ds003711_ReproVBM/sub-13/report/cat_sub-13_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.03296231547772 -0.0400698731561078 0.0594171847596211 5.54943974232715;0.0169879022502005 1.05503443585811 0.200724765625918 -31.1934386801632;-0.0756638874343346 -0.203506720373294 1.18471281232245 9.40055972652845;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[266.117855523406 350.605277887739 106.582639045759 175.381472122392 157.767343328679 24.1819226750187 59.2606948709066 331.154660155238 688.076798416839 466.93339938339 288.44021048928 247.426993731774 15.8177434387153]</mn>
      <vr>[987.621622099956;202.041524995578;365.726513318117;1509.30064888504;3117.19274408415;113.381768572828;493.646174032813;5847.85600583244;7354.68965270595;8579.44522402785;1504.5864835732;6274.65089872908;63.8570797778515]</vr>
      <ll>-5.5743350982666</ll>
      <Affine_translation>[5.54943974232715 -31.1934386801632 9.40055972652845]</Affine_translation>
      <Affine_rotation>[0.193113957696107 0.068623674447207 -0.0301176469924011]</Affine_rotation>
      <Affine_scaling>[1.03586908336992 1.07520116812861 1.20245985927113]</Affine_scaling>
      <Affine_shearing>[-0.00752055108472467 -0.0231629058368921 -0.0275879316977081]</Affine_shearing>
      <Affine0_translation>[5.54943974232715 -31.1934386801632 9.40055972652845]</Affine0_translation>
      <Affine0_rotation>[0.193113957696107 0.068623674447207 -0.0301176469924011]</Affine0_rotation>
      <Affine0_scaling>[1.03586908336992 1.07520116812861 1.20245985927113]</Affine0_scaling>
      <Affine0_shearing>[-0.00752055108472467 -0.0231629058368921 -0.0275879316977081]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_19088/ds/sub-13</path>
      <file>sub-13_T1w</file>
      <fname>/var/lib/condor/execute/dir_19088/ds/sub-13/sub-13_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_19088/ds/sub-13/sub-13_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_19088/ds/sub-13/mri/msub-13_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_19088/ds/sub-13/mri/p0sub-13_T1w.nii</Fp0>
      <fnames>..19088/ds/sub-13/sub-13_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>36</SurfaceEulerNumber>
      <SurfaceDefectArea>0.970826080347903</SurfaceDefectArea>
      <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0717821419239044</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0721943229436874</SurfacePositionRMSE>
      <res_vx_vol>[1 0.9765625 0.9765625]</res_vx_vol>
      <res_vx_voli>[1 0.9765625 0.9765625]</res_vx_voli>
      <res_RMS>0.984437002015619</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[5.38899993896484 105.499588012695 240.743118286133 359.073211669922]</tissue_mn>
      <tissue_mnr>[0.0150080816820264 0.293810814619064 0.670456945896149 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[5.62016192627743 39.1934501887223 34.8852656537012 23.7730527612006]</tissue_std>
      <tissue_stdr>[0.0158903393894434 0.110814817249775 0.0986339375376701 0.0672154799103737]</tissue_stdr>
      <contrast>120.13306427002</contrast>
      <contrastr>0.33456426858902</contrastr>
      <NCR>0.122640371322632</NCR>
      <ICR>0.271841496229172</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2 1.953125 1.953125]</res_vx_vol>
      <res_RMS>1.96887400403124</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>3.06486916542053</contrastr>
      <NCR>2.09159302711487</NCR>
      <ICR>1.13403153419495</ICR>
      <SurfaceEulerNumber>2.73469387755102</SurfaceEulerNumber>
      <SurfaceDefectArea>1.24270652008698</SurfaceDefectArea>
      <SurfaceDefectNumber>1.925</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.43564283847809</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.44388651847839</SurfacePositionRMSE>
      <IQR>2.03666714684209</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>1980</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20220712-143753</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>36</SurfaceEulerNumber>
         <SurfaceDefectArea>0.970826080347903</SurfaceDefectArea>
         <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0717821419239044</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0721943229436874</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>36</EC_abs>
      <defect_size>0.970826080347903</defect_size>
      <vol_abs_CGW>[239.644577923943 706.40448401956 467.948674220665 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.253045325185738</vol_abs_WMH>
      <vol_rel_WMH>0.000178957376461004</vol_rel_WMH>
      <surf_TSA>1951.65674342431</surf_TSA>
      <vol_TIV>1413.99773616417</vol_TIV>
