ds003554_ReproVBM/sub-sc016/report/cat_sub-sc016_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.09004269700377 -0.0265079569577068 0.024741962098866 -1.3192559452331;0.0357197061383935 0.984527639015152 0.013179517944869 -20.4188610045658;-0.0234436058552917 0.0379178762023215 1.08727968527376 -10.9227851326998;0 0 0 1]</Affine>
      <Affine0>[1.09004269700377 -0.0265079569577068 0.024741962098866 -1.3192559452331;0.0357197061383935 0.984527639015152 0.013179517944869 -20.4188610045658;-0.0234436058552917 0.0379178762023215 1.08727968527376 -10.9227851326998;0 0 0 1]</Affine0>
      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[253424.444185224 409583.936423265 47532.1263544397 134847.767816251 77182.1021520571 16049.7311807624 36835.023963161 215693.084671601 869097.226874634 453080.381811927 145623.117311158 27888.0891115608 10577.5236165618]</mn>
      <vr>[3357192350.74469;375822732.905839;436826698.097853;2350153280.83602;684005008.109922;43636688.2355649;173103668.522263;4209773017.95106;4087386375.39612;6660642647.56896;2797883055.48038;131227052.762205;21005136.9570413]</vr>
      <ll>-12.5203266143799</ll>
      <Affine_translation>[-1.3192559452331 -20.4188610045658 -10.9227851326998]</Affine_translation>
      <Affine_rotation>[-0.0378831348080097 0.0227288061421777 -0.0319119335479089]</Affine_rotation>
      <Affine_scaling>[1.09087972817968 0.985601723110244 1.08628222740751]</Affine_scaling>
      <Affine_shearing>[0.00452371197921102 0.00163930819063948 0.0551139176390573]</Affine_shearing>
      <Affine0_translation>[-1.3192559452331 -20.4188610045658 -10.9227851326998]</Affine0_translation>
      <Affine0_rotation>[-0.0378831348080097 0.0227288061421777 -0.0319119335479089]</Affine0_rotation>
      <Affine0_scaling>[1.09087972817968 0.985601723110244 1.08628222740751]</Affine0_scaling>
      <Affine0_shearing>[0.00452371197921102 0.00163930819063948 0.0551139176390573]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_9674/ds/sub-sc016</path>
      <file>sub-sc016_T1w</file>
      <fname>/var/lib/condor/execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_9674/ds/sub-sc016/mri/msub-sc016_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_9674/ds/sub-sc016/mri/p0sub-sc016_T1w.nii</Fp0>
      <fnames>..74/ds/sub-sc016/sub-sc016_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>64</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>6</SurfaceEulerNumber>
      <SurfaceDefectArea>0.0628218766688279</SurfaceDefectArea>
      <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0574171617627144</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0551595129072666</SurfacePositionRMSE>
      <res_vx_vol>[0.999999993821372 1.00000001816488 1.00000000727884]</res_vx_vol>
      <res_vx_voli>[0.999999993163534 1.00000002385505 1.00000001013407]</res_vx_voli>
      <res_RMS>1.0000000064217</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[0 39161.63671875 202904.265625 396720.03125]</tissue_mn>
      <tissue_mnr>[0 0.0987135395407677 0.511454582214355 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[1025.40666264445 37460.1868790541 51029.7614521108 36753.64263239]</tissue_std>
      <tissue_stdr>[0.00258471118286252 0.0944247394800186 0.128629148006439 0.0926437750458717]</tissue_stdr>
      <contrast>133148.84375</contrast>
      <contrastr>0.335624217987061</contrastr>
      <NCR>0.124074056744576</NCR>
      <ICR>0.311294674873352</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.99999998764274 2.00000003632976 2.00000001455768]</res_vx_vol>
      <res_RMS>2.00000001284339</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[1.89584374427795 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>3.04896998405457</contrastr>
      <NCR>2.11217427253723</NCR>
      <ICR>1.23188161849976</ICR>
      <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
      <SurfaceDefectArea>1.01570546916721</SurfaceDefectArea>
      <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.14834320545197</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.10319030284882</SurfacePositionRMSE>
      <IQR>2.06140366235492</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>20220711-191324</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>6</SurfaceEulerNumber>
         <SurfaceDefectArea>0.0628218766688279</SurfaceDefectArea>
         <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0574171617627144</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0551595129072666</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>6</EC_abs>
      <defect_size>0.0628218766688279</defect_size>
      <vol_abs_CGW>[311.785792779535 744.512530019408 529.76929673758 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.737109823936052</vol_abs_WMH>
