ds003768_ReproVBM/sub-11/report/cat_sub-11_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.0076045782601 -0.085675127889727 -0.0677780731741938 -2.77912011817895;0.081002331185788 1.02781712761526 0.175262877614973 -14.9770765713502;0.0516729692570197 -0.201232013959319 1.0470711180626 32.3427741682824;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>[238.467937677712 337.812882611293 88.0380613312308 165.902688768074 332.621806890944 32.3994564658685 102.424615220352 313.387935411613 553.631675766652 431.336097450776 261.765265802252 208.866815624511 18.5530203668881]</mn>
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      <ll>-5.67979907989502</ll>
      <Affine_translation>[-2.77912011817895 -14.9770765713502 32.3427741682824]</Affine_translation>
      <Affine_rotation>[0.187989962563232 -0.0653102978757191 -0.0691323663502896]</Affine_rotation>
      <Affine_scaling>[1.01217511308078 1.05074521860525 1.06353826451242]</Affine_scaling>
      <Affine_shearing>[-0.0131472363678189 8.27577109519706e-06 -0.0224253321191517]</Affine_shearing>
      <Affine0_translation>[-2.77912011817895 -14.9770765713502 32.3427741682824]</Affine0_translation>
      <Affine0_rotation>[0.187989962563232 -0.0653102978757191 -0.0691323663502896]</Affine0_rotation>
      <Affine0_scaling>[1.01217511308078 1.05074521860525 1.06353826451242]</Affine0_scaling>
      <Affine0_shearing>[-0.0131472363678189 8.27577109519706e-06 -0.0224253321191517]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_10502/ds/sub-11</path>
      <file>sub-11_T1w</file>
      <fname>/var/lib/condor/execute/dir_10502/ds/sub-11/sub-11_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_10502/ds/sub-11/sub-11_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_10502/ds/sub-11/mri/msub-11_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_10502/ds/sub-11/mri/p0sub-11_T1w.nii</Fp0>
      <fnames>..10502/ds/sub-11/sub-11_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>42</SurfaceEulerNumber>
      <SurfaceDefectArea>1.34195550947767</SurfaceDefectArea>
      <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0721261352300644</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0767283588647842</SurfacePositionRMSE>
      <res_vx_vol>[1.00000163049119 0.999999973153342 0.999999967996754]</res_vx_vol>
      <res_vx_voli>[1.00000162663464 0.999999970087758 0.999999966534547]</res_vx_voli>
      <res_RMS>1.00000052388073</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[4.27299976348877 71.3309097290039 204.627014160156 331.089874267578]</tissue_mn>
      <tissue_mnr>[0.0129058612510562 0.21544274687767 0.61804074048996 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[5.49839290364037 39.2585839637365 36.5709142031055 24.2755923970244]</tissue_std>
      <tissue_stdr>[0.0168240796774626 0.120124109089375 0.111900329589844 0.0742788836359978]</tissue_stdr>
      <contrast>117.849006652832</contrast>
      <contrastr>0.355942666530609</contrastr>
      <NCR>0.131874963641167</NCR>
      <ICR>0.38789963722229</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.00000326098237 1.99999994630668 1.99999993599351]</res_vx_vol>
      <res_RMS>2.00000104776147</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>2.74419331550598</contrastr>
      <NCR>2.22415971755981</NCR>
      <ICR>1.42187404632568</ICR>
      <SurfaceEulerNumber>3.04081632653061</SurfaceEulerNumber>
      <SurfaceDefectArea>1.33548887736942</SurfaceDefectArea>
      <SurfaceDefectNumber>1.875</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.44252276420593</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.53456711769104</SurfacePositionRMSE>
      <IQR>2.13234959837764</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>20220712-144205</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>42</SurfaceEulerNumber>
         <SurfaceDefectArea>1.34195550947767</SurfaceDefectArea>
         <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0721261352300644</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0767283588647842</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>42</EC_abs>
      <defect_size>1.34195550947767</defect_size>
      <vol_abs_CGW>[271.01314523112 807.542748669266 592.541118449374 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.848303286898161</vol_abs_WMH>
      <vol_rel_WMH>0.000507632579454706</vol_rel_WMH>
      <surf_TSA>2186.20332711656</surf_TSA>
      <vol_TIV>1671.09701234976</vol_TIV>
