ds003550_ReproVBM/sub-sc026/report/cat_sub-sc026_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>-12.5106868743896</ll>
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      <Affine_rotation>[0.13675086561537 0.0224491394806679 0.0492181546532936]</Affine_rotation>
      <Affine_scaling>[1.09749292717627 1.04432662964203 1.1487020844507]</Affine_scaling>
      <Affine_shearing>[-0.000111333729215948 -0.0020776350763665 -0.0216399308374788]</Affine_shearing>
      <Affine0_translation>[2.62804990112222 -23.7028270470435 -19.7566430499054]</Affine0_translation>
      <Affine0_rotation>[0.13675086561537 0.0224491394806679 0.0492181546532936]</Affine0_rotation>
      <Affine0_scaling>[1.09749292717627 1.04432662964203 1.1487020844507]</Affine0_scaling>
      <Affine0_shearing>[-0.000111333729215948 -0.0020776350763665 -0.0216399308374788]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_32266/ds/sub-sc026</path>
      <file>sub-sc026_T1w</file>
      <fname>/var/lib/condor/execute/dir_32266/ds/sub-sc026/sub-sc026_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_32266/ds/sub-sc026/sub-sc026_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_32266/ds/sub-sc026/mri/msub-sc026_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_32266/ds/sub-sc026/mri/p0sub-sc026_T1w.nii</Fp0>
      <fnames>..66/ds/sub-sc026/sub-sc026_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>8</SurfaceEulerNumber>
      <SurfaceDefectArea>0.112083598270889</SurfaceDefectArea>
      <SurfaceDefectNumber>10</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0638725608587265</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0619441121816635</SurfacePositionRMSE>
      <res_vx_vol>[0.999999992470947 1.00000002277828 0.999999993117216]</res_vx_vol>
      <res_vx_voli>[0.999999992657692 1.0000000209194 0.999999995784783]</res_vx_voli>
      <res_RMS>1.00000000278881</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[0 163823.09375 366844.3125 539447.9375]</tissue_mn>
      <tissue_mnr>[0 0.303686589002609 0.680036544799805 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[52356.4116053336 66251.8187933688 55925.0430425563 31985.8656226189]</tissue_std>
      <tissue_stdr>[0.0970555394887924 0.122814111411572 0.103670880198479 0.0592937022447586]</tissue_stdr>
      <contrast>172603.625</contrast>
      <contrastr>0.319963455200195</contrastr>
      <NCR>0.1038708537817</NCR>
      <ICR>0.245894312858582</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.99999998494189 2.00000004555656 1.99999998623443]</res_vx_vol>
      <res_RMS>2.00000000557763</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[1.89584374427795 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>3.28388142585754</contrastr>
      <NCR>1.82214832305908</NCR>
      <ICR>1.06967830657959</ICR>
      <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
      <SurfaceDefectArea>1.02802089956772</SurfaceDefectArea>
      <SurfaceDefectNumber>1.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.27745127677917</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.23888230323792</SurfacePositionRMSE>
      <IQR>1.92526109087571</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>20220711-171632</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>8</SurfaceEulerNumber>
         <SurfaceDefectArea>0.112083598270889</SurfaceDefectArea>
         <SurfaceDefectNumber>10</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0638725608587265</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0619441121816635</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>8</EC_abs>
      <defect_size>0.112083598270889</defect_size>
      <vol_abs_CGW>[178.254966374684 669.716994505104 532.673189300548 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.24685099206503</vol_abs_WMH>
      <vol_rel_WMH>0.000903093015538544</vol_rel_WMH>
      <surf_TSA>1868.46076576807</surf_TSA>
      <vol_TIV>1380.64515018034</vol_TIV>
