ds003721_ReproVBM/sub-28/report/cat_sub-28_acq-highres_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_rotation>[0.192091395299883 0.0239368914240581 -0.0250330916625503]</Affine_rotation>
      <Affine_scaling>[1.05533619625395 1.01051937190967 1.11897077330357]</Affine_scaling>
      <Affine_shearing>[0.00738569827323863 -0.00343189769114083 -0.00247149047889503]</Affine_shearing>
      <Affine0_translation>[-0.480123489467034 -24.960276320129 -2.86940992912766]</Affine0_translation>
      <Affine0_rotation>[0.192091395299883 0.0239368914240581 -0.0250330916625503]</Affine0_rotation>
      <Affine0_scaling>[1.05533619625395 1.01051937190967 1.11897077330357]</Affine0_scaling>
      <Affine0_shearing>[0.00738569827323863 -0.00343189769114083 -0.00247149047889503]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_13284/ds/sub-28</path>
      <file>sub-28_acq-highres_T1w</file>
      <fname>/var/lib/condor/execute/dir_13284/ds/sub-28/sub-28_acq-highres_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_13284/ds/sub-28/sub-28_acq-highres_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_13284/ds/sub-28/mri/msub-28_acq-highres_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_13284/ds/sub-28/mri/p0sub-28_acq-highres_T1w.nii</Fp0>
      <fnames>..13284/ds/sub-28/sub-28_acq-highres_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>
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   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>6</SurfaceEulerNumber>
      <SurfaceDefectArea>0.221392643535183</SurfaceDefectArea>
      <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0602023601531982</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.058834470808506</SurfacePositionRMSE>
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      <res_vx_voli>[0.99999997585094 1.0000000338103 0.999999648177134]</res_vx_voli>
      <res_RMS>0.999999887011151</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[1.25600004196167 62.7411766052246 144.536987304688 200.625015258789]</tissue_mn>
      <tissue_mnr>[0.00626043556258082 0.312728583812714 0.720433473587036 0.999999940395355]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.00825054571032524 0.107920154929161 0.0913805961608887 0.0496277287602425]</tissue_stdr>
      <contrast>56.4413757324219</contrast>
      <contrastr>0.281327694654465</contrastr>
      <NCR>0.131221175193787</NCR>
      <ICR>0.22987799346447</ICR>
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   <qualityratings>
      <res_vx_vol>[1.9999999531765 2.00000007102351 1.99999929786681]</res_vx_vol>
      <res_RMS>1.9999997740223</res_RMS>
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      <tissue_mn>[5.69818496704102 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.62399999999916 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>3.86341786384583</contrastr>
      <NCR>2.2147741317749</NCR>
      <ICR>1.02995538711548</ICR>
      <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
      <SurfaceDefectArea>1.0553481608838</SurfaceDefectArea>
      <SurfaceDefectNumber>1.375</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.20404720306396</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.1766893863678</SurfacePositionRMSE>
      <IQR>2.12607370271359</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>20220712-143108</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>6</SurfaceEulerNumber>
         <SurfaceDefectArea>0.221392643535183</SurfaceDefectArea>
         <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0602023601531982</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.058834470808506</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>6</EC_abs>
      <defect_size>0.221392643535183</defect_size>
      <vol_abs_CGW>[280.37629622282 690.657779369603 592.584930573439 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.50870536613168</vol_abs_WMH>
      <vol_rel_WMH>0.000964880421753867</vol_rel_WMH>
      <surf_TSA>2117.34117807776</surf_TSA>
      <vol_TIV>1563.61900616586</vol_TIV>
