ds003126_ReproVBM/sub-047EPKL013053/report/cat_sub-047EPKL013053_ses-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[320.460185740287 422.065103142823 174.013999748634 247.125488341288 231.434989710077 83.4105406291084 146.753142267408 214.904640689164 566.880194962775 325.107687920951 99.9457265592898 41.6955561348365 21.278944539842]</mn>
      <vr>[1042.17581950276;340.577689813796;1195.98324360345;956.783493377854;1155.86599699562;905.276744994553;908.836362023296;2920.71391808714;7510.9413682367;2833.05606112939;1422.7943479118;190.193450610125;54.6865025810296]</vr>
      <ll>-5.41484403610229</ll>
      <Affine_translation>[-7.42805317043419 -6.08845026544976 -35.8235632236242]</Affine_translation>
      <Affine_rotation>[0.00565325868834261 -0.0707943838537107 -0.204180152998067]</Affine_rotation>
      <Affine_scaling>[1.06774790246231 1.10453436872493 1.12721429627479]</Affine_scaling>
      <Affine_shearing>[0.00541790492450711 0.0101133292849935 -0.00629200640400951]</Affine_shearing>
      <Affine0_translation>[-7.42805317043419 -6.08845026544976 -35.8235632236242]</Affine0_translation>
      <Affine0_rotation>[0.00565325868834261 -0.0707943838537107 -0.204180152998067]</Affine0_rotation>
      <Affine0_scaling>[1.06774790246231 1.10453436872493 1.12721429627479]</Affine0_scaling>
      <Affine0_shearing>[0.00541790492450711 0.0101133292849935 -0.00629200640400951]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053</path>
      <file>sub-047EPKL013053_ses-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/sub-047EPKL013053_ses-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/sub-047EPKL013053_ses-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/mri/msub-047EPKL013053_ses-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/mri/p0sub-047EPKL013053_ses-1_T1w.nii</Fp0>
      <fnames>..b-047EPKL013053/sub-047EPKL013053_ses-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_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>58</SurfaceEulerNumber>
      <SurfaceDefectArea>1.96238148348068</SurfaceDefectArea>
      <SurfaceDefectNumber>28.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0845908671617508</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0915691256523132</SurfacePositionRMSE>
      <res_vx_vol>[1.00000397818536 0.999999981925692 1.00000002531022]</res_vx_vol>
      <res_vx_voli>[1.00000396725986 0.999999965352436 1.00000002531022]</res_vx_voli>
      <res_RMS>1.00000132847551</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[5.64099979400635 129.152328491211 291.190673828125 431.080230712891]</tissue_mn>
      <tissue_mnr>[0.0130857303738594 0.29960161447525 0.67549067735672 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[3.72490803623281 49.5275950515144 40.6544238142859 29.4711888751402]</tissue_std>
      <tissue_stdr>[0.00875544082373381 0.116415202617645 0.0955587103962898 0.0692723840475082]</tissue_stdr>
      <contrast>141.744384765625</contrast>
      <contrastr>0.328812062740326</contrastr>
      <NCR>0.133140996098518</NCR>
      <ICR>0.33826071023941</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.00000795637071 1.99999996385138 2.00000005062045]</res_vx_vol>
      <res_RMS>2.00000265695102</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>3.15115237236023</contrastr>
      <NCR>2.24233412742615</NCR>
      <ICR>1.29876172542572</ICR>
      <SurfaceEulerNumber>3.85714285714286</SurfaceEulerNumber>
      <SurfaceDefectArea>1.49059537087017</SurfaceDefectArea>
      <SurfaceDefectNumber>2.425</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.69181728363037</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.83138251304626</SurfacePositionRMSE>
      <IQR>2.14465962818077</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>20220711-113401</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>58</SurfaceEulerNumber>
         <SurfaceDefectArea>1.96238148348068</SurfaceDefectArea>
         <SurfaceDefectNumber>28.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0845908671617508</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0915691256523132</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>58</EC_abs>
      <defect_size>1.96238148348068</defect_size>
      <vol_abs_CGW>[132.730290040001 823.594408729528 460.21390775827 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.328542476811095</vol_abs_WMH>
      <vol_rel_WMH>0.000231933302274347</vol_rel_WMH>
      <surf_TSA>2026.35919914566</surf_TSA>
      <vol_TIV>1416.5386065278</vol_TIV>
