ds003717_ReproVBM/sub-11/report/cat_sub-11_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.05476052098478 -0.026939272335709 0.0452552784627009 3.03704705404191;0.0120842268874307 0.981478276170468 0.275511594687962 -28.3142538618846;-0.0470254213555545 -0.276328129291974 1.10969402512035 -2.59272696276285;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>-6.41304302215576</ll>
      <Affine_translation>[3.03704705404191 -28.3142538618846 -2.59272696276285]</Affine_translation>
      <Affine_rotation>[0.27548992988008 0.0397653625675518 -0.0231300651533335]</Affine_rotation>
      <Affine_scaling>[1.05587744337173 1.01998588259459 1.1436896572749]</Affine_scaling>
      <Affine_shearing>[-0.00319284322575079 -0.00100549497539489 -0.0360003741577881]</Affine_shearing>
      <Affine0_translation>[3.03704705404191 -28.3142538618846 -2.59272696276285]</Affine0_translation>
      <Affine0_rotation>[0.27548992988008 0.0397653625675518 -0.0231300651533335]</Affine0_rotation>
      <Affine0_scaling>[1.05587744337173 1.01998588259459 1.1436896572749]</Affine0_scaling>
      <Affine0_shearing>[-0.00319284322575079 -0.00100549497539489 -0.0360003741577881]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_28867/ds/sub-11</path>
      <file>sub-11_T1w</file>
      <fname>/var/lib/condor/execute/dir_28867/ds/sub-11/sub-11_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_28867/ds/sub-11/sub-11_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_28867/ds/sub-11/mri/msub-11_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_28867/ds/sub-11/mri/p0sub-11_T1w.nii</Fp0>
      <fnames>..28867/ds/sub-11/sub-11_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>26</SurfaceEulerNumber>
      <SurfaceDefectArea>1.21818871231332</SurfaceDefectArea>
      <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0720400512218475</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0796118229627609</SurfacePositionRMSE>
      <res_vx_vol>[0.800000005424959 0.800000001072016 0.799999919481871]</res_vx_vol>
      <res_vx_voli>[0.800000005424959 0.800000001072016 0.79999991965539]</res_vx_voli>
      <res_RMS>0.799999975326283</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[22.5935001373291 274.638000488281 720.4189453125 967.244384765625]</tissue_mn>
      <tissue_mnr>[0.0233586262911558 0.283938586711884 0.744815826416016 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[25.6025249825435 125.566538945641 82.2564787797203 43.8523508047399]</tissue_std>
      <tissue_stdr>[0.0271026324480772 0.132923752069473 0.0870760604739189 0.046421755105257]</tissue_stdr>
      <contrast>252.728851318359</contrast>
      <contrastr>0.261287480592728</contrastr>
      <NCR>0.107243925333023</NCR>
      <ICR>0.117022939026356</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.60000001084992 1.60000000214403 1.59999983896374]</res_vx_vol>
      <res_RMS>1.59999995065257</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>4.16402101516724</contrastr>
      <NCR>1.87057030200958</NCR>
      <ICR>0.750056862831116</ICR>
      <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
      <SurfaceDefectArea>1.30454717807833</SurfaceDefectArea>
      <SurfaceDefectNumber>1.725</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.44080102443695</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.59223651885986</SurfacePositionRMSE>
      <IQR>1.77020149087675</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>20220709-214348</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>26</SurfaceEulerNumber>
         <SurfaceDefectArea>1.21818871231332</SurfaceDefectArea>
         <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0720400512218475</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0796118229627609</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>26</EC_abs>
      <defect_size>1.21818871231332</defect_size>
      <vol_abs_CGW>[216.829885804138 701.379808385355 508.96019496321 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.06138594123962</vol_abs_WMH>
      <vol_rel_WMH>0.000743699786063843</vol_rel_WMH>
      <surf_TSA>1906.31388836615</surf_TSA>
      <vol_TIV>1427.1698891527</vol_TIV>
      <vol_rel_CGW>[0.151929975157245 0.491448014504957 0.356622010337798 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.54121430918905 0.641110794730386]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.55545592308044 0.809745302977824 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.89937184098849 0.272057805052548 0.269049355073913;2.56042430118557 0.185480616067312 0.44420211770627;3.24707432929642 0.285478689864916 0.286748527219817]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.747109984087612 0.337447269134421 0.631519274376417;4.17387836563004 0.313686921881075 0.368480725623583]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.01756741275195</vol_TIV>
