ds004169_ReproVBM/sub-0159/report/cat_sub-0159_ses-01_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>-3.78173518180847</ll>
      <Affine_translation>[-1.52209225244329 -16.8345965299302 31.3055122583143]</Affine_translation>
      <Affine_rotation>[0.321258635167228 0.00987874685658521 0.0071352598343586]</Affine_rotation>
      <Affine_scaling>[1.0761892472537 1.05017740377844 1.17627920503268]</Affine_scaling>
      <Affine_shearing>[0.000971054979531982 0.00842867392749164 -0.0626612253884857]</Affine_shearing>
      <Affine0_translation>[-1.52209225244329 -16.8345965299302 31.3055122583143]</Affine0_translation>
      <Affine0_rotation>[0.321258635167228 0.00987874685658521 0.0071352598343586]</Affine0_rotation>
      <Affine0_scaling>[1.0761892472537 1.05017740377844 1.17627920503268]</Affine0_scaling>
      <Affine0_shearing>[0.000971054979531982 0.00842867392749164 -0.0626612253884857]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_30963/ds/sub-0159</path>
      <file>sub-0159_ses-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_30963/ds/sub-0159/sub-0159_ses-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_30963/ds/sub-0159/sub-0159_ses-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_30963/ds/sub-0159/mri/msub-0159_ses-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_30963/ds/sub-0159/mri/p0sub-0159_ses-01_T1w.nii</Fp0>
      <fnames>..963/ds/sub-0159/sub-0159_ses-01_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>112</SurfaceEulerNumber>
      <SurfaceDefectArea>3.75670460069258</SurfaceDefectArea>
      <SurfaceDefectNumber>46.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0833915844559669</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0971287041902542</SurfacePositionRMSE>
      <res_vx_vol>[0.9375 0.900009155273438 0.9375]</res_vx_vol>
      <res_vx_voli>[0.9375 0.900009155273438 0.9375]</res_vx_voli>
      <res_RMS>0.925171872244289</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[2.93700003623962 17.5110721588135 36.6810111999512 61.6218299865723]</tissue_mn>
      <tissue_mnr>[0.0476616807281971 0.284169942140579 0.59526002407074 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[8.30818053042073 11.1364269437214 7.83571048339806 5.23656408842094]</tissue_std>
      <tissue_stdr>[0.141572877764702 0.189766705036163 0.133521914482117 0.0892319902777672]</tissue_stdr>
      <contrast>21.4649868011475</contrast>
      <contrastr>0.348334133625031</contrastr>
      <NCR>0.151048734784126</NCR>
      <ICR>0.514630734920502</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.875 1.80001831054688 1.875]</res_vx_vol>
      <res_RMS>1.85034374448858</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62028408050537 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>2.85832118988037</contrastr>
      <NCR>2.49940752983093</NCR>
      <ICR>1.73618733882904</ICR>
      <SurfaceEulerNumber>6.61224489795918</SurfaceEulerNumber>
      <SurfaceDefectArea>1.93917615017314</SurfaceDefectArea>
      <SurfaceDefectNumber>3.325</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.66783165931702</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.94257402420044</SurfacePositionRMSE>
      <IQR>2.31684936728289</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>20220709-173434</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>112</SurfaceEulerNumber>
         <SurfaceDefectArea>3.75670460069258</SurfaceDefectArea>
         <SurfaceDefectNumber>46.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0833915844559669</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0971287041902542</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>112</EC_abs>
      <defect_size>3.75670460069258</defect_size>
      <vol_abs_CGW>[175.49607749967 720.066760600016 489.406944332 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.526787642713855</vol_abs_WMH>
      <vol_rel_WMH>0.00038036038720566</vol_rel_WMH>
      <surf_TSA>2000.56498981647</surf_TSA>
      <vol_TIV>1384.96978243169</vol_TIV>
      <vol_rel_CGW>[0.126714733942815 0.519915141639947 0.353370124417238 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.47599866491906 0.654147479408358]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.51259112358093 0.80133356540327 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.84494647477671 0.285442880938869 0.288877840738922;2.52871326313684 0.189278757279075 0.423394391000683;3.20131484817523 0.27897693326312 0.287727768260396]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.746316799116744 0.299136027143389 0.696402507083369;4.06041992101734 0.290535742867786 0.303597492916631]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00538034538181</vol_TIV>
