ds003085_ReproVBM/sub-40/report/cat_sub-40_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine>[1.09640284108113 -0.0255326603462177 0.00803577044316552 3.69242037884124;0.0339685786230695 1.00751239719884 0.188661353949681 -17.4827641985075;-0.00969781866476068 -0.172146633248343 1.15712594752022 0.543306847136043;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-5.0492730140686</ll>
      <Affine_translation>[3.69242037884124 -17.4827641985075 0.543306847136043]</Affine_translation>
      <Affine_rotation>[0.169316217691462 0.00349792604911415 -0.0320181434146417]</Affine_rotation>
      <Affine_scaling>[1.09697178721756 1.02240684580461 1.17239125761204]</Affine_scaling>
      <Affine_shearing>[0.00656429849226049 0.00332190268386772 -0.0089428460211007]</Affine_shearing>
      <Affine0_translation>[3.69242037884124 -17.4827641985075 0.543306847136043]</Affine0_translation>
      <Affine0_rotation>[0.169316217691462 0.00349792604911415 -0.0320181434146417]</Affine0_rotation>
      <Affine0_scaling>[1.09697178721756 1.02240684580461 1.17239125761204]</Affine0_scaling>
      <Affine0_shearing>[0.00656429849226049 0.00332190268386772 -0.0089428460211007]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_4348/ds/sub-40</path>
      <file>sub-40_T1w</file>
      <fname>/var/lib/condor/execute/dir_4348/ds/sub-40/sub-40_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_4348/ds/sub-40/sub-40_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_4348/ds/sub-40/mri/msub-40_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_4348/ds/sub-40/mri/p0sub-40_T1w.nii</Fp0>
      <fnames>.._4348/ds/sub-40/sub-40_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>30</SurfaceEulerNumber>
      <SurfaceDefectArea>0.811185681117915</SurfaceDefectArea>
      <SurfaceDefectNumber>18</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0696141123771667</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0712136924266815</SurfacePositionRMSE>
      <res_vx_vol>[0.999998357974219 1.00000000556953 0.999999960378065]</res_vx_vol>
      <res_vx_voli>[0.999998356555231 1.00000000689052 0.999999961116397]</res_vx_voli>
      <res_RMS>0.999999441307564</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[1.40199995040894 93.6178894042969 214.237503051758 287.237030029297]</tissue_mn>
      <tissue_mnr>[0.00488098617643118 0.325925558805466 0.745856106281281 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[10.3910142364059 36.4179794243174 24.4330101350733 12.893149211794]</tissue_std>
      <tissue_stdr>[0.0363531894981861 0.127409085631371 0.0854794159531593 0.0451069623231888]</tissue_stdr>
      <contrast>73.3575897216797</contrast>
      <contrastr>0.25539043545723</contrastr>
      <NCR>0.141640365123749</NCR>
      <ICR>0.217432573437691</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.99999671594844 2.00000001113905 1.99999992075613]</res_vx_vol>
      <res_RMS>1.99999888261513</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[6.51440286636353 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>4.25247669219971</contrastr>
      <NCR>2.36434626579285</NCR>
      <ICR>0.999088704586029</ICR>
      <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
      <SurfaceDefectArea>1.20279642027948</SurfaceDefectArea>
      <SurfaceDefectNumber>1.9</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.39228224754333</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.42427384853363</SurfacePositionRMSE>
      <IQR>2.23213876640028</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>20220711-085046</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>30</SurfaceEulerNumber>
         <SurfaceDefectArea>0.811185681117915</SurfaceDefectArea>
         <SurfaceDefectNumber>18</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0696141123771667</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0712136924266815</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>30</EC_abs>
      <defect_size>0.811185681117915</defect_size>
      <vol_abs_CGW>[179.762447838304 671.331988948618 506.352371244521 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.579591185792139</vol_abs_WMH>
      <vol_rel_WMH>0.000426971563351832</vol_rel_WMH>
      <surf_TSA>1924.9282704135</surf_TSA>
      <vol_TIV>1357.44680803144</vol_TIV>
