ds004169_ReproVBM/sub-0663/report/cat_sub-0663_ses-01_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[47.4908417877053 67.077813739033 25.0191102348777 29.779215068137 24.5426331935936 7.33155271634258 13.2535634308627 49.0161662035636 109.823579129655 94.8372070809986 39.8126518328039 12.189285489165 6.3840831406724]</mn>
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      <ll>-3.8658127784729</ll>
      <Affine_translation>[0.787429818402958 -28.0422092386067 -2.46219828793129]</Affine_translation>
      <Affine_rotation>[0.187683924873063 -0.0232652010775434 -0.109534708160887]</Affine_rotation>
      <Affine_scaling>[1.1198960771429 1.07583195683998 1.17717270367937]</Affine_scaling>
      <Affine_shearing>[-0.00521141026413385 0.00261142647619423 -0.0012661535276269]</Affine_shearing>
      <Affine0_translation>[0.787429818402958 -28.0422092386067 -2.46219828793129]</Affine0_translation>
      <Affine0_rotation>[0.187683924873063 -0.0232652010775434 -0.109534708160887]</Affine0_rotation>
      <Affine0_scaling>[1.1198960771429 1.07583195683998 1.17717270367937]</Affine0_scaling>
      <Affine0_shearing>[-0.00521141026413385 0.00261142647619423 -0.0012661535276269]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_32611/ds/sub-0663</path>
      <file>sub-0663_ses-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_32611/ds/sub-0663/sub-0663_ses-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_32611/ds/sub-0663/sub-0663_ses-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_32611/ds/sub-0663/mri/msub-0663_ses-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_32611/ds/sub-0663/mri/p0sub-0663_ses-01_T1w.nii</Fp0>
      <fnames>..611/ds/sub-0663/sub-0663_ses-01_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>1.11612342897698</SurfaceDefectArea>
      <SurfaceDefectNumber>25</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0755171924829483</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0780005753040314</SurfacePositionRMSE>
      <res_vx_vol>[0.937500032668967 0.900008901924878 0.9375]</res_vx_vol>
      <res_vx_voli>[0.937500032018815 0.90000890176234 0.9375]</res_vx_voli>
      <res_RMS>0.925171801126389</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[3.19099998474121 19.7441349029541 40.8147430419922 67.7456970214844]</tissue_mn>
      <tissue_mnr>[0.0471026226878166 0.29144486784935 0.602469921112061 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[10.5698899346385 10.2528150798223 8.45086142835934 5.65034158670926]</tissue_std>
      <tissue_stdr>[0.163735419511795 0.158823698759079 0.130910098552704 0.0875279754400253]</tissue_stdr>
      <contrast>23.7040328979492</contrast>
      <contrastr>0.349897265434265</contrastr>
      <NCR>0.149171411991119</NCR>
      <ICR>0.461917281150818</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.87500006533793 1.80001780384976 1.875]</res_vx_vol>
      <res_RMS>1.85034360225278</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62322044372559 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>2.83487415313721</contrastr>
      <NCR>2.47245788574219</NCR>
      <ICR>1.60544967651367</ICR>
      <SurfaceEulerNumber>3.04081632653061</SurfaceEulerNumber>
      <SurfaceDefectArea>1.27903085724424</SurfaceDefectArea>
      <SurfaceDefectNumber>2.25</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.51034379005432</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.56001150608063</SurfacePositionRMSE>
      <IQR>2.29400910675126</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>20220709-185916</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>42</SurfaceEulerNumber>
         <SurfaceDefectArea>1.11612342897698</SurfaceDefectArea>
         <SurfaceDefectNumber>25</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0755171924829483</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0780005753040314</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>42</EC_abs>
      <defect_size>1.11612342897698</defect_size>
      <vol_abs_CGW>[187.968594430226 629.365832906339 472.711304894758 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.749642090859791</vol_abs_WMH>
      <vol_rel_WMH>0.000581097299212157</vol_rel_WMH>
      <surf_TSA>1809.45350903809</surf_TSA>
      <vol_TIV>1290.04573223132</vol_TIV>