      <vol_rel_CGW>[0.129109906590698 0.485075397119693 0.385814696289609 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.55896762678714 0.600921759465605]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.57391953468323 0.743648553441797 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.9623240038968 0.241195025136102 0.281084738636588;2.5783569836082 0.169126864082225 0.430177176605068;3.17709418734057 0.258072745842501 0.288738084758345]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.905754077272692 0.334656207831203 0.53760193295077;4.17091154984703 0.390316077184255 0.46239806704923]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00891986621979</vol_TIV>
      <vol_rel_CGW>[0.5 6.56169894252322 4.77899957416683 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.09030930155385</vol_rel_WMH>
      <surf_TSA>8.60771106142368</surf_TSA>
      <SQR>5.41728055784116</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.628134822845459 6033 2060 3899.28903262317 0.371735636570603]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0 0 0.340682506561279]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[804.592450669753 470.105294597148 243.523076789638 474.288682871606 1948.64624961554 7082.39292120647]</SPMvols0>
      <SPMvols1>[727.425602888502 445.466925739035 151.704840635929 364.745007336268 1158.05757554748 7638.41260092166]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[180317.5 395905.28125 533075.875]</T3th>
            <Tth>
               <T3th>[0 18062.125 5507.0634765625 180317.5 395905.28125 533075.875 709455.0625 955643.5]</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>[0.0188598856329918 0.066305972635746 0.0722232162952423 0 0]</dtc>
         <ll>[0.077758782956542 0 0.077758782956542 0;0.183968808470654 0.00895516669192091 0.192923975162575 1909.67138671875;0.183968808470654 0.00895516669192091 0.192923975162575 1909.67138671875]</ll>
         <rmsdtc>[0.0394815616309643 0.0858323350548744 0.0951557978987694]</rmsdtc>
         <rmsgdt>[0.028048999607563 0.0402311310172081 0.049341905862093]</rmsgdt>
         <rmsdt>0.0951557978987694</rmsdt>
         <dt>0.0722232162952423</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>[0.00868695043027401 0.0314060300588608 0.0439322516322136 0.0512632355093956 0.0556380338966846 0.0622355937957764]</dtc>
         <ll>[0.0789408210132447 0 0.0789408210132447 0;0.207275778388278 0.011601066468254 0.218876844856532 5938.2958984375;0.186534726737917 0.0148377357670499 0.201372462504967 10678.896484375;0.167223924019171 0.016823238796658 0.184047162815829 18140.02734375;0.153891467302483 0.0175368809568452 0.171428348259328 30678.1953125;0.153891467302483 0.0175368809568452 0.171428348259328 30678.1953125]</ll>
         <rmsdtc>[0.0101915635168552 0.0367209427058697 0.055375799536705 0.078936792910099 0.1009341776371 0.105667911469936]</rmsdtc>
         <rmsgdt>[0.00316912122070789 0.0123578039929271 0.0269382949918509 0.0459286831319332 0.0624048374593258 0.066411942243576]</rmsgdt>
         <rmsdt>0.105667911469936</rmsdt>
         <dt>0.0622355937957764</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_32266/ds/sub-sc026/sub-sc026_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 27s</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>37s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 10s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 5s</item>
      <item>Use initial fine affine registration. 64s</item>
      <item>SPM preprocessing 1 (estimate 2): 59s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 38s</item>
      <item>Update probability maps 8s</item>
      <item>80s</item>
      <item>Global intensity correction: 15s</item>
      <item>SANLM denoising after intensity normalization (medium): 18s</item>
      <item>Fast Optimized Shooting registration 32s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.20) 14s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 22s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 23s</item>
      <item>88s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 8s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 13s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 27s</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>71s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 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) 1s</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 | 0.0789 0.0000 0.0789 | 32.0000</item>
