ds003974_ReproVBM/sub-27/report/cat_sub-27_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.04365171056261 0.0293671959757431 -0.0267550655674922 0.302183405540212;-0.027138546051183 1.02504323470018 0.29594973304702 -21.2231361612071;0.0367580230171911 -0.240045486550657 1.12484578412216 1.79707761863818;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>[347.454365780584 432.836025620952 159.010439094353 252.264441509477 202.588148463134 44.4134812587336 96.3332143135086 548.29441953613 999.928592656231 751.530371718752 386.416594300763 393.596747403748 30.6477403205109]</mn>
      <vr>[1248.34975578658;289.538824634374;933.648106348041;1501.90304185139;3583.64717503719;327.501658595523;970.775506846722;15515.0358724383;12352.6282073609;29820.7764812416;3145.9129325339;12632.9389615554;302.56630683284]</vr>
      <ll>-5.76949453353882</ll>
      <Affine_translation>[0.302183405540212 -21.2231361612071 1.79707761863818]</Affine_translation>
      <Affine_rotation>[0.230826001387407 -0.0283297602864183 0.0333458501660166]</Affine_rotation>
      <Affine_scaling>[1.0446513992228 1.05316902405886 1.16301153737035]</Affine_scaling>
      <Affine_shearing>[-0.0054913178798001 0.0049413624912144 0.0293833730407152]</Affine_shearing>
      <Affine0_translation>[0.302183405540212 -21.2231361612071 1.79707761863818]</Affine0_translation>
      <Affine0_rotation>[0.230826001387407 -0.0283297602864183 0.0333458501660166]</Affine0_rotation>
      <Affine0_scaling>[1.0446513992228 1.05316902405886 1.16301153737035]</Affine0_scaling>
      <Affine0_shearing>[-0.0054913178798001 0.0049413624912144 0.0293833730407152]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_11428/ds/sub-27</path>
      <file>sub-27_T1w</file>
      <fname>/var/lib/condor/execute/dir_11428/ds/sub-27/sub-27_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_11428/ds/sub-27/sub-27_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_11428/ds/sub-27/mri/msub-27_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_11428/ds/sub-27/mri/p0sub-27_T1w.nii</Fp0>
      <fnames>..11428/ds/sub-27/sub-27_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>28</SurfaceEulerNumber>
      <SurfaceDefectArea>0.939245548123159</SurfaceDefectArea>
      <SurfaceDefectNumber>20</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0724707916378975</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0747916698455811</SurfacePositionRMSE>
      <res_vx_vol>[0.999999973286646 1 0.999999973286646]</res_vx_vol>
      <res_vx_voli>[0.99999997318384 1 0.999999973287865]</res_vx_voli>
      <res_RMS>0.999999982191097</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[5.19849967956543 138.516174316406 323.086242675781 443.096343994141]</tissue_mn>
      <tissue_mnr>[0.0117322104051709 0.312609612941742 0.729155719280243 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[6.06067899736536 50.0462844853234 41.7603099728886 23.2288814274783]</tissue_std>
      <tissue_stdr>[0.0138403940945864 0.114287577569485 0.0953654125332832 0.0530463457107544]</tissue_stdr>
      <contrast>121.434791564941</contrast>
      <contrastr>0.274059563875198</contrastr>
      <NCR>0.163042992353439</NCR>
      <ICR>0.420696943998337</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.99999994657329 2 1.99999994657329]</res_vx_vol>
      <res_RMS>1.99999996438219</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>3.97243976593018</contrastr>
      <NCR>2.67159056663513</NCR>
      <ICR>1.50321662425995</ICR>
      <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
      <SurfaceDefectArea>1.23481138703079</SurfaceDefectArea>
      <SurfaceDefectNumber>2</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.44941580295563</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.49583339691162</SurfacePositionRMSE>
      <IQR>2.47883938504421</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>20220712-163121</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>28</SurfaceEulerNumber>
         <SurfaceDefectArea>0.939245548123159</SurfaceDefectArea>
         <SurfaceDefectNumber>20</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0724707916378975</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0747916698455811</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>28</EC_abs>
      <defect_size>0.939245548123159</defect_size>
      <vol_abs_CGW>[201.809667628845 629.856174128009 536.320920311262 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.01382347514352</vol_abs_WMH>
      <vol_rel_WMH>0.00074110620311181</vol_rel_WMH>
      <surf_TSA>1925.25051392011</surf_TSA>
      <vol_TIV>1367.98676206812</vol_TIV>