      <vol_rel_WMH>0.000464740478184309</vol_rel_WMH>
      <surf_TSA>2002.49323762208</surf_TSA>
      <vol_TIV>1586.06761953652</vol_TIV>
      <vol_rel_CGW>[0.19657786902594 0.469407811400227 0.334014319573833 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.65572825396561 0.638470288019683]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.64437794685364 0.779875265970239 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.09676463694317 0.247902117150272 0.335166909012159;2.71328097295537 0.183611125137539 0.407189926677598;3.39416242194538 0.273688835298441 0.257643164310243]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.945515395392195 0.386256033170216 0.594617807042657;4.3042123185825 0.304921660545206 0.405382192957343]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.7817950256859</vol_TIV>
      <vol_rel_CGW>[1.38034965923025 6.28031270474546 3.84867671648406 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04647404781843</vol_rel_WMH>
      <surf_TSA>8.6215364234576</surf_TSA>
      <SQR>5.14848545866247</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.696983664772727 2118 659 3839.82307397453 0.496378724336795]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0 0 0.0907841175794601]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[920.863801474478 446.560090556661 533.690912530337 751.332192949678 1708.7000503173 9052.57757129164]</SPMvols0>
      <SPMvols1>[809.277151385782 423.732874250567 311.047098641831 972.868340141441 1347.45684835173 8807.65021954317]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[49729.03125 231828.171875 410933.65625]</T3th>
            <Tth>
               <T3th>[0 0 1051.23425292969 49729.03125 231828.171875 410933.65625 591536 1105798.375]</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>[0.0200188551098108 0.0734647810459137 0.0813822224736214 0 0]</dtc>
         <ll>[0.0852860858698948 0 0.0852860858698948 0;0.202671541028521 0.0103928038195259 0.213064344848047 2216.24462890625;0.202671541028521 0.0103928038195259 0.213064344848047 2216.24462890625]</ll>
         <rmsdtc>[0.0433654636144638 0.0998614355921745 0.112856589257717]</rmsdtc>
         <rmsgdt>[0.0310502704232931 0.0526283346116543 0.0659764111042023]</rmsgdt>
         <rmsdt>0.112856589257717</rmsdt>
         <dt>0.0813822224736214</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>[0.00907475873827934 0.0327237658202648 0.047443650662899 0.0565108731389046 0.0633211880922318 0.0704898610711098]</dtc>
         <ll>[0.0855339333320655 0 0.0855339333320655 0;0.223085485347985 0.0123827571733822 0.235468242521368 6338.423828125;0.201392362500556 0.0157381366174942 0.21713049911805 11326.92578125;0.181204901801215 0.0180322043916099 0.199237106192825 19443.62109375;0.163949721697107 0.0207974279455033 0.184747149642611 36382.04296875;0.163949721697107 0.0207974279455033 0.184747149642611 36382.04296875]</ll>
         <rmsdtc>[0.0104407723993063 0.0378784909844398 0.0589889474213123 0.0861159265041351 0.111298754811287 0.118558771908283]</rmsdtc>
         <rmsgdt>[0.0031620638910681 0.0129718128591776 0.0291583016514778 0.0511776022613049 0.0710096061229706 0.0780047625303268]</rmsgdt>
         <rmsdt>0.118558771908283</rmsdt>
         <dt>0.0704898610711098</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 41s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 9s</item>
      <item>Estimate background 9s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 4s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 6s</item>
      <item>52s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 105s</item>
      <item>SPM preprocessing 1 (estimate 2): 78s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 24s</item>
      <item>Update Segmentation 25s</item>
      <item>Update Skull-Stripping 57s</item>
      <item>Update probability maps 12s</item>
      <item>118s</item>
      <item>Global intensity correction: 22s</item>
      <item>SANLM denoising after intensity normalization (medium): 13s</item>
      <item>Fast Optimized Shooting registration 44s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.08) 20s</item>
      <item>Estimate local tissue thresholds (WM) 26s</item>
      <item>Estimate local tissue thresholds (GM) 37s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 13s</item>
      <item>108s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 10s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 15s</item>
      <item>Blood vessel detection 14s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.15) 31s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 6s</item>