      <vol_rel_CGW>[0.162176787600166 0.483241094144358 0.354582118255475 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.59857247582034 0.62911016265569]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.59157633781433 0.73045153343309 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.99401509177675 0.242823150318361 0.310866407176996;2.6348039592626 0.184521616850434 0.422768555174823;3.30880842731606 0.268604357195255 0.266365037648181]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.961847674726144 0.35586352529775 0.55215319449347;4.21551955415697 0.337394280199202 0.44784680550653]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.56446116546427</vol_TIV>
      <vol_rel_CGW>[0.762514145117931 6.52875528276505 4.21806965257679 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.05076325794547</vol_rel_WMH>
      <surf_TSA>8.62387727125751</surf_TSA>
      <SQR>5.35898617767063</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.150775671005249 1 1 10685.7317941098 0.393416398278987]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00914477929472923 0.00608599651604891 0.310428202152252]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[984.066667758314 518.227719925686 535.407950704326 1801.43326707888 2162.28791353943 7556.3000830076]</SPMvols0>
      <SPMvols1>[837.012492777189 487.156973314989 303.721180675826 1559.38315928121 1932.82803718821 7464.45547276444]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[90.0986022949219 225.681304931641 338.245910644531]</T3th>
            <Tth>
               <T3th>[0 0 5.50323677062988 90.0986022949219 225.681304931641 338.245910644531 462.319580078125 1214.54907226562]</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>[0.0191985815763474 0.0657286792993546 0.0722915753722191 0 0]</dtc>
         <ll>[0.0849069547252495 0 0.0849069547252495 0;0.200849755185277 0.0104716073135797 0.211321362498857 2233.04931640625;0.200849755185277 0.0104716073135797 0.211321362498857 2233.04931640625]</ll>
         <rmsdtc>[0.0485909394919872 0.0894294083118439 0.100814618170261]</rmsdtc>
         <rmsgdt>[0.0357355661690235 0.0452672280371189 0.0561535619199276]</rmsgdt>
         <rmsdt>0.100814618170261</rmsdt>
         <dt>0.0722915753722191</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>[0.00767746847122908 0.0283862762153149 0.0396190471947193 0.0488202646374702 0.0560529120266438 0.0621300488710403]</dtc>
         <ll>[0.0862826866079142 0 0.0862826866079142 0;0.223271886446886 0.0153374694749695 0.238609355921856 7850.8671875;0.205876295830832 0.0174489622780536 0.223325258108886 12558.2275390625;0.184730029853321 0.01984632479386 0.204576354647181 21399.736328125;0.167253746813822 0.0231939903281385 0.19044773714196 40574.4765625;0.167253746813822 0.0231939903281385 0.19044773714196 40574.4765625]</ll>
         <rmsdtc>[0.00933310203254223 0.0330324284732342 0.0521988421678543 0.0760933235287666 0.102730005979538 0.108473740518093]</rmsdtc>
         <rmsgdt>[0.00322284246794879 0.0125183779746294 0.0280409548431635 0.0486615374684334 0.0733207613229752 0.0753358379006386]</rmsgdt>
         <rmsdt>0.108473740518093</rmsdt>
         <dt>0.0621300488710403</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_10502/ds/sub-11/sub-11_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 87s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 7s</item>
      <item>Initial correction 7s</item>
      <item>Refine background 3s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 6s</item>
      <item>40s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 9s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 80s</item>
      <item>SPM preprocessing 1 (estimate 2): 60s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 17s</item>
      <item>Update Segmentation 19s</item>
      <item>Update Skull-Stripping 46s</item>
      <item>Update probability maps 9s</item>
      <item>91s</item>
      <item>Global intensity correction: 17s</item>
      <item>SANLM denoising after intensity normalization (medium): 24s</item>
      <item>Fast Optimized Shooting registration 33s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.23) 16s</item>
      <item>Estimate local tissue thresholds (WM) 20s</item>
      <item>Estimate local tissue thresholds (GM) 28s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 37s</item>
      <item>111s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 8s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 19s</item>
      <item>Blood vessel detection 10s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.04) 29s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 5s</item>
      <item>81s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 5s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>12s</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 | 0.0863 0.0000 0.0863 | 32.0000</item>