      <vol_rel_CGW>[0.5 7.18741274497031 4.19630252186131 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.03803603872057</vol_rel_WMH>
      <surf_TSA>8.62146402201989</surf_TSA>
      <SQR>5.88747854047702</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.169891476631165 1 1 11016.5154826194 0.538475396579308]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.044820386916399 0.043248325586319 0.257210969924927]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[881.148792347084 441.680034775804 300.012866310775 2257.37670850906 2385.79198458752 7691.74231982499]</SPMvols0>
      <SPMvols1>[767.634699214644 411.794794419408 165.698430384415 3083.89265064539 2079.06689156424 6764.17947215438]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[18.4587993621826 41.0153999328613 60.5652008056641]</T3th>
            <Tth>
               <T3th>[0 2.02390670776367 2.77258610725403 18.4587993621826 41.0153999328613 60.5652008056641 81.6184005737305 263.274108886719]</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>[0.0174926202744246 0.0608723647892475 0.0664648935198784 0 0]</dtc>
         <ll>[0.0809881264517526 0 0.0809881264517526 0;0.194463503174707 0.00865390005947447 0.203117403234182 1845.42687988281;0.194463503174707 0.00865390005947447 0.203117403234182 1845.42687988281]</ll>
         <rmsdtc>[0.0392210632562637 0.0819357261061668 0.0920950174331665]</rmsdtc>
         <rmsgdt>[0.0282725766301155 0.0424592755734921 0.052924606949091]</rmsgdt>
         <rmsdt>0.0920950174331665</rmsdt>
         <dt>0.0664648935198784</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>[0.0078631928190589 0.0280979685485363 0.0408536121249199 0.0502230450510979 0.0574707873165607 0.0649490132927895]</dtc>
         <ll>[0.083337507380281 0 0.083337507380281 0;0.221825457875458 0.0119559829059829 0.233781440781441 6119.96875;0.202507912887377 0.015353557601426 0.217861470488803 11050.1396484375;0.183060069143036 0.0181045043162811 0.201164573459317 19521.580078125;0.167586173288067 0.0215376435780829 0.18912381686615 37676.94140625;0.167586173288067 0.0215376435780829 0.18912381686615 37676.94140625]</ll>
         <rmsdtc>[0.00942948460578918 0.0340270437300205 0.0537389330565929 0.0824539586901665 0.111121170222759 0.118746712803841]</rmsdtc>
         <rmsgdt>[0.00298547581769526 0.0120816761627793 0.0281322859227657 0.0508411712944508 0.0722731128334999 0.0787884518504143]</rmsgdt>
         <rmsdt>0.118746712803841</rmsdt>
         <dt>0.0649490132927895</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_30963/ds/sub-0159/sub-0159_ses-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 192s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 9s</item>
      <item>Initial correction 16s</item>
      <item>Refine background 5s</item>
      <item>Final correction 9s</item>
      <item>Final scaling 7s</item>
      <item>63s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 21s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 93s</item>
      <item>SPM preprocessing 1 (estimate 2): 68s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 22s</item>
      <item>Update Segmentation 24s</item>
      <item>Update Skull-Stripping 55s</item>
      <item>Update probability maps 12s</item>
      <item>113s</item>
      <item>Global intensity correction: 22s</item>
      <item>SANLM denoising after intensity normalization (medium): 28s</item>
      <item>Fast Optimized Shooting registration 36s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 7s</item>
      <item>Prepare segments (LASmod = 1.03) 17s</item>
      <item>Estimate local tissue thresholds (WM) 24s</item>
      <item>Estimate local tissue thresholds (GM) 33s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 50s</item>
      <item>141s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 10s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 17s</item>
      <item>Blood vessel detection 11s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 34s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 6s</item>
      <item>88s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 5s</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>13s</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 | 0.0833 0.0000 0.0833 | 32.0000</item>