      <vol_rel_CGW>[0.093700439527976 0.581413316187909 0.324886244284115 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.79233782131129 0.683031818198826]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.82853674888611 0.855986388345784 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.08840575625597 0.298230899255585 0.2787198568582;2.83020219812636 0.205531702520402 0.428124110446911;3.55695074641222 0.291404440091381 0.293156032694888]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.910232296312929 0.348486625827055 0.678665585074022;4.40843961441242 0.242663017023946 0.321334414925979]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00651396082097</vol_TIV>
      <vol_rel_CGW>[0.5 8.29190582234033 3.68473858268884 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.02319333022743</vol_rel_WMH>
      <surf_TSA>8.6222860800872</surf_TSA>
      <SQR>6.78212198459944</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.273330716786004 8 8 6417.22457524157 0.316475641402387]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0133952833712101 0 0.384457796812057]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[924.717393278603 422.964623074171 207.010227170325 519.491248254813 1874.31528111032 5546.72460832107]</SPMvols0>
      <SPMvols1>[840.173850820003 397.662401361708 118.677787362682 349.995087208724 993.162472020984 6131.72580213265]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[156.14680480957 314.053009033203 423.427185058594]</T3th>
            <Tth>
               <T3th>[0 23.6837768554688 8.79196929931641 156.14680480957 314.053009033203 423.427185058594 557.0673828125 814.528137207031]</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>[0.0149363232776523 0.0490969568490982 0.0532397665083408 0 0]</dtc>
         <ll>[0.077726042809702 0 0.077726042809702 0;0.192761974174435 0.00796461048103323 0.200726584655469 1698.43725585938;0.192761974174435 0.00796461048103323 0.200726584655469 1698.43725585938]</ll>
         <rmsdtc>[0.0348606519401073 0.0684997364878654 0.0786954089999199]</rmsdtc>
         <rmsgdt>[0.0256223641335964 0.0378387160599232 0.0478904955089092]</rmsgdt>
         <rmsdt>0.0786954089999199</rmsdt>
         <dt>0.0532397665083408</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>[0.00618067057803273 0.0212920978665352 0.0325779616832733 0.0437304265797138 0.0529478713870049 0.059072732925415]</dtc>
         <ll>[0.0798871694268012 0 0.0798871694268012 0;0.215372222222222 0.010653962530525 0.226026184752747 5453.4970703125;0.19840392754324 0.0148314588422174 0.213235386385457 10674.37890625;0.178615921469722 0.0181753479177796 0.196791269387501 19597.96875;0.16170716044732 0.0216934221537906 0.18340058260111 37949.453125;0.16170716044732 0.0216934221537906 0.18340058260111 37949.453125]</ll>
         <rmsdtc>[0.00780550157651305 0.0272736568003893 0.0460260659456253 0.0760589689016342 0.10602043569088 0.113756999373436]</rmsdtc>
         <rmsgdt>[0.0028588930144906 0.0114156696945429 0.0280976127833128 0.052066870033741 0.0738421976566315 0.0807272121310234]</rmsgdt>
         <rmsdt>0.113756999373436</rmsdt>
         <dt>0.059072732925415</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-047EPKL013053/sub-047EPKL013053_ses-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 48s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 5s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 2s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 6s</item>
      <item>32s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 11s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 6s</item>
      <item>Use initial fine affine registration. 4s</item>
      <item>Use previous fine affine registration. 58s</item>
      <item>SPM preprocessing 1 (estimate 2): 45s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 13s</item>
      <item>Update Segmentation 16s</item>
      <item>Update Skull-Stripping 32s</item>
      <item>Update probability maps 6s</item>
      <item>69s</item>
      <item>Global intensity correction: 12s</item>
      <item>SANLM denoising after intensity normalization (medium): 15s</item>
      <item>Fast Optimized Shooting registration 28s</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) 13s</item>
      <item>Estimate local tissue thresholds (WM) 16s</item>
      <item>Estimate local tissue thresholds (GM) 22s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 27s</item>
      <item>85s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</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'=0.00) 27s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 3s</item>
