ds003799_ReproVBM/sub-season127/report/cat_sub-season127_ses-3_acq-MPrageHiRes_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine>[1.04581659356329 -0.0565244678811071 -0.0119834061252095 0.166535796279161;0.0327754365473015 0.968171022279529 0.11391005508655 -9.04531601326368;0.0313392294895301 -0.0824827385145731 1.11990985367192 -33.8057356952694;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>[905.636176117374 1183.76549033987 418.085041025904 634.970760424282 361.604510095639 78.3206881859326 172.340107254472 833.363576372693 1279.13582948118 959.449520541199 600.94669567887 979.357848965322 62.6145711751656]</mn>
      <vr>[11757.2736928561;1633.27750381566;9842.21503435236;8528.34626199933;12005.1875635446;1001.63903039166;3529.3677892458;70465.1660298467;219515.389498889;33416.2338538343;17723.6448874315;304259.22739652;927.238013568906]</vr>
      <ll>-6.5133638381958</ll>
      <Affine_translation>[0.166535796279161 -9.04531601326368 -33.8057356952694]</Affine_translation>
      <Affine_rotation>[0.0831006565905451 -0.0324528111595928 -0.0287210284758544]</Affine_rotation>
      <Affine_scaling>[1.0467992758491 0.972899804080256 1.12529649520902]</Affine_scaling>
      <Affine_shearing>[-0.0273473739616696 0.023999260210685 0.0203983400654224]</Affine_shearing>
      <Affine0_translation>[0.166535796279161 -9.04531601326368 -33.8057356952694]</Affine0_translation>
      <Affine0_rotation>[0.0831006565905451 -0.0324528111595928 -0.0287210284758544]</Affine0_rotation>
      <Affine0_scaling>[1.0467992758491 0.972899804080256 1.12529649520902]</Affine0_scaling>
      <Affine0_shearing>[-0.0273473739616696 0.023999260210685 0.0203983400654224]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_377798/ds/sub-season127</path>
      <file>sub-season127_ses-3_acq-MPrageHiRes_T1w</file>
      <fname>/var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_377798/ds/sub-season127/mri/msub-season127_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_377798/ds/sub-season127/mri/p0sub-season127_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
      <fnames>..s/sub-season127/..son127_ses-3_acq-MPrageHiRes_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>12</SurfaceEulerNumber>
      <SurfaceDefectArea>0.288366650590358</SurfaceDefectArea>
      <SurfaceDefectNumber>18</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0677556991577148</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0662119090557098</SurfacePositionRMSE>
      <res_vx_vol>[0.879998141040695 0.875000041249352 0.874999985053819]</res_vx_vol>
      <res_vx_voli>[0.879998140112651 0.875000047356633 0.874999982709038]</res_vx_voli>
      <res_RMS>0.876669221973265</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[9.90299987792969 334.443237304688 846.250549316406 1202.8134765625]</tissue_mn>
      <tissue_mnr>[0.00823319610208273 0.278050780296326 0.703559219837189 1]</tissue_mnr>
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      <tissue_stdr>[0.0172303970903158 0.108581833541393 0.0934712812304497 0.0543298497796059]</tissue_stdr>
      <contrast>359.52294921875</contrast>
      <contrastr>0.29890164732933</contrastr>
      <NCR>0.10830894857645</NCR>
      <ICR>0.329137563705444</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.75999628208139 1.7500000824987 1.74999997010764]</res_vx_vol>
      <res_RMS>1.75333844394653</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>3.59980869293213</contrastr>
      <NCR>1.88585913181305</NCR>
      <ICR>1.27613484859467</ICR>
      <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
      <SurfaceDefectArea>1.07209166264759</SurfaceDefectArea>
      <SurfaceDefectNumber>1.9</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.3551139831543</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.3242381811142</SurfacePositionRMSE>
      <IQR>1.82793684069946</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>20220712-180214</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>12</SurfaceEulerNumber>
         <SurfaceDefectArea>0.288366650590358</SurfaceDefectArea>
         <SurfaceDefectNumber>18</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0677556991577148</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0662119090557098</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>12</EC_abs>
      <defect_size>0.288366650590358</defect_size>
      <vol_abs_CGW>[229.61574200574 770.398107867405 568.443804202272 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.85219950265752</vol_abs_WMH>
      <vol_rel_WMH>0.00054333599663542</vol_rel_WMH>
      <surf_TSA>2138.10957533069</surf_TSA>
      <vol_TIV>1568.45765407542</vol_TIV>