      <vol_rel_CGW>[0.132426881683116 0.494554913663378 0.373018204653506 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.46514704047442 0.60452007521017]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.47120523452759 0.6745118364561 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.83433004091322 0.235773905356519 0.275206696188599;2.46833298283279 0.172658445680206 0.437664781017227;3.09143867418117 0.247595273095645 0.287128522794174]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.927324127117809 0.29354442529599 0.501276906238599;3.98893615461739 0.349937263225907 0.498723093761401]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.04301986166895</vol_TIV>
      <vol_rel_CGW>[0.5 6.73194888044859 4.54917752610463 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04269715633518</vol_rel_WMH>
      <surf_TSA>8.61642005518408</surf_TSA>
      <SQR>5.53452457811318</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.393122586337003 513 6 6124.92673412702 0.282284437157756]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00441252673044801 0 0.37595722079277]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[818.755690968569 450.444660993 266.980533082131 479.707227651582 2973.8860291953 5631.26455730758]</SPMvols0>
      <SPMvols1>[714.035784067612 418.936329469613 167.149814068062 1434.77638827425 2587.19970451625 4770.47405833446]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[114.366203308105 217.245300292969 277.414794921875]</T3th>
            <Tth>
               <T3th>[0 41.0002593994141 4.53242206573486 114.366203308105 217.245300292969 277.414794921875 358.939086914062 591.232666015625]</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>[0.0214090012013912 0.0758746191859245 0.0834368094801903 0 0]</dtc>
         <ll>[0.0813174757207571 0 0.0813174757207571 0;0.189809224471038 0.00997406866799454 0.199783293139033 2126.9501953125;0.189809224471038 0.00997406866799454 0.199783293139033 2126.9501953125]</ll>
         <rmsdtc>[0.0445604026317596 0.0982838794589043 0.108102455735207]</rmsdtc>
         <rmsgdt>[0.0313649959862232 0.0416485257446766 0.0506135635077953]</rmsgdt>
         <rmsdt>0.108102455735207</rmsdt>
         <dt>0.0834368094801903</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>[0.00991968996822834 0.0366826914250851 0.0515639670193195 0.0589436106383801 0.0646635293960571 0.0724878162145615]</dtc>
         <ll>[0.0817387200555287 0 0.0817387200555287 0;0.216521352258852 0.0133599196810134 0.229881271939866 6838.60888671875;0.196376402123349 0.0162758299934557 0.212652232116805 11713.91015625;0.176725121305199 0.0181680409430552 0.194893162248255 19590.08984375;0.160264877214604 0.0210914116354732 0.181356288850078 36896.32421875;0.160264877214604 0.0210914116354732 0.181356288850078 36896.32421875]</ll>
         <rmsdtc>[0.0116115529090166 0.0424637869000435 0.0626709833741188 0.0858538895845413 0.106974646449089 0.113944135606289]</rmsdtc>
         <rmsgdt>[0.00329216476529837 0.0126347607001662 0.0276019796729088 0.0479192212224007 0.0650925859808922 0.0704175978899002]</rmsgdt>
         <rmsdt>0.113944135606289</rmsdt>
         <dt>0.0724878162145615</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_4348/ds/sub-40/sub-40_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 23s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 6s</item>
      <item>Refine background 3s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 5s</item>
      <item>36s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 9s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 70s</item>
      <item>SPM preprocessing 1 (estimate 2): 56s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 14s</item>
      <item>Update Segmentation 16s</item>
      <item>Update Skull-Stripping 36s</item>
      <item>Update probability maps 7s</item>
      <item>73s</item>
      <item>Global intensity correction: 13s</item>
      <item>SANLM denoising after intensity normalization (medium): 7s</item>
      <item>Fast Optimized Shooting registration 29s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 12s</item>
      <item>Estimate local tissue thresholds (WM) 15s</item>
      <item>Estimate local tissue thresholds (GM) 21s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 24s</item>
