ds003085_ReproVBM/sub-32/report/cat_sub-32_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.02402030907768 0.0436172242310215 0.00192088314257037 -1.14690311806346;-0.0285567358091572 0.891130468077109 0.308857262513787 -15.9044191162658;0.00626247109252569 -0.29862584283971 0.98407190686493 17.8280027454471;0 0 0 1]</Affine>
      <Affine0>[1.02402030907768 0.0436172242310215 0.00192088314257037 -1.14690311806346;-0.0285567358091572 0.891130468077109 0.308857262513787 -15.9044191162658;0.00626247109252569 -0.29862584283971 0.98407190686493 17.8280027454471;0 0 0 1]</Affine0>
      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[212.528472343652 260.1977881731 88.4234835668231 138.510911146185 86.2668136690346 22.6214900909455 49.879066957133 192.452675614454 223.979567616047 202.931304559602 149.24842162075 228.687182808207 11.3319891098404]</mn>
      <vr>[529.649270091347;49.704837005865;114.022374877368;793.530697005292;544.247645900884;87.2463773317615;268.497926899138;4401.38547049199;191.458824563307;1670.93120151279;2355.60492802521;7434.7264748863;35.1364879417181]</vr>
      <ll>-5.01240110397339</ll>
      <Affine_translation>[-1.14690311806346 -15.9044191162658 17.8280027454471]</Affine_translation>
      <Affine_rotation>[0.323205876751844 0.00305816848301595 0.0283775622199702]</Affine_rotation>
      <Affine_scaling>[1.02443755256619 0.940694761327198 1.0312153221055]</Affine_scaling>
      <Affine_shearing>[0.0165292694207127 -0.000657673413454738 -0.0209536155782233]</Affine_shearing>
      <Affine0_translation>[-1.14690311806346 -15.9044191162658 17.8280027454471]</Affine0_translation>
      <Affine0_rotation>[0.323205876751844 0.00305816848301595 0.0283775622199702]</Affine0_rotation>
      <Affine0_scaling>[1.02443755256619 0.940694761327198 1.0312153221055]</Affine0_scaling>
      <Affine0_shearing>[0.0165292694207127 -0.000657673413454738 -0.0209536155782233]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_19926/ds/sub-32</path>
      <file>sub-32_T1w</file>
      <fname>/var/lib/condor/execute/dir_19926/ds/sub-32/sub-32_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_19926/ds/sub-32/sub-32_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_19926/ds/sub-32/mri/msub-32_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_19926/ds/sub-32/mri/p0sub-32_T1w.nii</Fp0>
      <fnames>..19926/ds/sub-32/sub-32_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>24</SurfaceEulerNumber>
      <SurfaceDefectArea>1.02414225944999</SurfaceDefectArea>
      <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0604261457920074</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0683512985706329</SurfacePositionRMSE>
      <res_vx_vol>[0.999997943062737 0.999999979493163 1.00000002523915]</res_vx_vol>
      <res_vx_voli>[0.999997943995247 0.999999985517663 1.00000002859579]</res_vx_voli>
      <res_RMS>0.999999315932153</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[1.27999997138977 85.3276062011719 202.999984741211 268.12939453125]</tissue_mn>
      <tissue_mnr>[0.0047738142311573 0.318232923746109 0.757097065448761 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[5.80607760430288 29.8477673638791 24.1707850510191 10.8846608473043]</tissue_std>
      <tissue_stdr>[0.0217578820884228 0.11185248196125 0.0905783772468567 0.0407895259559155]</tissue_stdr>
      <contrast>65.4418182373047</contrast>
      <contrastr>0.244068041443825</contrastr>
      <NCR>0.116322413086891</NCR>
      <ICR>0.23193347454071</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.99999588612547 1.99999995898633 2.00000005047829]</res_vx_vol>
      <res_RMS>1.99999863186431</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[5.84219169616699 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>4.42231273651123</contrastr>
      <NCR>2.00089597702026</NCR>
      <ICR>1.03505325317383</ICR>
      <SurfaceEulerNumber>2.12244897959184</SurfaceEulerNumber>
      <SurfaceDefectArea>1.2560355648625</SurfaceDefectArea>
      <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.20852291584015</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.36702597141266</SurfacePositionRMSE>
      <IQR>2.00044765665073</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>20220711-085727</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>24</SurfaceEulerNumber>
         <SurfaceDefectArea>1.02414225944999</SurfaceDefectArea>
         <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0604261457920074</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0683512985706329</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>24</EC_abs>
      <defect_size>1.02414225944999</defect_size>
