ds004169_ReproVBM/sub-0970/report/cat_sub-0970_ses-01_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.09332603249139 0.0524247723179661 0.0535877988016815 -1.32087367495972;-0.0399789440072035 0.946192160007383 0.398802736664002 -20.3173295310202;-0.038491526186184 -0.410835140506079 1.11826164322732 4.60893766968997;0 0 0 1]</Affine>
      <Affine0>[1.09332603249139 0.0524247723179661 0.0535877988016815 -1.32087367495972;-0.0399789440072035 0.946192160007383 0.398802736664002 -20.3173295310202;-0.038491526186184 -0.410835140506079 1.11826164322732 4.60893766968997;0 0 0 1]</Affine0>
      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[35.9520744185007 51.5502816369658 13.5457117477076 23.612065798159 18.0866493701737 6.16645320722817 10.9546989923314 34.4182240626566 78.054867178221 56.0876563217397 23.1881946513207 39.9912076724009 5.0955583269832]</mn>
      <vr>[34.2208308471377;6.49494743429311;11.3037368672521;29.3385676063982;21.8690466951425;3.39157865983402;9.42069534805342;44.8313768000977;558.806126876059;255.269533958513;57.4657356042336;343.481261882185;2.68142348575249]</vr>
      <ll>-3.57643270492554</ll>
      <Affine_translation>[-1.32087367495972 -20.3173295310202 4.60893766968997]</Affine_translation>
      <Affine_rotation>[0.407256934419886 0.046775934669455 0.0196068543598872]</Affine_rotation>
      <Affine_scaling>[1.094733632842 1.03236307641068 1.18597233415438]</Affine_scaling>
      <Affine_shearing>[0.0294576496420171 -0.00033241011187785 -0.0743648548008197]</Affine_shearing>
      <Affine0_translation>[-1.32087367495972 -20.3173295310202 4.60893766968997]</Affine0_translation>
      <Affine0_rotation>[0.407256934419886 0.046775934669455 0.0196068543598872]</Affine0_rotation>
      <Affine0_scaling>[1.094733632842 1.03236307641068 1.18597233415438]</Affine0_scaling>
      <Affine0_shearing>[0.0294576496420171 -0.00033241011187785 -0.0743648548008197]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_3050/ds/sub-0970</path>
      <file>sub-0970_ses-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_3050/ds/sub-0970/sub-0970_ses-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_3050/ds/sub-0970/sub-0970_ses-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_3050/ds/sub-0970/mri/msub-0970_ses-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3050/ds/sub-0970/mri/p0sub-0970_ses-01_T1w.nii</Fp0>
      <fnames>..050/ds/sub-0970/sub-0970_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>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>44</SurfaceEulerNumber>
      <SurfaceDefectArea>1.75917945292025</SurfaceDefectArea>
      <SurfaceDefectNumber>27</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0787749737501144</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0843027755618095</SurfacePositionRMSE>
      <res_vx_vol>[0.937500027692008 0.899992831404032 0.9375]</res_vx_vol>
      <res_vx_voli>[0.937500028342062 0.899992830233936 0.9375]</res_vx_voli>
      <res_RMS>0.925166588332639</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[2.39299988746643 13.8148193359375 30.1903228759766 52.2356758117676]</tissue_mn>
      <tissue_mnr>[0.0458116009831429 0.264470964670181 0.577963650226593 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[1.95267034652212 7.02296590752897 6.83682147899222 4.79515188382611]</tissue_std>
      <tissue_stdr>[0.0391766726970673 0.140902653336525 0.137168020009995 0.0962057411670685]</tissue_stdr>
      <contrast>18.0147037506104</contrast>
      <contrastr>0.344873577356339</contrastr>
      <NCR>0.164785176515579</NCR>
      <ICR>0.509719967842102</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.87500005538402 1.79998566280806 1.875]</res_vx_vol>
      <res_RMS>1.85033317666528</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.55950736999512 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>2.91022968292236</contrastr>
      <NCR>2.69660043716431</NCR>
      <ICR>1.72400784492493</ICR>
      <SurfaceEulerNumber>3.14285714285714</SurfaceEulerNumber>
      <SurfaceDefectArea>1.43979486323006</SurfaceDefectArea>
      <SurfaceDefectNumber>2.35</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.57549953460693</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.68605542182922</SurfacePositionRMSE>
      <IQR>2.4876668357679</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>20220709-140232</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>44</SurfaceEulerNumber>
         <SurfaceDefectArea>1.75917945292025</SurfaceDefectArea>
         <SurfaceDefectNumber>27</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0787749737501144</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0843027755618095</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>44</EC_abs>
      <defect_size>1.75917945292025</defect_size>
      <vol_abs_CGW>[214.638165376299 703.910439563992 469.355161344723 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.897054231866673</vol_abs_WMH>