      <item>2 | 2.50 | 0.0809 0.0011 0.0820 | 29.4886</item>
      <item>3 | 2.50 | 0.0802 0.0016 0.0819 | 26.9772</item>
      <item>4 | 2.50 | 0.0799 0.0018 0.0817 | 24.6107</item>
      <item>5 | 2.50 | 0.0796 0.0020 0.0815 | 22.6548</item>
      <item>6 | 2.50 | 0.0793 0.0020 0.0814 | 20.6989</item>
      <item>7 | 2.50 | 0.0791 0.0021 0.0812 | 18.9688</item>
      <item>8 | 2.50 | 0.0788 0.0022 0.0810 | 17.4455</item>
      <item>9 | 2.50 | 0.0786 0.0022 0.0808 | 15.9223</item>
      <item>10 | 2.50 | 0.0783 0.0023 0.0806 | 14.6627</item>
      <item>11 | 2.50 | 0.0780 0.0024 0.0804 | 13.4764</item>
      <item>12 | 2.50 | 0.0777 0.0024 0.0801 | 12.3015</item>
      <item>13 | 2.50 | 0.0774 0.0025 0.0799 | 11.3776</item>
      <item>14 | 2.50 | 0.0771 0.0026 0.0797 | 10.4537</item>
      <item>15 | 2.25 | 0.0768 0.0027 0.0795 | 9.5920</item>
      <item>16 | 2.25 | 0.0739 0.0040 0.0779 | 8.8725</item>
      <item>29 | 2.00 | 0.0754 0.0018 0.0772 | 3.3283</item>
      <item>30 | 2.00 | 0.0695 0.0042 0.0737 | 3.1221</item>
      <item>31 | 2.00 | 0.0675 0.0051 0.0726 | 2.9160</item>
      <item>43 | 1.75 | 0.0667 0.0030 0.0697 | 1.5785</item>
      <item>44 | 1.75 | 0.0624 0.0052 0.0677 | 1.5194</item>
      <item>45 | 1.75 | 0.0610 0.0060 0.0671 | 1.4626</item>
      <item>57 | 1.50 | 0.0601 0.0044 0.0645 | 1.0900</item>
      <item>58 | 1.50 | 0.0569 0.0065 0.0634 | 1.0730</item>
      <item>59 | 1.50 | 0.0559 0.0072 0.0630 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 155s</item>
      <item>Prepare output 12s</item>
      <item>167s</item>
      <item>Jacobian determinant (RMS): 0.009 0.034 0.054 0.082 0.111 | 0.118747</item>
      <item>Template Matching: 0.083 0.222 0.203 0.183 0.168 | 0.167586</item>
      <item>Write result maps: 33s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 30s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 44s</item>
      <item>95s</item>
      <item>Create initial surface 83s</item>
      <item>Topology correction: 101s</item>
      <item>Surface refinement: 93s</item>
      <item>Reduction of surface collisions with optimization: 77s</item>
      <item>Spherical mapping with areal smoothing 91s</item>
      <item>Spherical registration 295s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 34s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 44s</item>
      <item>99s</item>
      <item>Create initial surface 82s</item>
      <item>Topology correction: 98s</item>
      <item>Surface refinement: 82s</item>
      <item>Reduction of surface collisions with optimization: 75s</item>
      <item>Spherical mapping with areal smoothing 83s</item>
      <item>Spherical registration 275s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4760 0.6539 mm</item>
      <item>Surface intensity / position RMSE: 0.0834 / 0.0971</item>
      <item>Euler number / defect number / defect size: 112.0 / 46.5 / 3.76%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_30963/ds/sub-0159/surf/lh.thickness.sub-0159_ses-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_30963/ds/sub-0159/surf/rh.thickness.sub-0159_ses-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_30963/ds/sub-0159/sub-0159_ses-01_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1736s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 11s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 40s</item>
      <item>ROI estimation of 'lpba40' atlas 12s</item>
      <item>ROI estimation of 'hammers' atlas 29s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 10s</item>
      <item>ROI estimation of 'aal3' atlas 17s</item>
      <item>ROI estimation of 'mori' atlas 25s</item>
      <item>ROI estimation of 'anatomy3' atlas 35s</item>
      <item>ROI estimation of 'julichbrain' atlas 47s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 113s</item>
      <item>Write results 113s</item>
      <item>473s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_30963/ds/sub-0159/report/catreport_sub-0159_ses-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 57 minute(s) and 13 second(s).</item>
      <item>Image Quality Rating (IQR): 81.83% (B-)</item>
      <item>GM volume (GMV): 51.99% (720.07 / 1384.97 ml)</item>
      <item>GM thickness (GMT): 2.48 0.65 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_30963/ds/sub-0159/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_30963/ds/sub-0159/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_30963/ds/sub-0159/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>