      <vol_rel_CGW>[0.179312412497676 0.441704645854337 0.378982941647986 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.38124976196562 0.598659312563378]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.37459707260132 0.693248463096613 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.77568754034246 0.246140824191089 0.295265854089383;2.38517917902301 0.170422862009475 0.42501324854266;2.99785732422918 0.250311480865571 0.279720897367956]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.890950618469424 0.265381343614493 0.489759134851712;3.96020364902995 0.385823733548567 0.510240865148288]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.61187192914189</vol_TIV>
      <vol_rel_CGW>[1.0702660290531 5.78277022008508 4.65630283132159 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.09648804217539</vol_rel_WMH>
      <surf_TSA>8.6236006328741</surf_TSA>
      <SQR>4.82611954518084</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.406742095947266 993 285 7464.9094696442 0.339766485156894]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00507978722453117 0 0.354692041873932]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[840.9059201173 535.532557937716 468.817172922031 740.362401578269 2390.89916231793 8256.55662590257]</SPMvols0>
      <SPMvols1>[734.04552530829 504.56528618059 277.732567715638 715.430684618753 1509.04075817378 8842.18713532613]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[71.2854995727539 148.238998413086 196.120697021484]</T3th>
            <Tth>
               <T3th>[0 0 2.3412184715271 71.2854995727539 148.238998413086 196.120697021484 258.538299560547 485.759033203125]</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>[0.0194300599396229 0.0680927708745003 0.074062317609787 0 0]</dtc>
         <ll>[0.0832190847530418 0 0.0832190847530418 0;0.201139305819984 0.00969632161336214 0.210835627433346 2067.72119140625;0.201139305819984 0.00969632161336214 0.210835627433346 2067.72119140625]</ll>
         <rmsdtc>[0.0432212390005589 0.0867054313421249 0.0960595086216927]</rmsdtc>
         <rmsgdt>[0.0311626754701138 0.0411973185837269 0.0507057420909405]</rmsgdt>
         <rmsdt>0.0960595086216927</rmsdt>
         <dt>0.074062317609787</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>[0.00904553849250078 0.0348901152610779 0.0466406606137753 0.0551330931484699 0.061073649674654 0.067691445350647]</dtc>
         <ll>[0.0840743327863775 0 0.0840743327863775 0;0.221850747863248 0.0142865184294872 0.236137266292735 7312.91162109375;0.204187165317516 0.0167879312640855 0.220975096581601 12082.4755859375;0.182785164596688 0.0192905255758751 0.202075690172563 20800.43359375;0.165273871968665 0.0222372124865593 0.187511084455224 38900.734375;0.165273871968665 0.0222372124865593 0.187511084455224 38900.734375]</ll>
         <rmsdtc>[0.0104184402152896 0.0374165661633015 0.0563598424196243 0.0795329883694649 0.101127795875072 0.107559017837048]</rmsdtc>
         <rmsgdt>[0.00307701458223164 0.0119755696505308 0.0267472770065069 0.0459258332848549 0.062377754598856 0.0676864013075829]</rmsgdt>
         <rmsdt>0.107559017837048</rmsdt>
         <dt>0.067691445350647</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_13284/ds/sub-28/sub-28_acq-highres_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 32s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</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 4s</item>
      <item>Affine registration 9s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 62s</item>
      <item>SPM preprocessing 1 (estimate 2): 50s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 17s</item>
      <item>Update Skull-Stripping 39s</item>
      <item>Update probability maps 9s</item>
      <item>80s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 9s</item>
      <item>Fast Optimized Shooting registration 30s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.03) 14s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 24s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 38s</item>
      <item>104s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 8s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 14s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.06) 28s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>72s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</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) 2s</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 | 0.0841 0.0000 0.0841 | 32.0000</item>
      <item>2 | 2.50 | 0.0819 0.0010 0.0829 | 29.4886</item>
      <item>3 | 2.50 | 0.0812 0.0016 0.0828 | 26.9772</item>