      <vol_rel_WMH>0.000646337486544768</vol_rel_WMH>
      <surf_TSA>1882.73017767947</surf_TSA>
      <vol_TIV>1387.90376628501</vol_TIV>
      <vol_rel_CGW>[0.154649169913861 0.507175249944123 0.338175580142015 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.59160796358427 0.636184456684563]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.63403010368347 0.817682235568239 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.92287979804065 0.293996851310025 0.245600205088765;2.60208571867488 0.182060129437824 0.436230212138691;3.24669934383437 0.2679279352152 0.318169582772544]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.792004207959424 0.297700309934602 0.675167264617473;4.11893248437056 0.31744703431921 0.324832735382527]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00348525020994</vol_TIV>
      <vol_rel_CGW>[0.627319861958718 6.95860721882405 3.923411999677 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06463374865448</vol_rel_WMH>
      <surf_TSA>8.61051728432247</surf_TSA>
      <SQR>5.69774050600358</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.19012987613678 1 1 10747.733518539 0.522052270784517]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0445791520178318 0.0439849570393562 0.111722640693188]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[861.076580008786 416.981610426615 360.924015676104 919.403586780871 2082.00701139264 9405.46907734732]</SPMvols0>
      <SPMvols1>[749.456627501159 389.499197329553 203.943656960027 947.186955669622 1417.36715217163 9563.77355779291]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[13.9184999465942 34.5145988464355 51.6679000854492]</T3th>
            <Tth>
               <T3th>[0 0 2.42962574958801 13.9184999465942 34.5145988464355 51.6679000854492 70.5426025390625 174.82600402832]</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>[0.0188526585698128 0.0650127753615379 0.0713604390621185 0 0]</dtc>
         <ll>[0.081724553835206 0 0.081724553835206 0;0.196640582502532 0.00939101531725972 0.206031597819792 2002.615234375;0.196640582502532 0.00939101531725972 0.206031597819792 2002.615234375]</ll>
         <rmsdtc>[0.0403018854558468 0.0867759436368942 0.0977123081684113]</rmsdtc>
         <rmsgdt>[0.0285716820508242 0.0446338132023811 0.0554778687655926]</rmsgdt>
         <rmsdt>0.0977123081684113</rmsdt>
         <dt>0.0713604390621185</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>[0.00843323767185211 0.0296051427721977 0.0419199876487255 0.0509099885821342 0.0578445605933666 0.0642421022057533]</dtc>
         <ll>[0.0829786454626214 0 0.0829786454626214 0;0.221286584249084 0.011786330509768 0.233072914758852 6033.1279296875;0.201742480846505 0.0153592022203847 0.21710168306689 11054.2021484375;0.180919100189934 0.0182111818000236 0.199130281989957 19636.607421875;0.164142453667156 0.0212720476156042 0.18541450128276 37212.3203125;0.164142453667156 0.0212720476156042 0.18541450128276 37212.3203125]</ll>
         <rmsdtc>[0.00982278492301702 0.0342617258429527 0.0522083193063736 0.0771917998790741 0.100580543279648 0.106855161488056]</rmsdtc>
         <rmsgdt>[0.00298162968829274 0.0117693822830915 0.0268071182072163 0.0470810979604721 0.0647720396518707 0.0702613517642021]</rmsgdt>
         <rmsdt>0.106855161488056</rmsdt>
         <dt>0.0642421022057533</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_3050/ds/sub-0970/sub-0970_ses-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 233s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 11s</item>
      <item>Estimate background 12s</item>
      <item>Initial correction 18s</item>
      <item>Refine background 6s</item>
      <item>Final correction 11s</item>
      <item>Final scaling 9s</item>
      <item>77s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 20s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 115s</item>
      <item>SPM preprocessing 1 (estimate 2): 86s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 28s</item>
      <item>Update Segmentation 30s</item>
      <item>Update Skull-Stripping 67s</item>
      <item>Update probability maps 15s</item>
      <item>139s</item>
      <item>Global intensity correction: 27s</item>
      <item>SANLM denoising after intensity normalization (medium): 31s</item>
      <item>Fast Optimized Shooting registration 49s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 6s</item>
      <item>Prepare partitions 4s</item>
      <item>Prepare segments (LASmod = 1.15) 21s</item>
      <item>Estimate local tissue thresholds (WM) 26s</item>
      <item>Estimate local tissue thresholds (GM) 37s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 54s</item>
      <item>154s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 13s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 17s</item>
      <item>Blood vessel detection 12s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 35s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 8s</item>
