ds003717_ReproVBM/sub-57/report/cat_sub-57_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.0540167990903 0.0284549417481264 -0.0433712886272225 -3.52564821334361;-0.00820824692455928 1.0210123213413 0.253227220540986 -21.33582405982;0.0530557586067786 -0.225544952066891 1.15496609053034 -5.87762664315171;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>[847.649482818856 1089.83754866612 319.611157836912 539.553029748388 345.046342271375 78.5462713615087 168.482529771894 824.09249333024 1147.01355936469 1007.16703052616 579.719548580124 108.252830915515 46.2676630391009]</mn>
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      <ll>-6.60235643386841</ll>
      <Affine_translation>[-3.52564821334361 -21.33582405982 -5.87762664315171]</Affine_translation>
      <Affine_rotation>[0.218702921159261 -0.047412511187657 0.0185003961914859]</Affine_rotation>
      <Affine_scaling>[1.05538320130817 1.04597459530089 1.18312237442755]</Affine_scaling>
      <Affine_shearing>[0.00865910847135547 0.0121068196385803 -0.0030158730573742]</Affine_shearing>
      <Affine0_translation>[-3.52564821334361 -21.33582405982 -5.87762664315171]</Affine0_translation>
      <Affine0_rotation>[0.218702921159261 -0.047412511187657 0.0185003961914859]</Affine0_rotation>
      <Affine0_scaling>[1.05538320130817 1.04597459530089 1.18312237442755]</Affine0_scaling>
      <Affine0_shearing>[0.00865910847135547 0.0121068196385803 -0.0030158730573742]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_3991310/ds/sub-57</path>
      <file>sub-57_T1w</file>
      <fname>/var/lib/condor/execute/dir_3991310/ds/sub-57/sub-57_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_3991310/ds/sub-57/sub-57_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_3991310/ds/sub-57/mri/msub-57_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3991310/ds/sub-57/mri/p0sub-57_T1w.nii</Fp0>
      <fnames>..91310/ds/sub-57/sub-57_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>8</SurfaceEulerNumber>
      <SurfaceDefectArea>0.0750241474900539</SurfaceDefectArea>
      <SurfaceDefectNumber>9</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0670195966959</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0666096061468124</SurfacePositionRMSE>
      <res_vx_vol>[0.800000019074096 0.800000106205726 0.800000048447407]</res_vx_vol>
      <res_vx_voli>[0.800000019074096 0.800000106205726 0.800000048447407]</res_vx_voli>
      <res_RMS>0.800000057909077</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[22.0074996948242 317.929443359375 835.33935546875 1109.3515625]</tissue_mn>
      <tissue_mnr>[0.0198381654918194 0.286590337753296 0.752997875213623 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[69.1243285640148 138.33615996873 100.322440635381 47.1940246043454]</tissue_std>
      <tissue_stdr>[0.0635717138648033 0.127223894000053 0.0922637432813644 0.0434030257165432]</tissue_stdr>
      <contrast>279.55810546875</contrast>
      <contrastr>0.252001374959946</contrastr>
      <NCR>0.124588571488857</NCR>
      <ICR>0.133336365222931</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.60000003814819 1.60000021241145 1.60000009689481]</res_vx_vol>
      <res_RMS>1.60000011581815</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>4.3033127784729</contrastr>
      <NCR>2.11956024169922</NCR>
      <ICR>0.790516793727875</ICR>
      <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
      <SurfaceDefectArea>1.01875603687251</SurfaceDefectArea>
      <SurfaceDefectNumber>1.45</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.34039187431335</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.33219218254089</SurfacePositionRMSE>
      <IQR>1.96815263523208</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>1980</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20220709-215926</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>8</SurfaceEulerNumber>
         <SurfaceDefectArea>0.0750241474900539</SurfaceDefectArea>
         <SurfaceDefectNumber>9</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0670195966959</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0666096061468124</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>8</EC_abs>
      <defect_size>0.0750241474900539</defect_size>
      <vol_abs_CGW>[259.064028901223 630.472527689256 476.078910224037 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.841079649314684</vol_abs_WMH>
      <vol_rel_WMH>0.000615897864189117</vol_rel_WMH>
      <surf_TSA>1759.08022367883</surf_TSA>
      <vol_TIV>1365.61546681452</vol_TIV>