      <item>4 | 2.50 | 0.0809 0.0018 0.0827 | 24.6107</item>
      <item>5 | 2.50 | 0.0806 0.0019 0.0825 | 22.6548</item>
      <item>6 | 2.50 | 0.0804 0.0020 0.0824 | 20.6989</item>
      <item>7 | 2.50 | 0.0801 0.0021 0.0822 | 18.9688</item>
      <item>8 | 2.50 | 0.0799 0.0022 0.0821 | 17.4455</item>
      <item>9 | 2.50 | 0.0796 0.0023 0.0819 | 15.9223</item>
      <item>10 | 2.50 | 0.0793 0.0024 0.0817 | 14.6627</item>
      <item>11 | 2.50 | 0.0791 0.0025 0.0815 | 13.4764</item>
      <item>12 | 2.50 | 0.0788 0.0025 0.0813 | 12.3015</item>
      <item>13 | 2.50 | 0.0785 0.0026 0.0811 | 11.3776</item>
      <item>14 | 2.50 | 0.0782 0.0027 0.0809 | 10.4537</item>
      <item>15 | 2.25 | 0.0782 0.0027 0.0809 | 9.5920</item>
      <item>16 | 2.25 | 0.0752 0.0042 0.0794 | 8.8725</item>
      <item>17 | 2.25 | 0.0740 0.0048 0.0787 | 8.1530</item>
      <item>29 | 2.00 | 0.0761 0.0022 0.0783 | 3.3283</item>
      <item>30 | 2.00 | 0.0702 0.0046 0.0748 | 3.1221</item>
      <item>31 | 2.00 | 0.0681 0.0056 0.0737 | 2.9160</item>
      <item>43 | 1.75 | 0.0670 0.0032 0.0702 | 1.5785</item>
      <item>44 | 1.75 | 0.0625 0.0056 0.0680 | 1.5194</item>
      <item>45 | 1.75 | 0.0609 0.0064 0.0674 | 1.4626</item>
      <item>57 | 1.50 | 0.0593 0.0047 0.0640 | 1.0900</item>
      <item>58 | 1.50 | 0.0562 0.0067 0.0629 | 1.0730</item>
      <item>59 | 1.50 | 0.0551 0.0074 0.0625 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 160s</item>
      <item>Prepare output 11s</item>
      <item>171s</item>
      <item>Jacobian determinant (RMS): 0.010 0.037 0.056 0.080 0.101 | 0.107559</item>
      <item>Template Matching: 0.084 0.222 0.204 0.183 0.165 | 0.165274</item>
      <item>Write result maps: 25s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 43s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 43s</item>
      <item>107s</item>
      <item>Create initial surface 81s</item>
      <item>Topology correction: 96s</item>
      <item>Surface refinement: 77s</item>
      <item>Reduction of surface collisions with optimization: 78s</item>
      <item>Spherical mapping with areal smoothing 101s</item>
      <item>Spherical registration 303s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 43s</item>
      <item>97s</item>
      <item>Create initial surface 85s</item>
      <item>Topology correction: 98s</item>
      <item>Surface refinement: 87s</item>
      <item>Reduction of surface collisions with optimization: 79s</item>
      <item>Spherical mapping with areal smoothing 87s</item>
      <item>Spherical registration 302s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3813 0.5987 mm</item>
      <item>Surface intensity / position RMSE: 0.0602 / 0.0588</item>
      <item>Euler number / defect number / defect size: 6.0 / 7.5 / 0.22%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_13284/ds/sub-28/surf/lh.thickness.sub-28_acq-highres_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_13284/ds/sub-28/surf/rh.thickness.sub-28_acq-highres_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_13284/ds/sub-28/sub-28_acq-highres_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1771s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 9s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 32s</item>
      <item>ROI estimation of 'lpba40' atlas 9s</item>
      <item>ROI estimation of 'hammers' atlas 22s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 8s</item>
      <item>ROI estimation of 'aal3' atlas 13s</item>
      <item>ROI estimation of 'mori' atlas 19s</item>
      <item>ROI estimation of 'anatomy3' atlas 28s</item>
      <item>ROI estimation of 'julichbrain' atlas 37s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s</item>
      <item>Write results 95s</item>
      <item>378s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_13284/ds/sub-28/report/catreport_sub-28_acq-highres_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 50 minute(s) and 20 second(s).</item>
      <item>Image Quality Rating (IQR): 83.74% (B)</item>
      <item>GM volume (GMV): 44.17% (690.66 / 1563.62 ml)</item>
      <item>GM thickness (GMT): 2.38 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_13284/ds/sub-28/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_13284/ds/sub-28/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_13284/ds/sub-28/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>