      <vol_rel_CGW>[0.169480170862254 0.49957964284714 0.330940186290606 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.58630039507642 0.629545289631197]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.60192203521729 0.728133433747749 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.93520317274356 0.245984791019723 0.285429557166014;2.59058579832657 0.181287568896134 0.40727986023072;3.22425510370631 0.257108356293746 0.307290582603266]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.954183797377251 0.32794772478708 0.515283018867924;4.17022461866117 0.357618297019947 0.484716981132075]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00466676103802</vol_TIV>
      <vol_rel_CGW>[0.893681229566337 6.82219186147881 3.79346598941462 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.0178957376461</vol_rel_WMH>
      <surf_TSA>8.61880460442324</surf_TSA>
      <SQR>5.58530065967135</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.240159270051238 12 2 7313.46702575684 0.414165436247593]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0131944194436073 0.00850029103457928 0.371079385280609]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[838.565979751886 414.069175720215 401.652893365598 643.322062024883 1441.22386633181 6521.44172892851]</SPMvols0>
      <SPMvols1>[743.456451565611 386.636427337048 239.250901166131 675.026500926298 1306.56795875699 6274.65100007899]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[119.926002502441 258.670806884766 351.015197753906]</T3th>
            <Tth>
               <T3th>[0 0 8.47887992858887 119.926002502441 258.670806884766 351.015197753906 466.559814453125 1158.19348144531]</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>[0.019030787050724 0.0682469606399536 0.0747789964079857 0 0]</dtc>
         <ll>[0.0831100567668474 0 0.0831100567668474 0;0.194136089494392 0.00993060951187115 0.204066699006263 2117.6826171875;0.194136089494392 0.00993060951187115 0.204066699006263 2117.6826171875]</ll>
         <rmsdtc>[0.0425649620592594 0.0904956758022308 0.100438989698887]</rmsdtc>
         <rmsgdt>[0.0309409182518721 0.0428618229925632 0.0527624785900116]</rmsgdt>
         <rmsdt>0.100438989698887</rmsdt>
         <dt>0.0747789964079857</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>[0.00845250766724348 0.0310087017714977 0.0438985750079155 0.0522218011319637 0.0582273192703724 0.0648739114403725]</dtc>
         <ll>[0.0850081166111561 0 0.0850081166111561 0;0.220851007326007 0.0139470943986569 0.234798101724664 7139.1689453125;0.198894748871771 0.016624998523715 0.215519747395486 11965.2109375;0.179572791002641 0.0182471479106153 0.197819938913257 19675.388671875;0.166331905996103 0.0190589704808006 0.185390876476903 33340.8671875;0.166331905996103 0.0190589704808006 0.185390876476903 33340.8671875]</ll>
         <rmsdtc>[0.0100320819765329 0.0367833524942398 0.0563561469316483 0.0809950977563858 0.10465233027935 0.108880810439587]</rmsdtc>
         <rmsgdt>[0.00321103958413005 0.0124983564019203 0.0278106722980738 0.0475640967488289 0.0654821842908859 0.0693892389535904]</rmsgdt>
         <rmsdt>0.108880810439587</rmsdt>
         <dt>0.0648739114403725</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_19088/ds/sub-13/sub-13_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 85s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 7s</item>
      <item>Estimate background 8s</item>
      <item>Initial correction 10s</item>
      <item>Refine background 4s</item>
      <item>Final correction 8s</item>
      <item>Final scaling 7s</item>
      <item>54s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 16s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 91s</item>
      <item>SPM preprocessing 1 (estimate 2): 97s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 20s</item>
      <item>Update Segmentation 24s</item>
      <item>Update Skull-Stripping 50s</item>
      <item>Update probability maps 11s</item>
      <item>105s</item>
      <item>Global intensity correction: 20s</item>
      <item>SANLM denoising after intensity normalization (medium): 17s</item>
      <item>Fast Optimized Shooting registration 44s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 6s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 18s</item>
      <item>Estimate local tissue thresholds (WM) 20s</item>
      <item>Estimate local tissue thresholds (GM) 29s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 37s</item>
      <item>117s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 11s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 20s</item>
      <item>Blood vessel detection 11s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.01) 30s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 6s</item>