      <item>97s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s</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) 6s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>15s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0830 0.0000 0.0830 | 32.0000</item>
      <item>2 | 2.50 | 0.0806 0.0011 0.0817 | 29.4886</item>
      <item>3 | 2.50 | 0.0800 0.0016 0.0816 | 26.9772</item>
      <item>4 | 2.50 | 0.0797 0.0018 0.0815 | 24.6107</item>
      <item>5 | 2.50 | 0.0794 0.0019 0.0813 | 22.6548</item>
      <item>6 | 2.50 | 0.0792 0.0020 0.0812 | 20.6989</item>
      <item>7 | 2.50 | 0.0789 0.0021 0.0810 | 18.9688</item>
      <item>8 | 2.50 | 0.0787 0.0022 0.0808 | 17.4455</item>
      <item>9 | 2.50 | 0.0784 0.0022 0.0806 | 15.9223</item>
      <item>10 | 2.50 | 0.0782 0.0023 0.0805 | 14.6627</item>
      <item>11 | 2.50 | 0.0779 0.0024 0.0803 | 13.4764</item>
      <item>12 | 2.50 | 0.0776 0.0024 0.0800 | 12.3015</item>
      <item>13 | 2.50 | 0.0773 0.0025 0.0798 | 11.3776</item>
      <item>14 | 2.50 | 0.0771 0.0025 0.0796 | 10.4537</item>
      <item>15 | 2.25 | 0.0765 0.0026 0.0791 | 9.5920</item>
      <item>16 | 2.25 | 0.0738 0.0039 0.0777 | 8.8725</item>
      <item>29 | 2.00 | 0.0753 0.0018 0.0771 | 3.3283</item>
      <item>30 | 2.00 | 0.0693 0.0041 0.0735 | 3.1221</item>
      <item>31 | 2.00 | 0.0672 0.0051 0.0724 | 2.9160</item>
      <item>43 | 1.75 | 0.0662 0.0029 0.0692 | 1.5785</item>
      <item>44 | 1.75 | 0.0618 0.0053 0.0671 | 1.5194</item>
      <item>45 | 1.75 | 0.0603 0.0061 0.0664 | 1.4626</item>
      <item>57 | 1.50 | 0.0589 0.0044 0.0633 | 1.0900</item>
      <item>58 | 1.50 | 0.0557 0.0065 0.0622 | 1.0730</item>
      <item>59 | 1.50 | 0.0547 0.0071 0.0618 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 222s</item>
      <item>Prepare output 14s</item>
      <item>236s</item>
      <item>Jacobian determinant (RMS): 0.010 0.034 0.052 0.077 0.101 | 0.106855</item>
      <item>Template Matching: 0.083 0.221 0.202 0.181 0.164 | 0.164142</item>
      <item>Write result maps: 42s</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: 18s</item>
      <item>PBT2x thickness: 56s</item>
      <item>123s</item>
      <item>Create initial surface 95s</item>
      <item>Topology correction: 108s</item>
      <item>Surface refinement: 118s</item>
      <item>Reduction of surface collisions with optimization: 85s</item>
      <item>Spherical mapping with areal smoothing 93s</item>
      <item>Spherical registration 258s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 55s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 57s</item>
      <item>140s</item>
      <item>Create initial surface 98s</item>
      <item>Topology correction: 111s</item>
      <item>Surface refinement: 101s</item>
      <item>Reduction of surface collisions with optimization: 87s</item>
      <item>Spherical mapping with areal smoothing 97s</item>
      <item>Spherical registration 257s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5915 0.6359 mm</item>
      <item>Surface intensity / position RMSE: 0.0788 / 0.0843</item>
      <item>Euler number / defect number / defect size: 44.0 / 27.0 / 1.76%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3050/ds/sub-0970/surf/lh.thickness.sub-0970_ses-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3050/ds/sub-0970/surf/rh.thickness.sub-0970_ses-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3050/ds/sub-0970/sub-0970_ses-01_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1893s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 20s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 75s</item>
      <item>ROI estimation of 'lpba40' atlas 22s</item>
      <item>ROI estimation of 'hammers' atlas 53s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 18s</item>
      <item>ROI estimation of 'aal3' atlas 31s</item>
      <item>ROI estimation of 'mori' atlas 46s</item>
      <item>ROI estimation of 'anatomy3' atlas 65s</item>
      <item>ROI estimation of 'julichbrain' atlas 86s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 40s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 139s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 207s</item>
      <item>Write results 209s</item>
      <item>839s</item>
      <item>Quality check: 7s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3050/ds/sub-0970/report/catreport_sub-0970_ses-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 70 minute(s) and 44 second(s).</item>
      <item>Image Quality Rating (IQR): 80.12% (B-)</item>
      <item>GM volume (GMV): 50.72% (703.91 / 1387.90 ml)</item>
      <item>GM thickness (GMT): 2.59 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3050/ds/sub-0970/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3050/ds/sub-0970/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3050/ds/sub-0970/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>