      <item>87s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 6s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>14s</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 | 0.0855 0.0000 0.0855 | 32.0000</item>
      <item>2 | 2.50 | 0.0831 0.0011 0.0843 | 29.4886</item>
      <item>3 | 2.50 | 0.0825 0.0017 0.0841 | 26.9772</item>
      <item>4 | 2.50 | 0.0821 0.0019 0.0840 | 24.6107</item>
      <item>5 | 2.50 | 0.0819 0.0020 0.0838 | 22.6548</item>
      <item>6 | 2.50 | 0.0816 0.0021 0.0837 | 20.6989</item>
      <item>7 | 2.50 | 0.0814 0.0021 0.0835 | 18.9688</item>
      <item>8 | 2.50 | 0.0811 0.0022 0.0833 | 17.4455</item>
      <item>9 | 2.50 | 0.0809 0.0023 0.0831 | 15.9223</item>
      <item>10 | 2.50 | 0.0806 0.0024 0.0830 | 14.6627</item>
      <item>11 | 2.50 | 0.0803 0.0024 0.0827 | 13.4764</item>
      <item>12 | 2.50 | 0.0800 0.0025 0.0825 | 12.3015</item>
      <item>13 | 2.50 | 0.0797 0.0026 0.0823 | 11.3776</item>
      <item>14 | 2.50 | 0.0794 0.0026 0.0821 | 10.4537</item>
      <item>15 | 2.25 | 0.0773 0.0027 0.0800 | 9.5920</item>
      <item>16 | 2.25 | 0.0744 0.0041 0.0785 | 8.8725</item>
      <item>29 | 2.00 | 0.0749 0.0018 0.0767 | 3.3283</item>
      <item>30 | 2.00 | 0.0690 0.0043 0.0733 | 3.1221</item>
      <item>31 | 2.00 | 0.0671 0.0052 0.0724 | 2.9160</item>
      <item>43 | 1.75 | 0.0659 0.0030 0.0689 | 1.5785</item>
      <item>44 | 1.75 | 0.0617 0.0053 0.0670 | 1.5194</item>
      <item>45 | 1.75 | 0.0604 0.0060 0.0664 | 1.4626</item>
      <item>57 | 1.50 | 0.0586 0.0043 0.0629 | 1.0900</item>
      <item>58 | 1.50 | 0.0556 0.0063 0.0619 | 1.0730</item>
      <item>59 | 1.50 | 0.0546 0.0069 0.0616 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 207s</item>
      <item>Prepare output 14s</item>
      <item>221s</item>
      <item>Jacobian determinant (RMS): 0.010 0.038 0.059 0.086 0.111 | 0.118559</item>
      <item>Template Matching: 0.086 0.223 0.201 0.181 0.164 | 0.163950</item>
      <item>Write result maps: 68s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 55s</item>
      <item>CSF distance: 23s</item>
      <item>PBT2x thickness: 68s</item>
      <item>155s</item>
      <item>Create initial surface 117s</item>
      <item>Topology correction: 119s</item>
      <item>Surface refinement: 132s</item>
      <item>Reduction of surface collisions with optimization: 89s</item>
      <item>Spherical mapping with areal smoothing 116s</item>
      <item>Spherical registration 338s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 44s</item>
      <item>CSF distance: 22s</item>
      <item>PBT2x thickness: 62s</item>
      <item>136s</item>
      <item>Create initial surface 158s</item>
      <item>Topology correction: 133s</item>
      <item>Surface refinement: 157s</item>
      <item>Reduction of surface collisions with optimization: 82s</item>
      <item>Spherical mapping with areal smoothing 103s</item>
      <item>Spherical registration 339s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.6557 0.6384 mm</item>
      <item>Surface intensity / position RMSE: 0.0574 / 0.0552</item>
      <item>Euler number / defect number / defect size: 6.0 / 8.5 / 0.06%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/lh.thickness.sub-sc016_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_9674/ds/sub-sc016/surf/rh.thickness.sub-sc016_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_9674/ds/sub-sc016/sub-sc016_T1w.nii</item>
      <item>Surface ROI estimation: 119s</item>
      <item>Surface and thickness estimation takes: 2489s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 14s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 48s</item>
      <item>ROI estimation of 'lpba40' atlas 15s</item>
      <item>ROI estimation of 'hammers' atlas 36s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 13s</item>
      <item>ROI estimation of 'aal3' atlas 22s</item>
      <item>ROI estimation of 'mori' atlas 32s</item>
      <item>ROI estimation of 'anatomy3' atlas 46s</item>
      <item>ROI estimation of 'julichbrain' atlas 58s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 95s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s</item>
      <item>Write results 137s</item>
      <item>585s</item>
      <item>Quality check: 7s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_9674/ds/sub-sc016/report/catreport_sub-sc016_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 70 minute(s) and 18 second(s).</item>
      <item>Image Quality Rating (IQR): 84.39% (B)</item>
      <item>GM volume (GMV): 46.94% (744.51 / 1586.07 ml)</item>
      <item>GM thickness (GMT): 2.66 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_9674/ds/sub-sc016/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>