      <vol_rel_CGW>[0.14639588222807 0.491181962015763 0.362422155756166 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.57224515425267 0.591064580345943]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.56513428688049 0.705000922065248 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.00513816721681 0.232176384938348 0.301098431472199;2.58497597343203 0.167838665968443 0.412691445863845;3.20387826461637 0.249441260988166 0.286210122663956]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.943355182930956 0.412019512678192 0.532487822810403;4.08950295569223 0.351460347372779 0.467512177189597]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.64699337119834</vol_TIV>
      <vol_rel_CGW>[0.5 6.67137144424863 4.35887492378172 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.05433359966354</vol_rel_WMH>
      <surf_TSA>8.62371824095924</surf_TSA>
      <SQR>5.47794248534793</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.235485008784703 1 1 7561.56741756174 0.332987487622851]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00708739226683974 0 0.222820609807968]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[925.423607477202 500.958169446535 344.681132933971 818.714403366366 2662.46959788969 5316.58839895078]</SPMvols0>
      <SPMvols1>[831.282015653056 473.976133909033 211.772305644172 1265.15156529291 2321.77244346654 4786.75270664794]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[400.971893310547 881.012512207031 1183.685546875]</T3th>
            <Tth>
               <T3th>[0 0 19.5282859802246 400.971893310547 881.012512207031 1183.685546875 1575.04235839844 2964.49877929688]</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>[0.021118177101016 0.0750022903084755 0.0821364894509315 0 0]</dtc>
         <ll>[0.081204314000991 0 0.081204314000991 0;0.185257983808758 0.00968718442882524 0.194945168237583 2065.77270507812;0.185257983808758 0.00968718442882524 0.194945168237583 2065.77270507812]</ll>
         <rmsdtc>[0.0463035441935062 0.0960628241300583 0.105165973305702]</rmsdtc>
         <rmsgdt>[0.0331899859011173 0.0417297929525375 0.0512371771037579]</rmsgdt>
         <rmsdt>0.105165973305702</rmsdt>
         <dt>0.0821364894509315</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>[0.0103588048368692 0.0384414494037628 0.0530784130096436 0.0604050606489182 0.0650252625346184 0.0728262066841125]</dtc>
         <ll>[0.0823926729430749 0 0.0823926729430749 0;0.20976076007326 0.0140881820436508 0.223848942116911 7211.38818359375;0.188582746466642 0.0160071502016605 0.204589896668303 11520.5380859375;0.170110298584216 0.0173940124221903 0.187504311006407 18755.4765625;0.157038398625092 0.0181623153138618 0.175200713938953 31772.30078125;0.157038398625092 0.0181623153138618 0.175200713938953 31772.30078125]</ll>
         <rmsdtc>[0.0120372101664543 0.0438198894262314 0.0638512894511223 0.0875388011336327 0.110017918050289 0.114849880337715]</rmsdtc>
         <rmsgdt>[0.00331308203749359 0.0127156060189009 0.0272105075418949 0.0467989444732666 0.0645895823836327 0.0687049776315689]</rmsgdt>
         <rmsdt>0.114849880337715</rmsdt>
         <dt>0.0728262066841125</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-season127_ses-3_acq-MPrageHiRes_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 38s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 10s</item>
      <item>Estimate background 11s</item>
      <item>Initial correction 32s</item>
      <item>Refine background 5s</item>
      <item>Final correction 22s</item>
      <item>Final scaling 14s</item>
      <item>104s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 17s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 139s</item>
      <item>SPM preprocessing 1 (estimate 2): 111s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 26s</item>
      <item>Update Segmentation 32s</item>
      <item>Update Skull-Stripping 69s</item>
      <item>Update probability maps 13s</item>
      <item>141s</item>
      <item>Global intensity correction: 24s</item>
      <item>SANLM denoising after intensity normalization (medium): 15s</item>
      <item>Fast Optimized Shooting registration 43s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 7s</item>
      <item>Prepare partitions 4s</item>
      <item>Prepare segments (LASmod = 1.00) 28s</item>
      <item>Estimate local tissue thresholds (WM) 33s</item>
      <item>Estimate local tissue thresholds (GM) 48s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 38s</item>
      <item>164s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 13s</item>
      <item>Major structures 7s</item>
      <item>Ventricle detection 24s</item>
      <item>Blood vessel detection 20s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 50s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 3s</item>
      <item>Side alignment 6s</item>
      <item>Final corrections 7s</item>