      <vol_rel_CGW>[0.147523114422357 0.46042563538831 0.392051250189333 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.47232043128721 0.657315404454224]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.51326870918274 0.75837253285927 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.77953394153661 0.257012686961078 0.276557940470787;2.48321913775716 0.188556945726819 0.396225925685753;3.11753691262251 0.262342866392779 0.32721613384346]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.827780286114366 0.256737884159918 0.55004003202562;4.08174136704067 0.360710799183348 0.449959967974379]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.02437793156823</vol_TIV>
      <vol_rel_CGW>[0.5 6.11899488843947 4.89100664851532 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.07411062031118</vol_rel_WMH>
      <surf_TSA>8.61645404447314</surf_TSA>
      <SQR>5.10123512921423</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.0414129578892868 1 12172 4265.69677209785 0.430350916647195]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0229283478111029 0.00468142703175545 0.479249835014343]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[756.640469302245 503.544953438253 345.688824633121 528.567003079257 658.073435362685 2137.12735619145]</SPMvols0>
      <SPMvols1>[652.825396427917 468.073159258566 206.514086984868 554.564950707239 678.405093097895 1889.8534439374]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[166.886795043945 339.184204101562 432.862091064453]</T3th>
            <Tth>
               <T3th>[0 0 13.9503316879272 166.886795043945 339.184204101562 432.862091064453 565.849731445312 1516.63525390625]</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>[0.0239265765994787 0.09089345484972 0.103710226714611 0 0]</dtc>
         <ll>[0.0889164992168743 0 0.0889164992168743 0;0.184341833657291 0.0152931316416948 0.199634965298986 3261.22973632812;0.184341833657291 0.0152931316416948 0.199634965298986 3261.22973632812]</ll>
         <rmsdtc>[0.0515950918197632 0.133380204439163 0.152292683720589]</rmsdtc>
         <rmsgdt>[0.037035658955574 0.0692042037844658 0.0823762938380241]</rmsgdt>
         <rmsdt>0.152292683720589</rmsdt>
         <dt>0.103710226714611</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>[0.011252417229116 0.0450917482376099 0.0617153719067574 0.0713741183280945 0.0778183788061142 0.0935249701142311]</dtc>
         <ll>[0.0901730469308898 0 0.0901730469308898 0;0.222800106837607 0.0241410809676435 0.24694118780525 12357.2158203125;0.194582694188787 0.0245293321321584 0.219112026320945 17654.0546875;0.169821729234368 0.0247980572446006 0.194619786478968 26739.05078125;0.151981010979488 0.0266250713478069 0.178606082327295 46576.6484375;0.151981010979488 0.0266250713478069 0.178606082327295 46576.6484375]</ll>
         <rmsdtc>[0.0135421641170979 0.0547605007886887 0.0920648723840714 0.139850214123726 0.179582953453064 0.187614321708679]</rmsdtc>
         <rmsgdt>[0.00447488948702812 0.0208170525729656 0.0439081415534019 0.0745519548654556 0.0981487631797791 0.100846491754055]</rmsgdt>
         <rmsdt>0.187614321708679</rmsdt>
         <dt>0.0935249701142311</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_11428/ds/sub-27/sub-27_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 33s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 2s</item>
      <item>Estimate background 4s</item>
      <item>Initial correction 3s</item>
      <item>Refine background 1s</item>
      <item>Final correction 3s</item>
      <item>Final scaling 3s</item>
      <item>20s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 50s</item>
      <item>SPM preprocessing 1 (estimate 2): 33s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 8s</item>
      <item>Update Segmentation 12s</item>
      <item>Update Skull-Stripping 20s</item>
      <item>Update probability maps 3s</item>
      <item>44s</item>
      <item>Global intensity correction: 7s</item>
      <item>SANLM denoising after intensity normalization (medium): 8s</item>
      <item>Fast Optimized Shooting registration 26s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 1s</item>
      <item>Prepare segments (LASmod = 1.00) 11s</item>
      <item>Estimate local tissue thresholds (WM) 11s</item>
      <item>Estimate local tissue thresholds (GM) 17s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 14s</item>
      <item>57s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 4s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 10s</item>
      <item>Blood vessel detection 8s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 22s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 2s</item>
      <item>52s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s</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) 3s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>8s</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 | 0.0902 0.0000 0.0902 | 32.0000</item>
