ds003826_ReproVBM/sub-104/report/cat_sub-104_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.00291623810984 -0.047517093277342 -0.0389415856331655 1.2932622684571;0.0730744934378524 1.07353053980166 0.261474204452095 11.4203007897505;0.0304451937013506 -0.272891391063934 1.14578133866007 -6.3840702274326;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[112.955872384448 162.849872185994 35.4037449279041 70.3586668569493 145.767617058517 16.598472125514 49.759155670386 170.655181225469 320.201754034007 248.334446012309 128.291434624144 45.219605764664 16.4006591912838]</mn>
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      <ll>-5.01606035232544</ll>
      <Affine_translation>[1.2932622684571 11.4203007897505 -6.3840702274326]</Affine_translation>
      <Affine_rotation>[0.24690095475832 -0.0472084639997912 -0.0630790155563735]</Affine_rotation>
      <Affine_scaling>[1.00603567137309 1.10846557519873 1.17546791771224]</Affine_scaling>
      <Affine_shearing>[0.02221483256074 0.014756809180936 -0.0247862119444264]</Affine_shearing>
      <Affine0_translation>[1.2932622684571 11.4203007897505 -6.3840702274326]</Affine0_translation>
      <Affine0_rotation>[0.24690095475832 -0.0472084639997912 -0.0630790155563735]</Affine0_rotation>
      <Affine0_scaling>[1.00603567137309 1.10846557519873 1.17546791771224]</Affine0_scaling>
      <Affine0_shearing>[0.02221483256074 0.014756809180936 -0.0247862119444264]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_48883/ds/sub-104</path>
      <file>sub-104_T1w</file>
      <fname>/var/lib/condor/execute/dir_48883/ds/sub-104/sub-104_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_48883/ds/sub-104/sub-104_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_48883/ds/sub-104/mri/msub-104_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_48883/ds/sub-104/mri/p0sub-104_T1w.nii</Fp0>
      <fnames>..8883/ds/sub-104/sub-104_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>64</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>26</SurfaceEulerNumber>
      <SurfaceDefectArea>0.700875401856562</SurfaceDefectArea>
      <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0698014348745346</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0681026875972748</SurfacePositionRMSE>
      <res_vx_vol>[1.09999847412109 1 1]</res_vx_vol>
      <res_vx_voli>[1.09999847412109 1 1]</res_vx_voli>
      <res_RMS>1.03440750240073</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[5.19700002670288 33.6500015258789 104.740531921387 159.917114257812]</tissue_mn>
      <tissue_mnr>[0.0324980840086937 0.210421502590179 0.654967606067657 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[4.581057812014 21.3229317180622 17.4224216554332 10.1485893606258]</tissue_std>
      <tissue_stdr>[0.0296086743474007 0.137816146016121 0.112606048583984 0.0655932053923607]</tissue_stdr>
      <contrast>57.0299491882324</contrast>
      <contrastr>0.356621921062469</contrastr>
      <NCR>0.138058349490166</NCR>
      <ICR>0.366922438144684</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.19999694824219 2 2]</res_vx_vol>
      <res_RMS>2.06881500480146</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>2.73400449752808</contrastr>
      <NCR>2.31292486190796</NCR>
      <ICR>1.36984729766846</ICR>
      <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
      <SurfaceDefectArea>1.17521885046414</SurfaceDefectArea>
      <SurfaceDefectNumber>1.875</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.39602875709534</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.3620537519455</SurfacePositionRMSE>
      <IQR>2.21398238402342</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>20220703-111524</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>26</SurfaceEulerNumber>
         <SurfaceDefectArea>0.700875401856562</SurfaceDefectArea>
         <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0698014348745346</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0681026875972748</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>26</EC_abs>
      <defect_size>0.700875401856562</defect_size>
      <vol_abs_CGW>[248.664343689085 695.990016508095 466.191267825796 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.487795401778876</vol_abs_WMH>
      <vol_rel_WMH>0.000345746828774191</vol_rel_WMH>
      <surf_TSA>1874.43374425873</surf_TSA>
      <vol_TIV>1410.84562802298</vol_TIV>