      <item>81s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 15s</item>
      <item>Blood vessel detection 8s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 24s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>66s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0817 0.0000 0.0817 | 32.0000</item>
      <item>2 | 2.50 | 0.0793 0.0011 0.0804 | 29.4886</item>
      <item>3 | 2.50 | 0.0786 0.0017 0.0803 | 26.9772</item>
      <item>4 | 2.50 | 0.0782 0.0019 0.0801 | 24.6107</item>
      <item>5 | 2.50 | 0.0779 0.0021 0.0800 | 22.6548</item>
      <item>6 | 2.50 | 0.0777 0.0022 0.0798 | 20.6989</item>
      <item>7 | 2.50 | 0.0774 0.0023 0.0797 | 18.9688</item>
      <item>8 | 2.50 | 0.0771 0.0024 0.0795 | 17.4455</item>
      <item>9 | 2.50 | 0.0768 0.0024 0.0793 | 15.9223</item>
      <item>10 | 2.50 | 0.0765 0.0026 0.0791 | 14.6627</item>
      <item>11 | 2.50 | 0.0762 0.0026 0.0789 | 13.4764</item>
      <item>12 | 2.50 | 0.0759 0.0027 0.0786 | 12.3015</item>
      <item>13 | 2.50 | 0.0756 0.0028 0.0784 | 11.3776</item>
      <item>14 | 2.50 | 0.0753 0.0029 0.0782 | 10.4537</item>
      <item>15 | 2.25 | 0.0752 0.0030 0.0781 | 9.5920</item>
      <item>16 | 2.25 | 0.0722 0.0045 0.0766 | 8.8725</item>
      <item>29 | 2.00 | 0.0737 0.0020 0.0758 | 3.3283</item>
      <item>30 | 2.00 | 0.0677 0.0044 0.0721 | 3.1221</item>
      <item>31 | 2.00 | 0.0655 0.0054 0.0709 | 2.9160</item>
      <item>43 | 1.75 | 0.0645 0.0032 0.0677 | 1.5785</item>
      <item>44 | 1.75 | 0.0604 0.0053 0.0657 | 1.5194</item>
      <item>45 | 1.75 | 0.0589 0.0061 0.0650 | 1.4626</item>
      <item>57 | 1.50 | 0.0576 0.0045 0.0620 | 1.0900</item>
      <item>58 | 1.50 | 0.0545 0.0064 0.0609 | 1.0730</item>
      <item>59 | 1.50 | 0.0534 0.0070 0.0605 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 162s</item>
      <item>Prepare output 9s</item>
      <item>172s</item>
      <item>Jacobian determinant (RMS): 0.012 0.042 0.063 0.086 0.107 | 0.113944</item>
      <item>Template Matching: 0.082 0.217 0.196 0.177 0.160 | 0.160265</item>
      <item>Write result maps: 21s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 25s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 42s</item>
      <item>87s</item>
      <item>Create initial surface 82s</item>
      <item>Topology correction: 90s</item>
      <item>Surface refinement: 69s</item>
      <item>Reduction of surface collisions with optimization: 65s</item>
      <item>Spherical mapping with areal smoothing 80s</item>
      <item>Spherical registration 294s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 41s</item>
      <item>88s</item>
      <item>Create initial surface 79s</item>
      <item>Topology correction: 93s</item>
      <item>Surface refinement: 87s</item>
      <item>Reduction of surface collisions with optimization: 67s</item>
      <item>Spherical mapping with areal smoothing 79s</item>
      <item>Spherical registration 304s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4651 0.6043 mm</item>
      <item>Surface intensity / position RMSE: 0.0696 / 0.0712</item>
      <item>Euler number / defect number / defect size: 30.0 / 18.0 / 0.81%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_4348/ds/sub-40/surf/lh.thickness.sub-40_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_4348/ds/sub-40/surf/rh.thickness.sub-40_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4348/ds/sub-40/sub-40_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1652s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
      <item>ROI estimation of 'lpba40' atlas 7s</item>
      <item>ROI estimation of 'hammers' atlas 18s</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 15s</item>
      <item>ROI estimation of 'anatomy3' atlas 22s</item>
      <item>ROI estimation of 'julichbrain' atlas 28s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s</item>
      <item>Write results 79s</item>
      <item>299s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_4348/ds/sub-40/report/catreport_sub-40_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 46 minute(s) and 36 second(s).</item>
      <item>Image Quality Rating (IQR): 82.68% (B-)</item>
      <item>GM volume (GMV): 49.46% (671.33 / 1357.45 ml)</item>
      <item>GM thickness (GMT): 2.47 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>