0.5985 mm</item>
      <item>Surface intensity / position RMSE: 0.0627 / 0.0599</item>
      <item>Euler number / defect number / defect size: 10.0 / 10.5 / 0.16%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1497/ds/sub-16/surf/lh.thickness.sub-16_ses-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1497/ds/sub-16/surf/rh.thickness.sub-16_ses-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1497/ds/sub-16/sub-16_ses-01_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1804s</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 20s</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 25s</item>
      <item>ROI estimation of 'julichbrain' atlas 33s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 79s</item>
      <item>Write results 80s</item>
      <item>331s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_1497/ds/sub-16/report/catreport_sub-16_ses-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 50 minute(s) and 46 second(s).</item>
      <item>Image Quality Rating (IQR): 84.51% (B)</item>
      <item>GM volume (GMV): 47.73% (737.56 / 1545.41 ml)</item>
      <item>GM thickness (GMT): 2.60 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_1497/ds/sub-16/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_1497/ds/sub-16/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_1497/ds/sub-16/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>