      <vol_rel_CGW>[0.189704961020634 0.461676469701913 0.348618569277452 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.52610417823728 0.601250571465721]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.56164121627808 0.733492842089313 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.9117893635496 0.251845768871459 0.266419875312973;2.54638705627931 0.170611926322172 0.426654901032363;3.1443578963758 0.252245466274078 0.306925223654664]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.840201731478732 0.353288371184848 0.603024989039895;4.00729036475992 0.326781200946494 0.396975010960105]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.02811623295524</vol_TIV>
      <vol_rel_CGW>[1.25691381143381 6.14145958516367 4.11096568386229 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06158978641891</vol_rel_WMH>
      <surf_TSA>8.56089860376051</surf_TSA>
      <SQR>5.04714389547481</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.0872250100160256 22 13130 9331.86301849806 0.323939477097322]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.024615291506052 0.0252297837287188 0.1319390386343]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[730.957332192788 444.382449066355 374.956788060536 528.683502290735 1888.91683196784 6877.05657583043]</SPMvols0>
      <SPMvols1>[643.242386713326 419.659822960359 250.621448244311 421.428729132729 1352.38932935411 7136.33257880122]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[348.100402832031 830.297912597656 1089.41870117188]</T3th>
            <Tth>
               <T3th>[0 0 30.777172088623 348.100402832031 830.297912597656 1089.41870117188 1460.07788085938 2449.74853515625]</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>[0.024278687313199 0.092766247689724 0.10366179049015 0 0]</dtc>
         <ll>[0.0867076933312387 0 0.0867076933312387 0;0.189720804093122 0.0128986615092814 0.202619465602403 2750.61376953125;0.189720804093122 0.0128986615092814 0.202619465602403 2750.61376953125]</ll>
         <rmsdtc>[0.0507881231606007 0.119730785489082 0.131803065538406]</rmsdtc>
         <rmsgdt>[0.0358546078205109 0.0503321178257465 0.0608117952942848]</rmsgdt>
         <rmsdt>0.131803065538406</rmsdt>
         <dt>0.10366179049015</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>[0.0119652235880494 0.0456822402775288 0.0657691285014153 0.0739974528551102 0.0783105716109276 0.0884738117456436]</dtc>
         <ll>[0.0852734303545976 0 0.0852734303545976 0;0.214897145909646 0.0172598176129426 0.232156963522589 8834.869140625;0.186035395060802 0.0192936183262367 0.205329013387039 13885.8486328125;0.16552379350943 0.0194624803910794 0.184986273900509 20985.84765625;0.152005877315785 0.0196152453399914 0.171621122655776 34313.98828125;0.152005877315785 0.0196152453399914 0.171621122655776 34313.98828125]</ll>
         <rmsdtc>[0.0138977011665702 0.0521636754274368 0.0775788351893425 0.103718489408493 0.124021880328655 0.128787308931351]</rmsdtc>
         <rmsgdt>[0.00374071253463626 0.0148385334759951 0.030013071373105 0.048358578234911 0.0638675689697266 0.0676692873239517]</rmsgdt>
         <rmsdt>0.128787308931351</rmsdt>
         <dt>0.0884738117456436</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_3991310/ds/sub-57/sub-57_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 82s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 15s</item>
      <item>Estimate background 11s</item>
      <item>Initial correction 19s</item>
      <item>Refine background 11s</item>
      <item>Final correction 17s</item>
      <item>Final scaling 15s</item>
      <item>103s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 15s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 167s</item>
      <item>SPM preprocessing 1 (estimate 2): 104s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 39s</item>
      <item>Update Segmentation 42s</item>
      <item>Update Skull-Stripping 92s</item>
      <item>Update probability maps 19s</item>
      <item>191s</item>
      <item>Global intensity correction: 35s</item>
      <item>SANLM denoising after intensity normalization (medium): 19s</item>
      <item>Fast Optimized Shooting registration 64s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 10s</item>
      <item>Prepare partitions 5s</item>
      <item>Prepare segments (LASmod = 1.00) 31s</item>
      <item>Estimate local tissue thresholds (WM) 37s</item>
      <item>Estimate local tissue thresholds (GM) 52s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 59s</item>
      <item>203s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 20s</item>
      <item>Major structures 9s</item>
      <item>Ventricle detection 26s</item>
      <item>Blood vessel detection 22s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.11) 61s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 4s</item>
      <item>Side alignment 9s</item>
      <item>Final corrections 10s</item>
      <item>161s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 51s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 9s</item>
      <item>Level 1 cleanup (brain masking) 6s</item>
