ds003717_ReproVBM/sub-07/report/cat_sub-07_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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      <Affine_rotation>[0.0675941692660382 -0.0286100473974953 -0.0201184263246018]</Affine_rotation>
      <Affine_scaling>[1.04235249448741 1.0414206447762 1.16165633314265]</Affine_scaling>
      <Affine_shearing>[0.00404577853581491 0.0106912891492484 0.043099120347772]</Affine_shearing>
      <Affine0_translation>[-0.343705749039344 -31.9612344501303 1.03097300996234]</Affine0_translation>
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      <Affine0_scaling>[1.04235249448741 1.0414206447762 1.16165633314265]</Affine0_scaling>
      <Affine0_shearing>[0.00404577853581491 0.0106912891492484 0.043099120347772]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_4014670/ds/sub-07</path>
      <file>sub-07_T1w</file>
      <fname>/var/lib/condor/execute/dir_4014670/ds/sub-07/sub-07_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_4014670/ds/sub-07/sub-07_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_4014670/ds/sub-07/mri/msub-07_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_4014670/ds/sub-07/mri/p0sub-07_T1w.nii</Fp0>
      <fnames>..14670/ds/sub-07/sub-07_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>20</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>16</SurfaceEulerNumber>
      <SurfaceDefectArea>0.64229450296325</SurfaceDefectArea>
      <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0722125470638275</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0680347010493279</SurfacePositionRMSE>
      <res_vx_vol>[0.799999977581063 0.800000016636097 0.799999968787145]</res_vx_vol>
      <res_vx_voli>[0.800000036996425 0.800000016636097 0.799999968849344]</res_vx_voli>
      <res_RMS>0.799999987668102</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[24.5275001525879 263.303436279297 702.271789550781 948.449645996094]</tissue_mn>
      <tissue_mnr>[0.0258606243878603 0.277614563703537 0.740441858768463 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.0364266559481621 0.124973498284817 0.0879714712500572 0.0462825633585453]</tissue_stdr>
      <contrast>252.713180541992</contrast>
      <contrastr>0.266448706388474</contrastr>
      <NCR>0.127797394990921</NCR>
      <ICR>0.131926193833351</ICR>
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   <qualityratings>
      <res_vx_vol>[1.59999995516213 1.60000003327219 1.59999993757429]</res_vx_vol>
      <res_RMS>1.5999999753362</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>4.08660268783569</contrastr>
      <NCR>2.16562438011169</NCR>
      <ICR>0.787019371986389</ICR>
      <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
      <SurfaceDefectArea>1.16057362574081</SurfaceDefectArea>
      <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.44425094127655</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.36069393157959</SurfacePositionRMSE>
      <IQR>2.00711238849847</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>20220709-220420</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>16</SurfaceEulerNumber>
         <SurfaceDefectArea>0.64229450296325</SurfaceDefectArea>
         <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0722125470638275</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0680347010493279</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>16</EC_abs>
      <defect_size>0.64229450296325</defect_size>
      <vol_abs_CGW>[154.443043461778 677.39507748344 525.655398113318 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.94191939901915</vol_abs_WMH>
      <vol_rel_WMH>0.000693866590002139</vol_rel_WMH>
      <surf_TSA>1981.01135351144</surf_TSA>
      <vol_TIV>1357.49351905854</vol_TIV>
      <vol_rel_CGW>[0.113770740923234 0.499004281032026 0.38722497804474 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.42794955086194 0.590668997085682]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.43494606018066 0.709805200199416 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.88098509723428 0.229290436076401 0.308686672485647;2.47032668989314 0.166416525747588 0.427695069028681;3.07935628717998 0.250509025381756 0.263618258485672]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.810921678453398 0.390598011707031 0.563612392880686;3.96676551796621 0.335838506618805 0.436387607119314]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.04292573315512</vol_TIV>
      <vol_rel_CGW>[0.5 6.81185849554644 4.80432791028628 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06938665900021</vol_rel_WMH>
      <surf_TSA>8.62060823344266</surf_TSA>