      <vol_rel_CGW>[0.145706923199619 0.487863195220032 0.366429881580349 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.41431461951303 0.6031961299353]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.43094992637634 0.721369774692256 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.84648315171044 0.251739720975269 0.288582511695846;2.45058785026038 0.168309278224264 0.436174097576772;3.07118943962334 0.251350924138835 0.275243390727382]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.80640890837021 0.313476887304607 0.642628980737586;3.95800096584425 0.349009323517265 0.357371019262414]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.28266944497173</vol_TIV>
      <vol_rel_CGW>[0.5 6.61176715553218 4.43085275826776 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.05810972992122</vol_rel_WMH>
      <surf_TSA>8.58946534096985</surf_TSA>
      <SQR>5.43388996733071</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.165981471538544 1 1 11068.4031144471 0.541880658032394]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0435564927756786 0.0412325486540794 0.235695481300354]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[806.192957843127 418.844538769611 286.051050885345 1189.38617402685 2164.90239097133 8989.02931128531]</SPMvols0>
      <SPMvols1>[698.573122033759 391.209938212136 161.143701012875 888.668434262627 1537.01365946681 9594.95025996394]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[20.8472003936768 45.6814002990723 67.2076034545898]</T3th>
            <Tth>
               <T3th>[0 0.968528747558594 3.75993347167969 20.8472003936768 45.6814002990723 67.2076034545898 90.3878021240234 246.111114501953]</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>[0.0184920690953732 0.0633348673582077 0.0690758749842644 0 0]</dtc>
         <ll>[0.0794190967402586 0 0.0794190967402586 0;0.193182057979442 0.00865937653137427 0.201841434510816 1846.5947265625;0.193182057979442 0.00865937653137427 0.201841434510816 1846.5947265625]</ll>
         <rmsdtc>[0.0408489219844341 0.0828557014465332 0.0930960401892662]</rmsdtc>
         <rmsgdt>[0.0291995499283075 0.0425258874893188 0.0535675100982189]</rmsgdt>
         <rmsdt>0.0930960401892662</rmsdt>
         <dt>0.0690758749842644</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>[0.00856774114072323 0.0307317841798067 0.0431836247444153 0.051546648144722 0.0584840141236782 0.0661252811551094]</dtc>
         <ll>[0.0829138133164719 0 0.0829138133164719 0;0.22388485958486 0.0112685401404151 0.235153399725275 5768.083984375;0.206225958265251 0.0151064644065091 0.22133242267176 10872.3037109375;0.18622804299379 0.0183627336000332 0.204590776593823 19800.021484375;0.169558563223089 0.0219853269501639 0.191543890173253 38460.09765625;0.169558563223089 0.0219853269501639 0.191543890173253 38460.09765625]</ll>
         <rmsdtc>[0.0098690465092659 0.0353061258792877 0.0539080873131752 0.0807446092367172 0.108588546514511 0.116429716348648]</rmsdtc>
         <rmsgdt>[0.00308995298109949 0.0125386640429497 0.0288156401365995 0.0517700277268887 0.0731874629855156 0.079186387360096]</rmsgdt>
         <rmsdt>0.116429716348648</rmsdt>
         <dt>0.0661252811551094</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_32611/ds/sub-0663/sub-0663_ses-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 133s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 9s</item>
      <item>Estimate background 9s</item>
      <item>Initial correction 16s</item>
      <item>Refine background 5s</item>
      <item>Final correction 9s</item>
      <item>Final scaling 8s</item>
      <item>63s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 23s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 82s</item>
      <item>SPM preprocessing 1 (estimate 2): 52s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 21s</item>
      <item>Update Segmentation 22s</item>
      <item>Update Skull-Stripping 52s</item>
      <item>Update probability maps 11s</item>
      <item>106s</item>
      <item>Global intensity correction: 21s</item>
      <item>SANLM denoising after intensity normalization (medium): 9s</item>
      <item>Fast Optimized Shooting registration 36s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 7s</item>
      <item>Prepare segments (LASmod = 1.04) 16s</item>
      <item>Estimate local tissue thresholds (WM) 25s</item>
      <item>Estimate local tissue thresholds (GM) 32s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 53s</item>
      <item>143s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 9s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 20s</item>
      <item>Blood vessel detection 11s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 31s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 6s</item>
      <item>86s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s</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>13s</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 | 0.0829 0.0000 0.0829 | 32.0000</item>
