ds003949_ReproVBM/sub-203/report/cat_sub-203_ses-20110727_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-6.06266117095947</ll>
      <Affine_translation>[14.470706049268 -10.1856750522305 -27.7403553050683]</Affine_translation>
      <Affine_rotation>[0.0185238214489215 0.119980177569032 0.0817350981773108]</Affine_rotation>
      <Affine_scaling>[1.05043956044481 1.05522113182508 1.11063997470506]</Affine_scaling>
      <Affine_shearing>[0.0158022583294975 -0.00877246609751049 -0.040755031190948]</Affine_shearing>
      <Affine0_translation>[14.470706049268 -10.1856750522305 -27.7403553050683]</Affine0_translation>
      <Affine0_rotation>[0.0185238214489215 0.119980177569032 0.0817350981773108]</Affine0_rotation>
      <Affine0_scaling>[1.05043956044481 1.05522113182508 1.11063997470506]</Affine0_scaling>
      <Affine0_shearing>[0.0158022583294975 -0.00877246609751049 -0.040755031190948]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_16358/ds/sub-203</path>
      <file>sub-203_ses-20110727_T1w</file>
      <fname>/var/lib/condor/execute/dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_16358/ds/sub-203/mri/msub-203_ses-20110727_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_16358/ds/sub-203/mri/p0sub-203_ses-20110727_T1w.nii</Fp0>
      <fnames>..6358/ds/sub-203/sub-203_ses-20110727_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>106</SurfaceEulerNumber>
      <SurfaceDefectArea>3.60649455950174</SurfaceDefectArea>
      <SurfaceDefectNumber>71</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0794719755649567</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0929306745529175</SurfacePositionRMSE>
      <res_vx_vol>[3.89999890120861 0.558035695633878 0.558035700345394]</res_vx_vol>
      <res_vx_voli>[1.00000003236989 0.999999981171278 0.999999988483227]</res_vx_voli>
      <res_RMS>2.29730270171274</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[3.32200002670288 309.705749511719 594.101806640625 691.6982421875]</tissue_mn>
      <tissue_mnr>[0.00480267219245434 0.447746902704239 0.858903169631958 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[77.9048424329897 71.6008708016171 45.8950196465936 25.0698828947358]</tissue_std>
      <tissue_stdr>[0.113171882927418 0.10401414334774 0.0666714161634445 0.036418866366148]</tissue_stdr>
      <contrast>98.0674285888672</contrast>
      <contrastr>0.141777753829956</contrastr>
      <NCR>0.273671269416809</NCR>
      <ICR>0.249824792146683</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[7.79999780241723 1.11607139126776 1.11607140069079]</res_vx_vol>
      <res_RMS>4.59460540342548</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62367057800293 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>5.95666694641113</contrastr>
      <NCR>4.25970840454102</NCR>
      <ICR>1.07942652702332</ICR>
      <SurfaceEulerNumber>6.30612244897959</SurfaceEulerNumber>
      <SurfaceDefectArea>1.90162363987543</SurfaceDefectArea>
      <SurfaceDefectNumber>4.55</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.58943951129913</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.85861349105835</SurfacePositionRMSE>
      <IQR>4.44902146567926</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>20220712-161537</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>106</SurfaceEulerNumber>
         <SurfaceDefectArea>3.60649455950174</SurfaceDefectArea>
         <SurfaceDefectNumber>71</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0794719755649567</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0929306745529175</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>106</EC_abs>
      <defect_size>3.60649455950174</defect_size>
      <vol_abs_CGW>[294.825737851745 589.680785507471 553.056001119603 0 0]</vol_abs_CGW>
      <vol_abs_WMH>7.92635295722253</vol_abs_WMH>
      <vol_rel_WMH>0.00551374484396509</vol_rel_WMH>
      <surf_TSA>1936.7075209479</surf_TSA>
      <vol_TIV>1437.56252447882</vol_TIV>
      <vol_rel_CGW>[0.205087245132961 0.410194878807972 0.384717876059068 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.09139395819703 0.599688824167521]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.07148742675781 0.622486402520543 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.49836359849569 0.237263426308898 0.304634962353083;2.09226982844834 0.170540850077723 0.425366579728996;2.71987836226287 0.23643409355893 0.269998457917921]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.743326342563288 0.174962308233932 0.501160631383473;3.55267497741364 0.332313716658664 0.498839368616527]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.03354172243525</vol_TIV>