      <vol_rel_CGW>[0.176251985865767 0.493314082479306 0.330433931654927 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.6090379021134 0.618242166281243]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.60292983055115 0.748113990954723 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.02827286875422 0.248440660929911 0.30513565317051;2.63443761722625 0.175219803239419 0.421509540840859;3.28676385616691 0.267395535179074 0.273354805988631]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.949830052700056 0.361075038168984 0.558198233181245;4.20698015969079 0.31835707366058 0.441801766818755]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00280196368143</vol_TIV>
      <vol_rel_CGW>[1.01530147029035 6.70966383763122 3.7843737725382 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.03457468287742</vol_rel_WMH>
      <surf_TSA>8.60894531295542</surf_TSA>
      <SQR>5.49392409513408</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.116612319722553 22 3 10857.9474382401 0.54572454258251]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0361649766564369 0.037951834499836 0.125098258256912]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[845.215805193643 429.895709546257 461.807778220143 2763.51979948443 1871.56888970831 6695.60680581698]</SPMvols0>
      <SPMvols1>[725.37821848692 403.463147389042 246.551186228225 3900.14792514711 1685.90112647573 5330.55116800124]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[41.8566017150879 108.579803466797 163.223907470703]</T3th>
            <Tth>
               <T3th>[0 0 6.32338047027588 41.8566017150879 108.579803466797 163.223907470703 223.907562255859 570.084655761719]</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>[0.0199451576918364 0.071880429983139 0.0792658925056458 0 0]</dtc>
         <ll>[0.0853347992028843 0 0.0853347992028843 0;0.203268538860857 0.0106678421185369 0.213936380979394 2274.89599609375;0.203268538860857 0.0106678421185369 0.213936380979394 2274.89599609375]</ll>
         <rmsdtc>[0.0436212532222271 0.0954575538635254 0.106334775686264]</rmsdtc>
         <rmsgdt>[0.0311661530286074 0.0443073995411396 0.05488371104002]</rmsgdt>
         <rmsdt>0.106334775686264</rmsdt>
         <dt>0.0792658925056458</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>[0.00969092175364494 0.0398828610777855 0.0513310469686985 0.0598359331488609 0.0666058957576752 0.07512366771698]</dtc>
         <ll>[0.087107676375132 0 0.087107676375132 0;0.223790369352869 0.0184335851648352 0.242223954517705 9435.69140625;0.207603614362412 0.0195926026660664 0.227196217028478 14101.03125;0.186298743498857 0.0215039773997192 0.207802720898577 23187.13671875;0.169023847673969 0.0246739928633615 0.19369784053733 43163.5234375;0.169023847673969 0.0246739928633615 0.19369784053733 43163.5234375]</ll>
         <rmsdtc>[0.0113977249711752 0.0421694666147232 0.0651567131280899 0.0898120105266571 0.114948816597462 0.121805742383003]</rmsdtc>
         <rmsgdt>[0.00338015938177705 0.0136240953579545 0.0305224768817425 0.0522646978497505 0.0734571218490601 0.0783574804663658]</rmsgdt>
         <rmsdt>0.121805742383003</rmsdt>
         <dt>0.07512366771698</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_48883/ds/sub-104/sub-104_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 96s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 14s</item>
      <item>Initial correction 11s</item>
      <item>Refine background 5s</item>
      <item>Final correction 7s</item>
      <item>Final scaling 11s</item>
      <item>63s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 11s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 79s</item>
      <item>SPM preprocessing 1 (estimate 2): 64s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 20s</item>
      <item>Update Segmentation 23s</item>
      <item>Update Skull-Stripping 48s</item>
      <item>Update probability maps 11s</item>
      <item>102s</item>
      <item>Global intensity correction: 19s</item>
      <item>SANLM denoising after intensity normalization (medium): 7s</item>
      <item>Fast Optimized Shooting registration 43s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 16s</item>
      <item>Estimate local tissue thresholds (WM) 25s</item>
      <item>Estimate local tissue thresholds (GM) 36s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 36s</item>
      <item>123s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 13s</item>
      <item>Blood vessel detection 10s</item>
      <item>WMH detection (WMHCstr=0.48 &gt; WMHCstr'=0.02) 25s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 5s</item>
      <item>69s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.24):</item>
      <item>Level 1 cleanup (ROI estimation) 5s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>12s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0871 0.0000 0.0871 | 32.0000</item>