      <vol_rel_CGW>[0.578483749232126 6.67614968579305 4.2547056454346 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.07436997860638</vol_rel_WMH>
      <surf_TSA>8.61419753168083</surf_TSA>
      <SQR>5.47787708577426</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.0999482171474359 24 13164 9201.78295659167 0.297527896959429]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0281931050121784 0.028827328234911 0.161093354225159]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[826.647800963099 463.813691585565 347.49533369541 906.984954582506 1614.55183263987 6672.23866678666]</SPMvols0>
      <SPMvols1>[729.852551419793 437.99079125554 224.680172263795 712.904830945014 1266.39200131168 6851.82523229538]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[346.828704833984 722.169494628906 956.388793945312]</T3th>
            <Tth>
               <T3th>[0 0 28.7483062744141 346.828704833984 722.169494628906 956.388793945312 1261.16882324219 1965.501953125]</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>[0.0230044107884169 0.0861941054463387 0.095802441239357 0 0]</dtc>
         <ll>[0.0849011113234356 0 0.0849011113234356 0;0.190650051524516 0.0116319244219905 0.202281975946507 2480.48461914062;0.190650051524516 0.0116319244219905 0.202281975946507 2480.48461914062]</ll>
         <rmsdtc>[0.0478631258010864 0.111823089420795 0.122901745140553]</rmsdtc>
         <rmsgdt>[0.03351741284132 0.0458961948752403 0.0558279231190681]</rmsgdt>
         <rmsdt>0.122901745140553</rmsdt>
         <dt>0.095802441239357</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>[0.011398496106267 0.0436748974025249 0.0625154003500938 0.0710141733288765 0.0768601819872856 0.0872276276350021]</dtc>
         <ll>[0.0849521490087785 0 0.0849521490087785 0;0.218192277167277 0.0163725026709402 0.234564779838217 8380.6748046875;0.193522265677104 0.0186816697164977 0.212203935393602 13445.421875;0.17245439926104 0.0200837942270132 0.192538193488053 21655.79296875;0.15513732076945 0.023008971031004 0.178146291800454 40250.8125;0.15513732076945 0.023008971031004 0.178146291800454 40250.8125]</ll>
         <rmsdtc>[0.0133370803669095 0.0501371510326862 0.0742167383432388 0.101011462509632 0.12559375166893 0.132038787007332]</rmsdtc>
         <rmsgdt>[0.0035774321295321 0.0139642283320427 0.029654486104846 0.0509581789374352 0.0750702694058418 0.0761801302433014]</rmsgdt>
         <rmsdt>0.132038787007332</rmsdt>
         <dt>0.0872276276350021</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_28867/ds/sub-11/sub-11_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 192s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 11s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 10s</item>
      <item>Refine background 5s</item>
      <item>Final correction 9s</item>
      <item>Final scaling 11s</item>
      <item>66s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 129s</item>
      <item>SPM preprocessing 1 (estimate 2): 75s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 30s</item>
      <item>Update Segmentation 33s</item>
      <item>Update Skull-Stripping 70s</item>
      <item>Update probability maps 14s</item>
      <item>147s</item>
      <item>Global intensity correction: 28s</item>
      <item>SANLM denoising after intensity normalization (medium): 40s</item>
      <item>Fast Optimized Shooting registration 40s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 8s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 27s</item>
      <item>Estimate local tissue thresholds (WM) 31s</item>
      <item>Estimate local tissue thresholds (GM) 44s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 64s</item>
      <item>184s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 13s</item>
      <item>Major structures 6s</item>
      <item>Ventricle detection 26s</item>
      <item>Blood vessel detection 18s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.03) 56s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 3s</item>
      <item>Side alignment 7s</item>
      <item>Final corrections 7s</item>
      <item>137s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 54s</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) 7s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
      <item>19s</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 | 0.0850 0.0000 0.0850 | 32.0000</item>