      <vol_rel_CGW>[1.53317609793392 5.21686204755697 4.75930093496889 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.55137448439651</vol_rel_WMH>
      <surf_TSA>8.61757448437664</surf_TSA>
      <SQR>4.48039122563683</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.287151816083576 1 1 5701.39125041319 0.369249139973777]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00433571683242917 0.0022030770778656 0.461840003728867]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[688.685409237307 573.681961945672 496.727502966356 752.466319170347 1405.9370616697 4740.7487272442]</SPMvols0>
      <SPMvols1>[541.521761880567 513.151397117252 326.605361445491 708.300287708388 1012.51804518699 4854.20602159153]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[374.393005371094 568.930297851562 654.214599609375]</T3th>
            <Tth>
               <T3th>[-201.380920410156 162.401245117188 21.2246017456055 374.393005371094 568.930297851562 654.214599609375 794.125366210938 1732.06762695312]</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>[0.0243368912488222 0.101050175726414 0.113535411655903 0 0]</dtc>
         <ll>[0.0933746362314457 0 0.0933746362314457 0;0.206052709169605 0.0152146613039747 0.22126737047358 3244.49609375;0.206052709169605 0.0152146613039747 0.22126737047358 3244.49609375]</ll>
         <rmsdtc>[0.051864568144083 0.128773510456085 0.144160717725754]</rmsdtc>
         <rmsgdt>[0.0367755182087421 0.0630597397685051 0.0775596424937248]</rmsgdt>
         <rmsdt>0.144160717725754</rmsdt>
         <dt>0.113535411655903</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>[0.0116812381893396 0.0574752241373062 0.0692990347743034 0.0798667967319489 0.0874810814857483 0.0999135002493858]</dtc>
         <ll>[0.092120013442978 0 0.092120013442978 0;0.224018528693529 0.0222697496947497 0.246288278388278 11399.328125;0.208987566380719 0.0227845478469165 0.231772114227635 16398.3125;0.187148584146672 0.0233197588073788 0.210468342954051 25145.04296875;0.170990092479905 0.0260624727220578 0.197052565201963 45592.46484375;0.170990092479905 0.0260624727220578 0.197052565201963 45592.46484375]</ll>
         <rmsdtc>[0.013421569019556 0.0518482178449631 0.0843635573983192 0.111207388341427 0.139183640480042 0.147830277681351]</rmsdtc>
         <rmsgdt>[0.00395473185926676 0.0160288512706757 0.0350086614489555 0.0591383650898933 0.0823578462004662 0.089386448264122]</rmsgdt>
         <rmsdt>0.147830277681351</rmsdt>
         <dt>0.0999135002493858</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 26s</item>
      <item>Internal resampling (3.90x0.56x0.56mm &gt; 1.00x1.00x1.00mm): 1s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 4s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 2s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 4s</item>
      <item>31s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 66s</item>
      <item>SPM preprocessing 1 (estimate 2): 67s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 12s</item>
      <item>Update Segmentation 16s</item>
      <item>Update Skull-Stripping 30s</item>
      <item>Update probability maps 11s</item>
      <item>70s</item>
      <item>Global intensity correction: 11s</item>
      <item>SANLM denoising after intensity normalization (medium): 12s</item>
      <item>Fast Optimized Shooting registration 27s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 1s</item>
      <item>Prepare segments (LASmod = 1.63) 12s</item>
      <item>Estimate local tissue thresholds (WM) 11s</item>
      <item>Estimate local tissue thresholds (GM) 13s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 21s</item>
      <item>64s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 10s</item>
      <item>Blood vessel detection 8s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.23) 20s</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>54s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.97 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>9s</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 | 0.0921 0.0000 0.0921 | 32.0000</item>
      <item>2 | 2.50 | 0.0883 0.0015 0.0898 | 29.4886</item>
      <item>3 | 2.50 | 0.0871 0.0024 0.0895 | 26.9772</item>
      <item>4 | 2.50 | 0.0865 0.0027 0.0892 | 24.6107</item>