      <item>2 | 2.50 | 0.0808 0.0010 0.0818 | 29.4886</item>
      <item>3 | 2.50 | 0.0802 0.0015 0.0817 | 26.9772</item>
      <item>4 | 2.50 | 0.0799 0.0017 0.0816 | 24.6107</item>
      <item>5 | 2.50 | 0.0796 0.0018 0.0815 | 22.6548</item>
      <item>6 | 2.50 | 0.0794 0.0019 0.0813 | 20.6989</item>
      <item>7 | 2.50 | 0.0792 0.0020 0.0812 | 18.9688</item>
      <item>8 | 2.50 | 0.0789 0.0021 0.0810 | 17.4455</item>
      <item>9 | 2.50 | 0.0787 0.0021 0.0808 | 15.9223</item>
      <item>10 | 2.50 | 0.0784 0.0022 0.0807 | 14.6627</item>
      <item>11 | 2.50 | 0.0782 0.0023 0.0805 | 13.4764</item>
      <item>12 | 2.50 | 0.0779 0.0023 0.0803 | 12.3015</item>
      <item>13 | 2.50 | 0.0777 0.0024 0.0801 | 11.3776</item>
      <item>14 | 2.50 | 0.0774 0.0025 0.0799 | 10.4537</item>
      <item>15 | 2.25 | 0.0771 0.0025 0.0796 | 9.5920</item>
      <item>16 | 2.25 | 0.0746 0.0038 0.0784 | 8.8725</item>
      <item>29 | 2.00 | 0.0764 0.0017 0.0781 | 3.3283</item>
      <item>30 | 2.00 | 0.0707 0.0040 0.0747 | 3.1221</item>
      <item>31 | 2.00 | 0.0687 0.0050 0.0738 | 2.9160</item>
      <item>43 | 1.75 | 0.0680 0.0029 0.0709 | 1.5785</item>
      <item>44 | 1.75 | 0.0636 0.0053 0.0688 | 1.5194</item>
      <item>45 | 1.75 | 0.0621 0.0061 0.0682 | 1.4626</item>
      <item>57 | 1.50 | 0.0610 0.0044 0.0654 | 1.0900</item>
      <item>58 | 1.50 | 0.0576 0.0066 0.0642 | 1.0730</item>
      <item>59 | 1.50 | 0.0565 0.0073 0.0638 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 163s</item>
      <item>Prepare output 12s</item>
      <item>174s</item>
      <item>Jacobian determinant (RMS): 0.010 0.035 0.054 0.081 0.109 | 0.116430</item>
      <item>Template Matching: 0.083 0.224 0.206 0.186 0.170 | 0.169559</item>
      <item>Write result maps: 30s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 25s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 40s</item>
      <item>84s</item>
      <item>Create initial surface 79s</item>
      <item>Topology correction: 87s</item>
      <item>Surface refinement: 95s</item>
      <item>Reduction of surface collisions with optimization: 60s</item>
      <item>Spherical mapping with areal smoothing 75s</item>
      <item>Spherical registration 299s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 27s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 39s</item>
      <item>86s</item>
      <item>Create initial surface 76s</item>
      <item>Topology correction: 83s</item>
      <item>Surface refinement: 79s</item>
      <item>Reduction of surface collisions with optimization: 60s</item>
      <item>Spherical mapping with areal smoothing 78s</item>
      <item>Spherical registration 296s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4143 0.6032 mm</item>
      <item>Surface intensity / position RMSE: 0.0755 / 0.0780</item>
      <item>Euler number / defect number / defect size: 42.0 / 25.0 / 1.12%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_32611/ds/sub-0663/surf/lh.thickness.sub-0663_ses-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_32611/ds/sub-0663/surf/rh.thickness.sub-0663_ses-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_32611/ds/sub-0663/sub-0663_ses-01_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1634s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 12s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 44s</item>
      <item>ROI estimation of 'lpba40' atlas 12s</item>
      <item>ROI estimation of 'hammers' atlas 30s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 11s</item>
      <item>ROI estimation of 'aal3' atlas 17s</item>
      <item>ROI estimation of 'mori' atlas 25s</item>
      <item>ROI estimation of 'anatomy3' atlas 35s</item>
      <item>ROI estimation of 'julichbrain' atlas 48s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 116s</item>
      <item>Write results 117s</item>
      <item>485s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_32611/ds/sub-0663/report/catreport_sub-0663_ses-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 54 minute(s) and 3 second(s).</item>
      <item>Image Quality Rating (IQR): 82.06% (B-)</item>
      <item>GM volume (GMV): 48.79% (629.37 / 1290.05 ml)</item>
      <item>GM thickness (GMT): 2.41 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_32611/ds/sub-0663/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_32611/ds/sub-0663/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_32611/ds/sub-0663/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>