      <item>2 | 2.50 | 0.0816 0.0014 0.0830 | 29.4886</item>
      <item>3 | 2.50 | 0.0806 0.0021 0.0828 | 26.9772</item>
      <item>4 | 2.50 | 0.0802 0.0024 0.0826 | 24.6107</item>
      <item>5 | 2.50 | 0.0798 0.0026 0.0824 | 22.6548</item>
      <item>6 | 2.50 | 0.0794 0.0027 0.0821 | 20.6989</item>
      <item>7 | 2.50 | 0.0791 0.0028 0.0819 | 18.9688</item>
      <item>8 | 2.50 | 0.0787 0.0030 0.0817 | 17.4455</item>
      <item>9 | 2.50 | 0.0783 0.0031 0.0814 | 15.9223</item>
      <item>10 | 2.50 | 0.0779 0.0032 0.0811 | 14.6627</item>
      <item>11 | 2.50 | 0.0775 0.0033 0.0808 | 13.4764</item>
      <item>12 | 2.50 | 0.0771 0.0034 0.0805 | 12.3015</item>
      <item>13 | 2.50 | 0.0766 0.0036 0.0802 | 11.3776</item>
      <item>14 | 2.50 | 0.0762 0.0036 0.0799 | 10.4537</item>
      <item>15 | 2.25 | 0.0761 0.0038 0.0799 | 9.5920</item>
      <item>16 | 2.25 | 0.0727 0.0055 0.0782 | 8.8725</item>
      <item>29 | 2.00 | 0.0735 0.0025 0.0760 | 3.3283</item>
      <item>30 | 2.00 | 0.0669 0.0051 0.0720 | 3.1221</item>
      <item>31 | 2.00 | 0.0645 0.0062 0.0707 | 2.9160</item>
      <item>43 | 1.75 | 0.0634 0.0036 0.0670 | 1.5785</item>
      <item>44 | 1.75 | 0.0590 0.0059 0.0649 | 1.5194</item>
      <item>45 | 1.75 | 0.0575 0.0067 0.0642 | 1.4626</item>
      <item>57 | 1.50 | 0.0560 0.0049 0.0610 | 1.0900</item>
      <item>58 | 1.50 | 0.0528 0.0070 0.0598 | 1.0730</item>
      <item>59 | 1.50 | 0.0517 0.0077 0.0594 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 155s</item>
      <item>Prepare output 15s</item>
      <item>170s</item>
      <item>Jacobian determinant (RMS): 0.013 0.050 0.074 0.101 0.126 | 0.132039</item>
      <item>Template Matching: 0.085 0.218 0.194 0.172 0.155 | 0.155137</item>
      <item>Write result maps: 38s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 33s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 42s</item>
      <item>95s</item>
      <item>Create initial surface 70s</item>
      <item>Topology correction: 87s</item>
      <item>Surface refinement: 74s</item>
      <item>Reduction of surface collisions with optimization: 68s</item>
      <item>Spherical mapping with areal smoothing 77s</item>
      <item>Spherical registration 275s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 42s</item>
      <item>95s</item>
      <item>Create initial surface 71s</item>
      <item>Topology correction: 90s</item>
      <item>Surface refinement: 75s</item>
      <item>Reduction of surface collisions with optimization: 62s</item>
      <item>Spherical mapping with areal smoothing 74s</item>
      <item>Spherical registration 298s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5411 0.6410 mm</item>
      <item>Surface intensity / position RMSE: 0.0720 / 0.0796</item>
      <item>Euler number / defect number / defect size: 26.0 / 14.5 / 1.22%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28867/ds/sub-11/surf/lh.thickness.sub-11_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28867/ds/sub-11/surf/rh.thickness.sub-11_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_28867/ds/sub-11/sub-11_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1620s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 13s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 47s</item>
      <item>ROI estimation of 'lpba40' atlas 14s</item>
      <item>ROI estimation of 'hammers' atlas 33s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 12s</item>
      <item>ROI estimation of 'aal3' atlas 20s</item>
      <item>ROI estimation of 'mori' atlas 31s</item>
      <item>ROI estimation of 'anatomy3' atlas 44s</item>
      <item>ROI estimation of 'julichbrain' atlas 59s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 41s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 96s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 148s</item>
      <item>Write results 148s</item>
      <item>585s</item>
      <item>Quality check: 9s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_28867/ds/sub-11/report/catreport_sub-11_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 61 minute(s) and 31 second(s).</item>
      <item>Image Quality Rating (IQR): 87.30% (B+)</item>
      <item>GM volume (GMV): 49.14% (701.38 / 1427.17 ml)</item>
      <item>GM thickness (GMT): 2.54 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_28867/ds/sub-11/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_28867/ds/sub-11/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_28867/ds/sub-11/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>