      <item>2 | 2.50 | 0.0769 0.0010 0.0779 | 29.4886</item>
      <item>3 | 2.50 | 0.0763 0.0015 0.0778 | 26.9772</item>
      <item>4 | 2.50 | 0.0760 0.0017 0.0777 | 24.6107</item>
      <item>5 | 2.50 | 0.0758 0.0018 0.0776 | 22.6548</item>
      <item>6 | 2.50 | 0.0756 0.0019 0.0774 | 20.6989</item>
      <item>7 | 2.50 | 0.0754 0.0019 0.0773 | 18.9688</item>
      <item>8 | 2.50 | 0.0751 0.0020 0.0772 | 17.4455</item>
      <item>9 | 2.50 | 0.0749 0.0021 0.0770 | 15.9223</item>
      <item>10 | 2.50 | 0.0747 0.0022 0.0769 | 14.6627</item>
      <item>11 | 2.50 | 0.0744 0.0023 0.0767 | 13.4764</item>
      <item>12 | 2.50 | 0.0742 0.0023 0.0765 | 12.3015</item>
      <item>13 | 2.50 | 0.0739 0.0024 0.0763 | 11.3776</item>
      <item>14 | 2.50 | 0.0737 0.0025 0.0761 | 10.4537</item>
      <item>15 | 2.25 | 0.0718 0.0025 0.0743 | 9.5920</item>
      <item>16 | 2.25 | 0.0691 0.0039 0.0730 | 8.8725</item>
      <item>29 | 2.00 | 0.0698 0.0018 0.0716 | 3.3283</item>
      <item>30 | 2.00 | 0.0641 0.0040 0.0681 | 3.1221</item>
      <item>31 | 2.00 | 0.0622 0.0049 0.0671 | 2.9160</item>
      <item>43 | 1.75 | 0.0609 0.0028 0.0638 | 1.5785</item>
      <item>44 | 1.75 | 0.0570 0.0049 0.0619 | 1.5194</item>
      <item>45 | 1.75 | 0.0557 0.0056 0.0613 | 1.4626</item>
      <item>57 | 1.50 | 0.0540 0.0041 0.0581 | 1.0900</item>
      <item>58 | 1.50 | 0.0513 0.0058 0.0571 | 1.0730</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 138s</item>
      <item>Prepare output 9s</item>
      <item>148s</item>
      <item>Jacobian determinant (RMS): 0.010 0.037 0.055 0.079 0.101 | 0.105668</item>
      <item>Template Matching: 0.079 0.207 0.187 0.167 0.154 | 0.153891</item>
      <item>Write result maps: 23s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 41s</item>
      <item>90s</item>
      <item>Create initial surface 81s</item>
      <item>Topology correction: 90s</item>
      <item>Surface refinement: 78s</item>
      <item>Reduction of surface collisions with optimization: 65s</item>
      <item>Spherical mapping with areal smoothing 81s</item>
      <item>Spherical registration 297s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 24s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 42s</item>
      <item>85s</item>
      <item>Create initial surface 81s</item>
      <item>Topology correction: 88s</item>
      <item>Surface refinement: 72s</item>
      <item>Reduction of surface collisions with optimization: 69s</item>
      <item>Spherical mapping with areal smoothing 95s</item>
      <item>Spherical registration 306s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5590 0.6009 mm</item>
      <item>Surface intensity / position RMSE: 0.0639 / 0.0619</item>
      <item>Euler number / defect number / defect size: 8.0 / 10.0 / 0.11%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_32266/ds/sub-sc026/surf/lh.thickness.sub-sc026_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_32266/ds/sub-sc026/surf/rh.thickness.sub-sc026_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_32266/ds/sub-sc026/sub-sc026_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1668s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 28s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 11s</item>
      <item>ROI estimation of 'mori' atlas 17s</item>
      <item>ROI estimation of 'anatomy3' atlas 24s</item>
      <item>ROI estimation of 'julichbrain' atlas 33s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 50s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 76s</item>
      <item>Write results 76s</item>
      <item>317s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_32266/ds/sub-sc026/report/catreport_sub-sc026_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 46 minute(s) and 41 second(s).</item>
      <item>Image Quality Rating (IQR): 85.75% (B)</item>
      <item>GM volume (GMV): 48.51% (669.72 / 1380.65 ml)</item>
      <item>GM thickness (GMT): 2.56 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_32266/ds/sub-sc026/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_32266/ds/sub-sc026/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_32266/ds/sub-sc026/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>