      <item>130s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 57s</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) 8s</item>
      <item>Level 1 cleanup (brain masking) 5s</item>
      <item>Level 2 cleanup (CSF correction) 3s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
      <item>21s</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 | 0.0824 0.0000 0.0824 | 32.0000</item>
      <item>2 | 2.50 | 0.0792 0.0013 0.0805 | 29.4886</item>
      <item>3 | 2.50 | 0.0783 0.0020 0.0803 | 26.9772</item>
      <item>4 | 2.50 | 0.0779 0.0022 0.0801 | 24.6107</item>
      <item>5 | 2.50 | 0.0775 0.0024 0.0799 | 22.6548</item>
      <item>6 | 2.50 | 0.0772 0.0025 0.0797 | 20.6989</item>
      <item>7 | 2.50 | 0.0769 0.0026 0.0794 | 18.9688</item>
      <item>8 | 2.50 | 0.0765 0.0027 0.0792 | 17.4455</item>
      <item>9 | 2.50 | 0.0762 0.0027 0.0790 | 15.9223</item>
      <item>10 | 2.50 | 0.0759 0.0029 0.0787 | 14.6627</item>
      <item>11 | 2.50 | 0.0755 0.0029 0.0785 | 13.4764</item>
      <item>12 | 2.50 | 0.0752 0.0030 0.0782 | 12.3015</item>
      <item>13 | 2.50 | 0.0748 0.0031 0.0779 | 11.3776</item>
      <item>14 | 2.50 | 0.0745 0.0032 0.0776 | 10.4537</item>
      <item>15 | 2.25 | 0.0727 0.0032 0.0760 | 9.5920</item>
      <item>16 | 2.25 | 0.0699 0.0047 0.0746 | 8.8725</item>
      <item>29 | 2.00 | 0.0705 0.0021 0.0726 | 3.3283</item>
      <item>30 | 2.00 | 0.0648 0.0044 0.0692 | 3.1221</item>
      <item>31 | 2.00 | 0.0629 0.0053 0.0682 | 2.9160</item>
      <item>43 | 1.75 | 0.0618 0.0031 0.0648 | 1.5785</item>
      <item>44 | 1.75 | 0.0579 0.0051 0.0630 | 1.5194</item>
      <item>45 | 1.75 | 0.0567 0.0058 0.0625 | 1.4626</item>
      <item>57 | 1.50 | 0.0552 0.0042 0.0594 | 1.0900</item>
      <item>58 | 1.50 | 0.0523 0.0061 0.0584 | 1.0730</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 162s</item>
      <item>Prepare output 16s</item>
      <item>178s</item>
      <item>Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.110 | 0.114850</item>
      <item>Template Matching: 0.082 0.210 0.189 0.170 0.157 | 0.157038</item>
      <item>Write result maps: 40s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 67s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 59s</item>
      <item>153s</item>
      <item>Create initial surface 103s</item>
      <item>Topology correction: 114s</item>
      <item>Surface refinement: 98s</item>
      <item>Reduction of surface collisions with optimization: 89s</item>
      <item>Spherical mapping with areal smoothing 99s</item>
      <item>Spherical registration 322s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 48s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 60s</item>
      <item>136s</item>
      <item>Create initial surface 103s</item>
      <item>Topology correction: 107s</item>
      <item>Surface refinement: 119s</item>
      <item>Reduction of surface collisions with optimization: 82s</item>
      <item>Spherical mapping with areal smoothing 97s</item>
      <item>Spherical registration 290s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5723 0.5909 mm</item>
      <item>Surface intensity / position RMSE: 0.0678 / 0.0662</item>
      <item>Euler number / defect number / defect size: 12.0 / 18.0 / 0.29%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_377798/ds/sub-season127/surf/lh.thickness.sub-season127_ses-3_acq-MPrageHiRes_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_377798/ds/sub-season127/surf/rh.thickness.sub-season127_ses-3_acq-MPrageHiRes_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_377798/ds/sub-season127/sub-season127_ses-3_acq-MPrageHiRes_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 2033s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 12s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 42s</item>
      <item>ROI estimation of 'lpba40' atlas 12s</item>
      <item>ROI estimation of 'hammers' atlas 30s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 10s</item>
      <item>ROI estimation of 'aal3' atlas 18s</item>
      <item>ROI estimation of 'mori' atlas 26s</item>
      <item>ROI estimation of 'anatomy3' atlas 31s</item>
      <item>ROI estimation of 'julichbrain' atlas 41s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s</item>
      <item>Write results 96s</item>
      <item>427s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_377798/ds/sub-season127/report/catreport_sub-season127_ses-3_acq-MPrageHiRes_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 64 minute(s) and 1 second(s).</item>
      <item>Image Quality Rating (IQR): 86.72% (B+)</item>
      <item>GM volume (GMV): 49.12% (770.40 / 1568.46 ml)</item>
      <item>GM thickness (GMT): 2.57 0.59 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_377798/ds/sub-season127/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>