      <item>2 | 2.50 | 0.0859 0.0016 0.0875 | 29.4886</item>
      <item>3 | 2.50 | 0.0845 0.0026 0.0871 | 26.9772</item>
      <item>4 | 2.50 | 0.0838 0.0030 0.0868 | 24.6107</item>
      <item>5 | 2.50 | 0.0832 0.0033 0.0865 | 22.6548</item>
      <item>6 | 2.50 | 0.0828 0.0034 0.0862 | 20.6989</item>
      <item>7 | 2.50 | 0.0823 0.0036 0.0859 | 18.9688</item>
      <item>8 | 2.50 | 0.0818 0.0038 0.0856 | 17.4455</item>
      <item>9 | 2.50 | 0.0813 0.0039 0.0852 | 15.9223</item>
      <item>10 | 2.50 | 0.0807 0.0041 0.0849 | 14.6627</item>
      <item>11 | 2.50 | 0.0802 0.0043 0.0845 | 13.4764</item>
      <item>12 | 2.50 | 0.0797 0.0044 0.0841 | 12.3015</item>
      <item>13 | 2.50 | 0.0791 0.0046 0.0837 | 11.3776</item>
      <item>14 | 2.50 | 0.0786 0.0047 0.0833 | 10.4537</item>
      <item>15 | 2.25 | 0.0807 0.0048 0.0855 | 9.5920</item>
      <item>16 | 2.25 | 0.0763 0.0071 0.0834 | 8.8725</item>
      <item>17 | 2.25 | 0.0743 0.0080 0.0823 | 8.1530</item>
      <item>29 | 2.00 | 0.0749 0.0037 0.0786 | 3.3283</item>
      <item>30 | 2.00 | 0.0676 0.0069 0.0745 | 3.1221</item>
      <item>31 | 2.00 | 0.0649 0.0082 0.0730 | 2.9160</item>
      <item>43 | 1.75 | 0.0633 0.0048 0.0681 | 1.5785</item>
      <item>44 | 1.75 | 0.0583 0.0074 0.0657 | 1.5194</item>
      <item>45 | 1.75 | 0.0566 0.0083 0.0649 | 1.4626</item>
      <item>57 | 1.50 | 0.0550 0.0062 0.0611 | 1.0900</item>
      <item>58 | 1.50 | 0.0517 0.0082 0.0600 | 1.0730</item>
      <item>59 | 1.50 | 0.0507 0.0089 0.0595 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 157s</item>
      <item>Prepare output 8s</item>
      <item>165s</item>
      <item>Jacobian determinant (RMS): 0.014 0.055 0.092 0.140 0.180 | 0.187614</item>
      <item>Template Matching: 0.090 0.223 0.195 0.170 0.152 | 0.151981</item>
      <item>Write result maps: 12s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 33s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 41s</item>
      <item>95s</item>
      <item>Create initial surface 83s</item>
      <item>Topology correction: 90s</item>
      <item>Surface refinement: 76s</item>
      <item>Reduction of surface collisions with optimization: 69s</item>
      <item>Spherical mapping with areal smoothing 101s</item>
      <item>Spherical registration 289s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 34s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 40s</item>
      <item>92s</item>
      <item>Create initial surface 77s</item>
      <item>Topology correction: 82s</item>
      <item>Surface refinement: 65s</item>
      <item>Reduction of surface collisions with optimization: 65s</item>
      <item>Spherical mapping with areal smoothing 81s</item>
      <item>Spherical registration 297s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4722 0.6570 mm</item>
      <item>Surface intensity / position RMSE: 0.0725 / 0.0748</item>
      <item>Euler number / defect number / defect size: 28.0 / 20.0 / 0.94%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_11428/ds/sub-27/surf/lh.thickness.sub-27_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_11428/ds/sub-27/surf/rh.thickness.sub-27_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_11428/ds/sub-27/sub-27_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1639s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 3s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 12s</item>
      <item>ROI estimation of 'lpba40' atlas 3s</item>
      <item>ROI estimation of 'hammers' atlas 8s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 3s</item>
      <item>ROI estimation of 'aal3' atlas 5s</item>
      <item>ROI estimation of 'mori' atlas 7s</item>
      <item>ROI estimation of 'anatomy3' atlas 10s</item>
      <item>ROI estimation of 'julichbrain' atlas 13s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 5s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 9s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 20s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 31s</item>
      <item>Write results 32s</item>
      <item>130s</item>
      <item>Quality check: 4s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_11428/ds/sub-27/report/catreport_sub-27_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 39 minute(s) and 55 second(s).</item>
      <item>Image Quality Rating (IQR): 80.21% (B-)</item>
      <item>GM volume (GMV): 46.04% (629.86 / 1367.99 ml)</item>
      <item>GM thickness (GMT): 2.47 0.66 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_11428/ds/sub-27/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_11428/ds/sub-27/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_11428/ds/sub-27/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>