      <vol_abs_CGW>[322.270949799537 779.892164404448 740.710554213123 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.92543136258802</vol_abs_WMH>
      <vol_rel_WMH>0.00104479834705209</vol_rel_WMH>
      <surf_TSA>2343.73160612769</surf_TSA>
      <vol_TIV>1842.87366841711</vol_TIV>
      <vol_rel_CGW>[0.174874141034498 0.423193503586341 0.401932355379161 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.36213008573341 0.573102155807535]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.37626218795776 0.690623209755385 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.77773771398222 0.244607029494695 0.270655930068575;2.3821262828105 0.162204278914625 0.460851966283063;2.96283498442152 0.251291444508767 0.268492103648362]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.84816479918027 0.269278612604911 0.544228820824565;3.92996551212632 0.41726294141811 0.455771179175434]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>4.49360612345899</vol_TIV>
      <vol_rel_CGW>[0.990555693866709 5.45031436038687 5.0684690262062 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.10447983470521</vol_rel_WMH>
      <surf_TSA>8.6239935757141</surf_TSA>
      <SQR>4.71157842974456</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.276987249200994 250 4 7297.02302498239 0.301824914015432]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00655331928282976 0.00373510480858386 0.440136849880219]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[973.736258791143 657.588657272683 490.415790779069 655.198607250955 3301.94587737943 4902.87568687944]</SPMvols0>
      <SPMvols1>[831.159157761821 618.258188561782 316.981878246327 1411.85224263546 2948.02146672276 3966.67606124633]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[95.4467010498047 207.033203125 260.310699462891]</T3th>
            <Tth>
               <T3th>[0 0 7.19120740890503 95.4467010498047 207.033203125 260.310699462891 342.742706298828 664.09326171875]</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>[0.0201271325349808 0.0772159025073051 0.08488380163908 0 0]</dtc>
         <ll>[0.0839956832342312 0 0.0839956832342312 0;0.19659601511503 0.0107362845650956 0.207332299680126 2289.4912109375;0.19659601511503 0.0107362845650956 0.207332299680126 2289.4912109375]</ll>
         <rmsdtc>[0.0449723154306412 0.0998389944434166 0.111779257655144]</rmsdtc>
         <rmsgdt>[0.0326032489538193 0.0498935095965862 0.0623299740254879]</rmsgdt>
         <rmsdt>0.111779257655144</rmsdt>
         <dt>0.08488380163908</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>[0.00898321904242039 0.0347438156604767 0.0503315404057503 0.0599885508418083 0.0670201256871223 0.0757851079106331]</dtc>
         <ll>[0.084901055844277 0 0.084901055844277 0;0.222679517704518 0.0135607486263736 0.236240266330891 6941.408203125;0.201063650286503 0.0171738698734702 0.218237520159974 12360.240234375;0.179279309279106 0.0197899466113374 0.199069255890443 21338.9453125;0.161419500523908 0.0228961614665536 0.184315661990462 40053.46875;0.161419500523908 0.0228961614665536 0.184315661990462 40053.46875]</ll>
         <rmsdtc>[0.0103588374331594 0.0400754176080227 0.0627334415912628 0.0918555334210396 0.118062019348145 0.126897782087326]</rmsdtc>
         <rmsgdt>[0.00338258501142263 0.0139559069648385 0.0314650572836399 0.0549930296838284 0.0739621669054031 0.0801632329821587]</rmsgdt>
         <rmsdt>0.126897782087326</rmsdt>
         <dt>0.0757851079106331</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_19926/ds/sub-32/sub-32_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 35s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 7s</item>
      <item>Initial correction 7s</item>
      <item>Refine background 3s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 7s</item>
      <item>39s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 10s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 74s</item>
      <item>SPM preprocessing 1 (estimate 2): 61s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 19s</item>
      <item>Update Skull-Stripping 39s</item>
      <item>Update probability maps 8s</item>
      <item>81s</item>
      <item>Global intensity correction: 14s</item>
      <item>SANLM denoising after intensity normalization (medium): 11s</item>
      <item>Fast Optimized Shooting registration 31s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 17s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 24s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 37s</item>
      <item>106s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 8s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 20s</item>