      <SQR>5.6120347904367</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.0823680388621795 54 10889 9381.51636615533 0.325255883327579]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0330638960003853 0.0334034189581871 0.161595165729523]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[804.48027760385 487.376305335626 251.289819893202 2001.00940299381 2023.42317943546 5216.77345132506]</SPMvols0>
      <SPMvols1>[711.810760709424 460.282467272265 147.906983795747 2021.03206106238 1998.67153262223 4883.93741725003]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[348.777099609375 702.257873535156 939.843017578125]</T3th>
            <Tth>
               <T3th>[0 89.0560913085938 31.569465637207 348.777099609375 702.257873535156 939.843017578125 1235.3759765625 2046.1513671875]</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>[0.0240723937749863 0.0835583657026291 0.0917111188173294 0 0]</dtc>
         <ll>[0.0838927001464648 0 0.0838927001464648 0;0.184686576046434 0.0110742424716469 0.195760818518081 2361.56005859375;0.184686576046434 0.0110742424716469 0.195760818518081 2361.56005859375]</ll>
         <rmsdtc>[0.0497879907488823 0.104301482439041 0.113830834627151]</rmsdtc>
         <rmsgdt>[0.0352253988385201 0.0442504361271858 0.0535465255379677]</rmsgdt>
         <rmsdt>0.113830834627151</rmsdt>
         <dt>0.0917111188173294</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>[0.0120840184390545 0.0481375232338905 0.0634552240371704 0.0710432827472687 0.0765803158283234 0.0865446701645851]</dtc>
         <ll>[0.0850132315873309 0 0.0850132315873309 0;0.20814300976801 0.0203517628205128 0.228494772588523 10417.55859375;0.186785630050631 0.0195272838410538 0.206312913891685 14054.0205078125;0.167077668598461 0.0198321926627743 0.186909861261236 21384.498046875;0.15090263014383 0.0222166379155608 0.173119268059391 38864.7421875;0.15090263014383 0.0222166379155608 0.173119268059391 38864.7421875]</ll>
         <rmsdtc>[0.0139608876779675 0.0513267703354359 0.0760923996567726 0.100487813353539 0.122895479202271 0.129962250590324]</rmsdtc>
         <rmsgdt>[0.00387796922586858 0.0148158203810453 0.0305877290666103 0.0511451400816441 0.0696268230676651 0.0753485783934593]</rmsgdt>
         <rmsdt>0.129962250590324</rmsdt>
         <dt>0.0865446701645851</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_4014670/ds/sub-07/sub-07_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 70s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 23s</item>
      <item>Estimate background 17s</item>
      <item>Initial correction 21s</item>
      <item>Refine background 9s</item>
      <item>Final correction 13s</item>
      <item>Final scaling 16s</item>
      <item>112s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 15s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 175s</item>
      <item>SPM preprocessing 1 (estimate 2): 133s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 38s</item>
      <item>Update Segmentation 41s</item>
      <item>Update Skull-Stripping 128s</item>
      <item>Update probability maps 20s</item>
      <item>226s</item>
      <item>Global intensity correction: 34s</item>
      <item>SANLM denoising after intensity normalization (medium): 20s</item>
      <item>Fast Optimized Shooting registration 58s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 10s</item>
      <item>Prepare partitions 6s</item>
      <item>Prepare segments (LASmod = 1.00) 30s</item>
      <item>Estimate local tissue thresholds (WM) 42s</item>
      <item>Estimate local tissue thresholds (GM) 52s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 53s</item>
      <item>202s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 19s</item>
      <item>Major structures 8s</item>
      <item>Ventricle detection 32s</item>
      <item>Blood vessel detection 21s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 64s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 4s</item>
      <item>Side alignment 9s</item>
      <item>Final corrections 10s</item>
      <item>167s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 53s</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) 9s</item>
      <item>Level 1 cleanup (brain masking) 6s</item>
      <item>Level 2 cleanup (CSF correction) 3s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
      <item>23s</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 | 0.0810 0.0016 0.0826 | 29.4886</item>
      <item>3 | 2.50 | 0.0798 0.0024 0.0822 | 26.9772</item>
      <item>4 | 2.50 | 0.0793 0.0027 0.0820 | 24.6107</item>
      <item>5 | 2.50 | 0.0788 0.0029 0.0818 | 22.6548</item>