      <item>2 | 2.50 | 0.0831 0.0013 0.0844 | 29.4886</item>
      <item>3 | 2.50 | 0.0823 0.0020 0.0842 | 26.9772</item>
      <item>4 | 2.50 | 0.0818 0.0022 0.0840 | 24.6107</item>
      <item>5 | 2.50 | 0.0815 0.0023 0.0838 | 22.6548</item>
      <item>6 | 2.50 | 0.0812 0.0024 0.0836 | 20.6989</item>
      <item>7 | 2.50 | 0.0809 0.0025 0.0834 | 18.9688</item>
      <item>8 | 2.50 | 0.0806 0.0026 0.0832 | 17.4455</item>
      <item>9 | 2.50 | 0.0803 0.0027 0.0830 | 15.9223</item>
      <item>10 | 2.50 | 0.0800 0.0028 0.0827 | 14.6627</item>
      <item>11 | 2.50 | 0.0797 0.0028 0.0825 | 13.4764</item>
      <item>12 | 2.50 | 0.0793 0.0029 0.0822 | 12.3015</item>
      <item>13 | 2.50 | 0.0790 0.0030 0.0820 | 11.3776</item>
      <item>14 | 2.50 | 0.0787 0.0030 0.0817 | 10.4537</item>
      <item>15 | 2.25 | 0.0788 0.0031 0.0818 | 9.5920</item>
      <item>16 | 2.25 | 0.0756 0.0046 0.0802 | 8.8725</item>
      <item>17 | 2.25 | 0.0744 0.0051 0.0795 | 8.1530</item>
      <item>29 | 2.00 | 0.0766 0.0023 0.0789 | 3.3283</item>
      <item>30 | 2.00 | 0.0706 0.0049 0.0755 | 3.1221</item>
      <item>31 | 2.00 | 0.0686 0.0058 0.0744 | 2.9160</item>
      <item>43 | 1.75 | 0.0678 0.0033 0.0711 | 1.5785</item>
      <item>44 | 1.75 | 0.0631 0.0058 0.0689 | 1.5194</item>
      <item>45 | 1.75 | 0.0616 0.0066 0.0682 | 1.4626</item>
      <item>57 | 1.50 | 0.0603 0.0048 0.0651 | 1.0900</item>
      <item>58 | 1.50 | 0.0569 0.0071 0.0639 | 1.0730</item>
      <item>59 | 1.50 | 0.0558 0.0077 0.0635 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 164s</item>
      <item>Prepare output 11s</item>
      <item>174s</item>
      <item>Jacobian determinant (RMS): 0.009 0.033 0.052 0.076 0.103 | 0.108474</item>
      <item>Template Matching: 0.086 0.223 0.206 0.185 0.167 | 0.167254</item>
      <item>Write result maps: 24s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 46s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 49s</item>
      <item>118s</item>
      <item>Create initial surface 96s</item>
      <item>Topology correction: 108s</item>
      <item>Surface refinement: 96s</item>
      <item>Reduction of surface collisions with optimization: 84s</item>
      <item>Spherical mapping with areal smoothing 88s</item>
      <item>Spherical registration 282s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 46s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 50s</item>
      <item>120s</item>
      <item>Create initial surface 93s</item>
      <item>Topology correction: 105s</item>
      <item>Surface refinement: 121s</item>
      <item>Reduction of surface collisions with optimization: 94s</item>
      <item>Spherical mapping with areal smoothing 102s</item>
      <item>Spherical registration 321s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5982 0.6290 mm</item>
      <item>Surface intensity / position RMSE: 0.0721 / 0.0767</item>
      <item>Euler number / defect number / defect size: 42.0 / 17.5 / 1.34%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_10502/ds/sub-11/surf/lh.thickness.sub-11_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_10502/ds/sub-11/surf/rh.thickness.sub-11_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_10502/ds/sub-11/sub-11_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1929s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 10s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 35s</item>
      <item>ROI estimation of 'lpba40' atlas 11s</item>
      <item>ROI estimation of 'hammers' atlas 24s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 8s</item>
      <item>ROI estimation of 'aal3' atlas 14s</item>
      <item>ROI estimation of 'mori' atlas 19s</item>
      <item>ROI estimation of 'anatomy3' atlas 28s</item>
      <item>ROI estimation of 'julichbrain' atlas 36s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 56s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
      <item>Write results 86s</item>
      <item>370s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_10502/ds/sub-11/report/catreport_sub-11_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 54 minute(s) and 30 second(s).</item>
      <item>Image Quality Rating (IQR): 83.68% (B)</item>
      <item>GM volume (GMV): 48.32% (807.54 / 1671.10 ml)</item>
      <item>GM thickness (GMT): 2.60 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_10502/ds/sub-11/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_10502/ds/sub-11/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_10502/ds/sub-11/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>