      <item>66s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 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 | 0.0799 0.0000 0.0799 | 32.0000</item>
      <item>2 | 2.50 | 0.0779 0.0010 0.0789 | 29.4886</item>
      <item>3 | 2.50 | 0.0773 0.0015 0.0788 | 26.9772</item>
      <item>4 | 2.50 | 0.0771 0.0016 0.0787 | 24.6107</item>
      <item>5 | 2.50 | 0.0768 0.0017 0.0786 | 22.6548</item>
      <item>6 | 2.50 | 0.0767 0.0018 0.0784 | 20.6989</item>
      <item>7 | 2.50 | 0.0765 0.0018 0.0783 | 18.9688</item>
      <item>8 | 2.50 | 0.0763 0.0019 0.0782 | 17.4455</item>
      <item>9 | 2.50 | 0.0761 0.0020 0.0780 | 15.9223</item>
      <item>10 | 2.50 | 0.0759 0.0020 0.0779 | 14.6627</item>
      <item>11 | 2.50 | 0.0757 0.0021 0.0777 | 13.4764</item>
      <item>12 | 2.50 | 0.0755 0.0021 0.0776 | 12.3015</item>
      <item>13 | 2.50 | 0.0752 0.0022 0.0774 | 11.3776</item>
      <item>14 | 2.50 | 0.0750 0.0022 0.0772 | 10.4537</item>
      <item>15 | 2.25 | 0.0745 0.0022 0.0767 | 9.5920</item>
      <item>16 | 2.25 | 0.0718 0.0036 0.0753 | 8.8725</item>
      <item>29 | 2.00 | 0.0741 0.0016 0.0757 | 3.3283</item>
      <item>30 | 2.00 | 0.0681 0.0041 0.0721 | 3.1221</item>
      <item>31 | 2.00 | 0.0661 0.0049 0.0711 | 2.9160</item>
      <item>43 | 1.75 | 0.0657 0.0028 0.0685 | 1.5785</item>
      <item>44 | 1.75 | 0.0610 0.0053 0.0663 | 1.5194</item>
      <item>45 | 1.75 | 0.0595 0.0061 0.0656 | 1.4626</item>
      <item>57 | 1.50 | 0.0584 0.0044 0.0627 | 1.0900</item>
      <item>58 | 1.50 | 0.0550 0.0066 0.0616 | 1.0730</item>
      <item>59 | 1.50 | 0.0539 0.0072 0.0611 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 160s</item>
      <item>Prepare output 9s</item>
      <item>169s</item>
      <item>Jacobian determinant (RMS): 0.008 0.027 0.046 0.076 0.106 | 0.113757</item>
      <item>Template Matching: 0.080 0.215 0.198 0.179 0.162 | 0.161707</item>
      <item>Write result maps: 19s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 23s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 44s</item>
      <item>87s</item>
      <item>Create initial surface 79s</item>
      <item>Topology correction: 96s</item>
      <item>Surface refinement: 70s</item>
      <item>Reduction of surface collisions with optimization: 78s</item>
      <item>Spherical mapping with areal smoothing 82s</item>
      <item>Spherical registration 333s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 44s</item>
      <item>92s</item>
      <item>Create initial surface 79s</item>
      <item>Topology correction: 96s</item>
      <item>Surface refinement: 86s</item>
      <item>Reduction of surface collisions with optimization: 85s</item>
      <item>Spherical mapping with areal smoothing 90s</item>
      <item>Spherical registration 296s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.7921 0.6826 mm</item>
      <item>Surface intensity / position RMSE: 0.0846 / 0.0916</item>
      <item>Euler number / defect number / defect size: 58.0 / 28.5 / 1.96%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/surf/lh.thickness.sub-047EPKL013053_ses-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/surf/rh.thickness.sub-047EPKL013053_ses-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/sub-047EPKL013053_ses-1_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1738s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 6s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 23s</item>
      <item>ROI estimation of 'lpba40' atlas 7s</item>
      <item>ROI estimation of 'hammers' atlas 17s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 6s</item>
      <item>ROI estimation of 'aal3' atlas 10s</item>
      <item>ROI estimation of 'mori' atlas 14s</item>
      <item>ROI estimation of 'anatomy3' atlas 20s</item>
      <item>ROI estimation of 'julichbrain' atlas 27s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 43s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s</item>
      <item>Write results 64s</item>
      <item>270s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/report/catreport_sub-047EPKL013053_ses-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 47 minute(s) and 6 second(s).</item>
      <item>Image Quality Rating (IQR): 83.55% (B)</item>
      <item>GM volume (GMV): 58.14% (823.59 / 1416.54 ml)</item>
      <item>GM thickness (GMT): 2.79 0.68 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_7857/ds/sub-047EPKL013053/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>