      <item>5 | 2.50 | 0.0860 0.0029 0.0890 | 22.6548</item>
      <item>6 | 2.50 | 0.0856 0.0031 0.0887 | 20.6989</item>
      <item>7 | 2.50 | 0.0852 0.0032 0.0884 | 18.9688</item>
      <item>8 | 2.50 | 0.0848 0.0034 0.0881 | 17.4455</item>
      <item>9 | 2.50 | 0.0843 0.0035 0.0878 | 15.9223</item>
      <item>10 | 2.50 | 0.0838 0.0036 0.0875 | 14.6627</item>
      <item>11 | 2.50 | 0.0834 0.0038 0.0871 | 13.4764</item>
      <item>12 | 2.50 | 0.0829 0.0039 0.0868 | 12.3015</item>
      <item>13 | 2.50 | 0.0824 0.0040 0.0864 | 11.3776</item>
      <item>14 | 2.50 | 0.0819 0.0041 0.0860 | 10.4537</item>
      <item>15 | 2.25 | 0.0832 0.0043 0.0875 | 9.5920</item>
      <item>16 | 2.25 | 0.0794 0.0062 0.0856 | 8.8725</item>
      <item>17 | 2.25 | 0.0778 0.0069 0.0847 | 8.1530</item>
      <item>18 | 2.25 | 0.0768 0.0072 0.0840 | 7.5234</item>
      <item>19 | 2.25 | 0.0760 0.0074 0.0834 | 6.9630</item>
      <item>20 | 2.25 | 0.0753 0.0074 0.0827 | 6.4027</item>
      <item>21 | 2.25 | 0.0747 0.0074 0.0821 | 5.9447</item>
      <item>29 | 2.00 | 0.0765 0.0044 0.0809 | 3.3283</item>
      <item>30 | 2.00 | 0.0715 0.0067 0.0783 | 3.1221</item>
      <item>31 | 2.00 | 0.0697 0.0076 0.0773 | 2.9160</item>
      <item>43 | 1.75 | 0.0687 0.0043 0.0730 | 1.5785</item>
      <item>44 | 1.75 | 0.0639 0.0069 0.0708 | 1.5194</item>
      <item>45 | 1.75 | 0.0624 0.0078 0.0702 | 1.4626</item>
      <item>57 | 1.50 | 0.0615 0.0057 0.0672 | 1.0900</item>
      <item>58 | 1.50 | 0.0581 0.0080 0.0661 | 1.0730</item>
      <item>59 | 1.50 | 0.0570 0.0087 0.0657 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 171s</item>
      <item>Prepare output 9s</item>
      <item>180s</item>
      <item>Jacobian determinant (RMS): 0.013 0.052 0.084 0.111 0.139 | 0.147830</item>
      <item>Template Matching: 0.092 0.224 0.209 0.187 0.171 | 0.170990</item>
      <item>Write result maps: 52s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 27s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 40s</item>
      <item>87s</item>
      <item>Create initial surface 89s</item>
      <item>Topology correction: 98s</item>
      <item>Surface refinement: 97s</item>
      <item>Reduction of surface collisions with optimization: 62s</item>
      <item>Spherical mapping with areal smoothing 77s</item>
      <item>Spherical registration 300s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 30s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 38s</item>
      <item>87s</item>
      <item>Create initial surface 84s</item>
      <item>Topology correction: 95s</item>
      <item>Surface refinement: 83s</item>
      <item>Reduction of surface collisions with optimization: 61s</item>
      <item>Spherical mapping with areal smoothing 75s</item>
      <item>Spherical registration 309s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.0914 0.5996 mm</item>
      <item>Surface intensity / position RMSE: 0.0795 / 0.0929</item>
      <item>Euler number / defect number / defect size: 106.0 / 71.0 / 3.61%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_16358/ds/sub-203/surf/lh.thickness.sub-203_ses-20110727_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_16358/ds/sub-203/surf/rh.thickness.sub-203_ses-20110727_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_16358/ds/sub-203/sub-203_ses-20110727_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1690s</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 6s</item>
      <item>ROI estimation of 'hammers' atlas 15s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 5s</item>
      <item>ROI estimation of 'aal3' atlas 10s</item>
      <item>ROI estimation of 'mori' atlas 13s</item>
      <item>ROI estimation of 'anatomy3' atlas 18s</item>
      <item>ROI estimation of 'julichbrain' atlas 23s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 36s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 53s</item>
      <item>Write results 54s</item>
      <item>238s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_16358/ds/sub-203/report/catreport_sub-203_ses-20110727_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 45 minute(s) and 19 second(s).</item>
      <item>Image Quality Rating (IQR): 60.51% (D-)</item>
      <item>GM volume (GMV): 41.02% (589.68 / 1437.56 ml)</item>
      <item>GM thickness (GMT): 2.09 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_16358/ds/sub-203/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>