      <item>6 | 2.50 | 0.0784 0.0031 0.0815 | 20.6989</item>
      <item>7 | 2.50 | 0.0780 0.0032 0.0812 | 18.9688</item>
      <item>8 | 2.50 | 0.0776 0.0033 0.0809 | 17.4455</item>
      <item>9 | 2.50 | 0.0771 0.0034 0.0806 | 15.9223</item>
      <item>10 | 2.50 | 0.0767 0.0036 0.0803 | 14.6627</item>
      <item>11 | 2.50 | 0.0762 0.0037 0.0799 | 13.4764</item>
      <item>12 | 2.50 | 0.0758 0.0038 0.0795 | 12.3015</item>
      <item>13 | 2.50 | 0.0753 0.0039 0.0792 | 11.3776</item>
      <item>14 | 2.50 | 0.0748 0.0040 0.0788 | 10.4537</item>
      <item>15 | 2.25 | 0.0750 0.0041 0.0791 | 9.5920</item>
      <item>16 | 2.25 | 0.0710 0.0061 0.0771 | 8.8725</item>
      <item>17 | 2.25 | 0.0694 0.0068 0.0762 | 8.1530</item>
      <item>29 | 2.00 | 0.0701 0.0031 0.0732 | 3.3283</item>
      <item>30 | 2.00 | 0.0643 0.0056 0.0699 | 3.1221</item>
      <item>31 | 2.00 | 0.0623 0.0065 0.0688 | 2.9160</item>
      <item>43 | 1.75 | 0.0611 0.0037 0.0648 | 1.5785</item>
      <item>44 | 1.75 | 0.0570 0.0059 0.0629 | 1.5194</item>
      <item>45 | 1.75 | 0.0557 0.0066 0.0623 | 1.4626</item>
      <item>57 | 1.50 | 0.0542 0.0049 0.0591 | 1.0900</item>
      <item>58 | 1.50 | 0.0513 0.0068 0.0580 | 1.0730</item>
      <item>59 | 1.50 | 0.0503 0.0074 0.0577 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 234s</item>
      <item>Prepare output 18s</item>
      <item>252s</item>
      <item>Jacobian determinant (RMS): 0.014 0.051 0.076 0.100 0.123 | 0.129962</item>
      <item>Template Matching: 0.085 0.208 0.187 0.167 0.151 | 0.150903</item>
      <item>Write result maps: 58s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 36s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 55s</item>
      <item>117s</item>
      <item>Create initial surface 85s</item>
      <item>Topology correction: 107s</item>
      <item>Surface refinement: 100s</item>
      <item>Reduction of surface collisions with optimization: 71s</item>
      <item>Spherical mapping with areal smoothing 109s</item>
      <item>Spherical registration 301s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 34s</item>
      <item>CSF distance: 18s</item>
      <item>PBT2x thickness: 55s</item>
      <item>116s</item>
      <item>Create initial surface 84s</item>
      <item>Topology correction: 108s</item>
      <item>Surface refinement: 83s</item>
      <item>Reduction of surface collisions with optimization: 70s</item>
      <item>Spherical mapping with areal smoothing 102s</item>
      <item>Spherical registration 301s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4280 0.5906 mm</item>
      <item>Surface intensity / position RMSE: 0.0722 / 0.0680</item>
      <item>Euler number / defect number / defect size: 16.0 / 10.5 / 0.64%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_4014670/ds/sub-07/surf/lh.thickness.sub-07_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_4014670/ds/sub-07/surf/rh.thickness.sub-07_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4014670/ds/sub-07/sub-07_T1w.nii</item>
      <item>Surface ROI estimation: 10s</item>
      <item>Surface and thickness estimation takes: 1894s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 30s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 113s</item>
      <item>ROI estimation of 'lpba40' atlas 33s</item>
      <item>ROI estimation of 'hammers' atlas 80s</item>
      <item>ROI estimation of 'thalamus' atlas 6s</item>
      <item>ROI estimation of 'ibsr' atlas 28s</item>
      <item>ROI estimation of 'aal3' atlas 44s</item>
      <item>ROI estimation of 'mori' atlas 65s</item>
      <item>ROI estimation of 'anatomy3' atlas 94s</item>
      <item>ROI estimation of 'julichbrain' atlas 124s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 46s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 58s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 199s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 293s</item>
      <item>Write results 294s</item>
      <item>1214s</item>
      <item>Quality check: 11s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_4014670/ds/sub-07/report/catreport_sub-07_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 81 minute(s) and 44 second(s).</item>
      <item>Image Quality Rating (IQR): 84.93% (B)</item>
      <item>GM volume (GMV): 49.90% (677.40 / 1357.49 ml)</item>
      <item>GM thickness (GMT): 2.43 0.59 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_4014670/ds/sub-07/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_4014670/ds/sub-07/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_4014670/ds/sub-07/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>