      <item>Level 2 cleanup (CSF correction) 3s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 6s</item>
      <item>24s</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 | 0.0853 0.0000 0.0853 | 32.0000</item>
      <item>2 | 2.50 | 0.0819 0.0014 0.0833 | 29.4886</item>
      <item>3 | 2.50 | 0.0809 0.0022 0.0831 | 26.9772</item>
      <item>4 | 2.50 | 0.0804 0.0025 0.0829 | 24.6107</item>
      <item>5 | 2.50 | 0.0799 0.0027 0.0826 | 22.6548</item>
      <item>6 | 2.50 | 0.0796 0.0028 0.0824 | 20.6989</item>
      <item>7 | 2.50 | 0.0792 0.0030 0.0822 | 18.9688</item>
      <item>8 | 2.50 | 0.0788 0.0031 0.0819 | 17.4455</item>
      <item>9 | 2.50 | 0.0784 0.0032 0.0816 | 15.9223</item>
      <item>10 | 2.50 | 0.0780 0.0034 0.0814 | 14.6627</item>
      <item>11 | 2.50 | 0.0776 0.0035 0.0811 | 13.4764</item>
      <item>12 | 2.50 | 0.0771 0.0036 0.0807 | 12.3015</item>
      <item>13 | 2.50 | 0.0767 0.0038 0.0804 | 11.3776</item>
      <item>14 | 2.50 | 0.0762 0.0039 0.0801 | 10.4537</item>
      <item>15 | 2.25 | 0.0752 0.0040 0.0791 | 9.5920</item>
      <item>16 | 2.25 | 0.0716 0.0058 0.0774 | 8.8725</item>
      <item>29 | 2.00 | 0.0713 0.0026 0.0739 | 3.3283</item>
      <item>30 | 2.00 | 0.0643 0.0053 0.0697 | 3.1221</item>
      <item>31 | 2.00 | 0.0620 0.0064 0.0684 | 2.9160</item>
      <item>43 | 1.75 | 0.0604 0.0038 0.0641 | 1.5785</item>
      <item>44 | 1.75 | 0.0565 0.0058 0.0623 | 1.5194</item>
      <item>45 | 1.75 | 0.0552 0.0065 0.0617 | 1.4626</item>
      <item>57 | 1.50 | 0.0534 0.0048 0.0582 | 1.0900</item>
      <item>58 | 1.50 | 0.0507 0.0065 0.0572 | 1.0730</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 201s</item>
      <item>Prepare output 19s</item>
      <item>219s</item>
      <item>Jacobian determinant (RMS): 0.014 0.052 0.078 0.104 0.124 | 0.128787</item>
      <item>Template Matching: 0.085 0.215 0.186 0.166 0.152 | 0.152006</item>
      <item>Write result maps: 60s</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: 17s</item>
      <item>PBT2x thickness: 53s</item>
      <item>118s</item>
      <item>Create initial surface 77s</item>
      <item>Topology correction: 83s</item>
      <item>Surface refinement: 96s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 85s</item>
      <item>Spherical registration 283s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 45s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 53s</item>
      <item>123s</item>
      <item>Create initial surface 78s</item>
      <item>Topology correction: 81s</item>
      <item>Surface refinement: 87s</item>
      <item>Reduction of surface collisions with optimization: 53s</item>
      <item>Spherical mapping with areal smoothing 85s</item>
      <item>Spherical registration 290s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5261 0.6011 mm</item>
      <item>Surface intensity / position RMSE: 0.0670 / 0.0666</item>
      <item>Euler number / defect number / defect size: 8.0 / 9.0 / 0.08%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3991310/ds/sub-57/surf/lh.thickness.sub-57_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3991310/ds/sub-57/surf/rh.thickness.sub-57_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3991310/ds/sub-57/sub-57_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1731s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 30s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 114s</item>
      <item>ROI estimation of 'lpba40' atlas 33s</item>
      <item>ROI estimation of 'hammers' atlas 80s</item>
      <item>ROI estimation of 'thalamus' atlas 6s</item>
      <item>ROI estimation of 'ibsr' atlas 28s</item>
      <item>ROI estimation of 'aal3' atlas 44s</item>
      <item>ROI estimation of 'mori' atlas 65s</item>
      <item>ROI estimation of 'anatomy3' atlas 94s</item>
      <item>ROI estimation of 'julichbrain' atlas 125s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 46s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 56s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 201s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 301s</item>
      <item>Write results 301s</item>
      <item>1223s</item>
      <item>Quality check: 10s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3991310/ds/sub-57/report/catreport_sub-57_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 77 minute(s) and 42 second(s).</item>
      <item>Image Quality Rating (IQR): 85.32% (B)</item>
      <item>GM volume (GMV): 46.17% (630.47 / 1365.62 ml)</item>
      <item>GM thickness (GMT): 2.53 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3991310/ds/sub-57/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3991310/ds/sub-57/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3991310/ds/sub-57/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>