      <item>Blood vessel detection 12s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.11) 36s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 4s</item>
      <item>91s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</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>14s</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 | 0.0849 0.0000 0.0849 | 32.0000</item>
      <item>2 | 2.50 | 0.0819 0.0013 0.0832 | 29.4886</item>
      <item>3 | 2.50 | 0.0811 0.0019 0.0830 | 26.9772</item>
      <item>4 | 2.50 | 0.0807 0.0021 0.0828 | 24.6107</item>
      <item>5 | 2.50 | 0.0803 0.0023 0.0826 | 22.6548</item>
      <item>6 | 2.50 | 0.0801 0.0023 0.0824 | 20.6989</item>
      <item>7 | 2.50 | 0.0798 0.0024 0.0822 | 18.9688</item>
      <item>8 | 2.50 | 0.0795 0.0025 0.0820 | 17.4455</item>
      <item>9 | 2.50 | 0.0792 0.0026 0.0818 | 15.9223</item>
      <item>10 | 2.50 | 0.0789 0.0027 0.0816 | 14.6627</item>
      <item>11 | 2.50 | 0.0785 0.0028 0.0813 | 13.4764</item>
      <item>12 | 2.50 | 0.0782 0.0028 0.0810 | 12.3015</item>
      <item>13 | 2.50 | 0.0779 0.0029 0.0808 | 11.3776</item>
      <item>14 | 2.50 | 0.0775 0.0030 0.0805 | 10.4537</item>
      <item>15 | 2.25 | 0.0772 0.0031 0.0802 | 9.5920</item>
      <item>16 | 2.25 | 0.0742 0.0045 0.0787 | 8.8725</item>
      <item>29 | 2.00 | 0.0755 0.0020 0.0776 | 3.3283</item>
      <item>30 | 2.00 | 0.0692 0.0046 0.0738 | 3.1221</item>
      <item>31 | 2.00 | 0.0670 0.0057 0.0727 | 2.9160</item>
      <item>43 | 1.75 | 0.0659 0.0033 0.0692 | 1.5785</item>
      <item>44 | 1.75 | 0.0613 0.0057 0.0670 | 1.5194</item>
      <item>45 | 1.75 | 0.0598 0.0066 0.0664 | 1.4626</item>
      <item>57 | 1.50 | 0.0582 0.0048 0.0630 | 1.0900</item>
      <item>58 | 1.50 | 0.0549 0.0069 0.0618 | 1.0730</item>
      <item>59 | 1.50 | 0.0538 0.0076 0.0614 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 166s</item>
      <item>Prepare output 11s</item>
      <item>177s</item>
      <item>Jacobian determinant (RMS): 0.010 0.040 0.063 0.092 0.118 | 0.126898</item>
      <item>Template Matching: 0.085 0.223 0.201 0.179 0.161 | 0.161420</item>
      <item>Write result maps: 23s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 58s</item>
      <item>CSF distance: 18s</item>
      <item>PBT2x thickness: 48s</item>
      <item>132s</item>
      <item>Create initial surface 107s</item>
      <item>Topology correction: 112s</item>
      <item>Surface refinement: 134s</item>
      <item>Reduction of surface collisions with optimization: 90s</item>
      <item>Spherical mapping with areal smoothing 96s</item>
      <item>Spherical registration 291s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 45s</item>
      <item>CSF distance: 18s</item>
      <item>PBT2x thickness: 51s</item>
      <item>121s</item>
      <item>Create initial surface 106s</item>
      <item>Topology correction: 114s</item>
      <item>Surface refinement: 125s</item>
      <item>Reduction of surface collisions with optimization: 89s</item>
      <item>Spherical mapping with areal smoothing 96s</item>
      <item>Spherical registration 300s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3621 0.5730 mm</item>
      <item>Surface intensity / position RMSE: 0.0604 / 0.0684</item>
      <item>Euler number / defect number / defect size: 24.0 / 8.5 / 1.02%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_19926/ds/sub-32/surf/lh.thickness.sub-32_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_19926/ds/sub-32/surf/rh.thickness.sub-32_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_19926/ds/sub-32/sub-32_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 2012s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 11s</item>
      <item>ROI estimation of 'mori' atlas 16s</item>
      <item>ROI estimation of 'anatomy3' atlas 23s</item>
      <item>ROI estimation of 'julichbrain' atlas 30s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 50s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s</item>
      <item>Write results 74s</item>
      <item>307s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_19926/ds/sub-32/report/catreport_sub-32_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 54 minute(s) and 8 second(s).</item>
      <item>Image Quality Rating (IQR): 85.00% (B)</item>
      <item>GM volume (GMV): 42.32% (779.89 / 1842.87 ml)</item>
      <item>GM thickness (GMT): 2.36 0.57 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_19926/ds/sub-32/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_19926/ds/sub-32/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_19926/ds/sub-32/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>