      <item>90s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 48s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>15s</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 | 0.0823 0.0012 0.0835 | 29.4886</item>
      <item>3 | 2.50 | 0.0815 0.0019 0.0833 | 26.9772</item>
      <item>4 | 2.50 | 0.0811 0.0021 0.0832 | 24.6107</item>
      <item>5 | 2.50 | 0.0808 0.0022 0.0830 | 22.6548</item>
      <item>6 | 2.50 | 0.0805 0.0023 0.0828 | 20.6989</item>
      <item>7 | 2.50 | 0.0802 0.0024 0.0826 | 18.9688</item>
      <item>8 | 2.50 | 0.0799 0.0025 0.0824 | 17.4455</item>
      <item>9 | 2.50 | 0.0796 0.0026 0.0822 | 15.9223</item>
      <item>10 | 2.50 | 0.0793 0.0027 0.0820 | 14.6627</item>
      <item>11 | 2.50 | 0.0790 0.0028 0.0817 | 13.4764</item>
      <item>12 | 2.50 | 0.0786 0.0028 0.0815 | 12.3015</item>
      <item>13 | 2.50 | 0.0783 0.0030 0.0812 | 11.3776</item>
      <item>14 | 2.50 | 0.0780 0.0030 0.0810 | 10.4537</item>
      <item>15 | 2.25 | 0.0769 0.0031 0.0800 | 9.5920</item>
      <item>16 | 2.25 | 0.0736 0.0046 0.0783 | 8.8725</item>
      <item>29 | 2.00 | 0.0745 0.0021 0.0766 | 3.3283</item>
      <item>30 | 2.00 | 0.0682 0.0046 0.0729 | 3.1221</item>
      <item>31 | 2.00 | 0.0663 0.0055 0.0718 | 2.9160</item>
      <item>43 | 1.75 | 0.0653 0.0032 0.0684 | 1.5785</item>
      <item>44 | 1.75 | 0.0611 0.0054 0.0665 | 1.5194</item>
      <item>45 | 1.75 | 0.0599 0.0061 0.0659 | 1.4626</item>
      <item>57 | 1.50 | 0.0584 0.0044 0.0628 | 1.0900</item>
      <item>58 | 1.50 | 0.0554 0.0064 0.0618 | 1.0730</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 210s</item>
      <item>Prepare output 12s</item>
      <item>221s</item>
      <item>Jacobian determinant (RMS): 0.010 0.037 0.056 0.081 0.105 | 0.108881</item>
      <item>Template Matching: 0.085 0.221 0.199 0.180 0.166 | 0.166332</item>
      <item>Write result maps: 38s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 41s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 58s</item>
      <item>127s</item>
      <item>Create initial surface 102s</item>
      <item>Topology correction: 119s</item>
      <item>Surface refinement: 94s</item>
      <item>Reduction of surface collisions with optimization: 95s</item>
      <item>Spherical mapping with areal smoothing 106s</item>
      <item>Spherical registration 298s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 52s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 58s</item>
      <item>137s</item>
      <item>Create initial surface 103s</item>
      <item>Topology correction: 116s</item>
      <item>Surface refinement: 95s</item>
      <item>Reduction of surface collisions with optimization: 96s</item>
      <item>Spherical mapping with areal smoothing 106s</item>
      <item>Spherical registration 284s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5863 0.6291 mm</item>
      <item>Surface intensity / position RMSE: 0.0718 / 0.0722</item>
      <item>Euler number / defect number / defect size: 36.0 / 18.5 / 0.97%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_19088/ds/sub-13/surf/lh.thickness.sub-13_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_19088/ds/sub-13/surf/rh.thickness.sub-13_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_19088/ds/sub-13/sub-13_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1992s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 16s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 57s</item>
      <item>ROI estimation of 'lpba40' atlas 17s</item>
      <item>ROI estimation of 'hammers' atlas 41s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 14s</item>
      <item>ROI estimation of 'aal3' atlas 24s</item>
      <item>ROI estimation of 'mori' atlas 36s</item>
      <item>ROI estimation of 'anatomy3' atlas 50s</item>
      <item>ROI estimation of 'julichbrain' atlas 68s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 26s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 108s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 161s</item>
      <item>Write results 162s</item>
      <item>659s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_19088/ds/sub-13/report/catreport_sub-13_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 64 minute(s) and 16 second(s).</item>
      <item>Image Quality Rating (IQR): 84.63% (B)</item>
      <item>GM volume (GMV): 49.96% (706.40 / 1414.00 ml)</item>
      <item>GM thickness (GMT): 2.59 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_19088/ds/sub-13/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_19088/ds/sub-13/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_19088/ds/sub-13/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>