      <item>2 | 2.50 | 0.0841 0.0013 0.0854 | 29.4886</item>
      <item>3 | 2.50 | 0.0832 0.0020 0.0852 | 26.9772</item>
      <item>4 | 2.50 | 0.0827 0.0023 0.0850 | 24.6107</item>
      <item>5 | 2.50 | 0.0824 0.0024 0.0848 | 22.6548</item>
      <item>6 | 2.50 | 0.0821 0.0025 0.0846 | 20.6989</item>
      <item>7 | 2.50 | 0.0817 0.0027 0.0844 | 18.9688</item>
      <item>8 | 2.50 | 0.0814 0.0028 0.0842 | 17.4455</item>
      <item>9 | 2.50 | 0.0810 0.0029 0.0839 | 15.9223</item>
      <item>10 | 2.50 | 0.0807 0.0030 0.0836 | 14.6627</item>
      <item>11 | 2.50 | 0.0803 0.0031 0.0834 | 13.4764</item>
      <item>12 | 2.50 | 0.0799 0.0031 0.0831 | 12.3015</item>
      <item>13 | 2.50 | 0.0795 0.0033 0.0828 | 11.3776</item>
      <item>14 | 2.50 | 0.0792 0.0033 0.0825 | 10.4537</item>
      <item>15 | 2.25 | 0.0807 0.0034 0.0841 | 9.5920</item>
      <item>16 | 2.25 | 0.0770 0.0052 0.0822 | 8.8725</item>
      <item>17 | 2.25 | 0.0755 0.0059 0.0814 | 8.1530</item>
      <item>18 | 2.25 | 0.0746 0.0061 0.0807 | 7.5234</item>
      <item>29 | 2.00 | 0.0772 0.0030 0.0802 | 3.3283</item>
      <item>30 | 2.00 | 0.0714 0.0055 0.0769 | 3.1221</item>
      <item>31 | 2.00 | 0.0692 0.0065 0.0757 | 2.9160</item>
      <item>43 | 1.75 | 0.0685 0.0037 0.0723 | 1.5785</item>
      <item>44 | 1.75 | 0.0638 0.0063 0.0701 | 1.5194</item>
      <item>45 | 1.75 | 0.0621 0.0072 0.0693 | 1.4626</item>
      <item>57 | 1.50 | 0.0610 0.0053 0.0662 | 1.0900</item>
      <item>58 | 1.50 | 0.0575 0.0075 0.0650 | 1.0730</item>
      <item>59 | 1.50 | 0.0563 0.0082 0.0646 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 212s</item>
      <item>Prepare output 14s</item>
      <item>225s</item>
      <item>Jacobian determinant (RMS): 0.011 0.042 0.065 0.090 0.115 | 0.121806</item>
      <item>Template Matching: 0.087 0.224 0.208 0.186 0.169 | 0.169024</item>
      <item>Write result maps: 29s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 46s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 58s</item>
      <item>131s</item>
      <item>Create initial surface 98s</item>
      <item>Topology correction: 109s</item>
      <item>Surface refinement: 67s</item>
      <item>Reduction of surface collisions with optimization: 75s</item>
      <item>Spherical mapping with areal smoothing 95s</item>
      <item>Spherical registration 346s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 36s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 57s</item>
      <item>118s</item>
      <item>Create initial surface 93s</item>
      <item>Topology correction: 106s</item>
      <item>Surface refinement: 85s</item>
      <item>Reduction of surface collisions with optimization: 72s</item>
      <item>Spherical mapping with areal smoothing 101s</item>
      <item>Spherical registration 322s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.6092 0.6180 mm</item>
      <item>Surface intensity / position RMSE: 0.0698 / 0.0681</item>
      <item>Euler number / defect number / defect size: 26.0 / 17.5 / 0.70%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_48883/ds/sub-104/surf/lh.thickness.sub-104_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_48883/ds/sub-104/surf/rh.thickness.sub-104_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_48883/ds/sub-104/sub-104_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1927s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 9s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 33s</item>
      <item>ROI estimation of 'lpba40' atlas 10s</item>
      <item>ROI estimation of 'hammers' atlas 23s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 8s</item>
      <item>ROI estimation of 'aal3' atlas 13s</item>
      <item>ROI estimation of 'mori' atlas 20s</item>
      <item>ROI estimation of 'anatomy3' atlas 28s</item>
      <item>ROI estimation of 'julichbrain' atlas 37s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
      <item>Write results 86s</item>
      <item>366s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_48883/ds/sub-104/report/catreport_sub-104_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 56 minute(s) and 20 second(s).</item>
      <item>Image Quality Rating (IQR): 82.86% (B-)</item>
      <item>GM volume (GMV): 49.33% (695.99 / 1410.85 ml)</item>
      <item>GM thickness (GMT): 2.61 0.62 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_48883/ds/sub-104/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_48883/ds/sub-104/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_48883/ds/sub-104/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>