ds003799_ReproVBM/sub-season108/report/cat_sub-season108_ses-3_acq-MPrageHiRes_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-6.32667207717896</ll>
      <Affine_translation>[1.79203959933246 7.89427697539324 -16.063726894061]</Affine_translation>
      <Affine_rotation>[0.220576659646018 0.0447700800612438 0.0333532822266892]</Affine_rotation>
      <Affine_scaling>[1.09230257849454 1.09654129683503 1.15899041569396]</Affine_scaling>
      <Affine_shearing>[0.00439397919985101 -0.000197743342773651 0.00507026836182279]</Affine_shearing>
      <Affine0_translation>[1.79203959933246 7.89427697539324 -16.063726894061]</Affine0_translation>
      <Affine0_rotation>[0.220576659646018 0.0447700800612438 0.0333532822266892]</Affine0_rotation>
      <Affine0_scaling>[1.09230257849454 1.09654129683503 1.15899041569396]</Affine0_scaling>
      <Affine0_shearing>[0.00439397919985101 -0.000197743342773651 0.00507026836182279]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_10175/ds/sub-season108</path>
      <file>sub-season108_ses-3_acq-MPrageHiRes_T1w</file>
      <fname>/var/lib/condor/execute/dir_10175/ds/sub-season108/sub-season108_ses-3_acq-MPrageHiRes_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_10175/ds/sub-season108/sub-season108_ses-3_acq-MPrageHiRes_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_10175/ds/sub-season108/mri/msub-season108_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_10175/ds/sub-season108/mri/p0sub-season108_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
      <fnames>..s/sub-season108/..son108_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>28</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>
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   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>22</SurfaceEulerNumber>
      <SurfaceDefectArea>0.623732055935441</SurfaceDefectArea>
      <SurfaceDefectNumber>15</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0725946426391602</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0763023570179939</SurfacePositionRMSE>
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      <res_vx_voli>[0.880005873347893 0.87499997616593 0.875000020771293]</res_vx_voli>
      <res_RMS>0.876671800646971</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[12.289999961853 279.501525878906 710.55078125 1022.97747802734]</tissue_mn>
      <tissue_mnr>[0.0120139494538307 0.273223549127579 0.69459080696106 1]</tissue_mnr>
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      <contrast>316.225830078125</contrast>
      <contrastr>0.309122949838638</contrastr>
      <NCR>0.125995606184006</NCR>
      <ICR>0.272923529148102</ICR>
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   <qualityratings>
      <res_vx_vol>[1.76001174815353 1.74999995336229 1.75000004633964]</res_vx_vol>
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      <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>3.44648909568787</contrastr>
      <NCR>2.1397590637207</NCR>
      <ICR>1.13671517372131</ICR>
      <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
      <SurfaceDefectArea>1.15593301398386</SurfaceDefectArea>
      <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.4518928527832</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.52604711055756</SurfacePositionRMSE>
      <IQR>2.00807684521269</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>20220712-172044</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>22</SurfaceEulerNumber>
         <SurfaceDefectArea>0.623732055935441</SurfaceDefectArea>
         <SurfaceDefectNumber>15</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0725946426391602</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0763023570179939</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>22</EC_abs>
      <defect_size>0.623732055935441</defect_size>
      <vol_abs_CGW>[186.25706259507 653.772072254052 462.299251532816 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.913597883565998</vol_abs_WMH>
      <vol_rel_WMH>0.00070151114966027</vol_rel_WMH>
      <surf_TSA>1863.14398464974</surf_TSA>
      <vol_TIV>1302.32838638194</vol_TIV>
      <vol_rel_CGW>[0.143018507883807 0.502002474253308 0.354979017862885 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.46615720845059 0.609204818699067]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.48467540740967 0.710943029986135 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.8398649191256 0.2473800161166 0.271577968858936;2.47851785909249 0.174361710320359 0.431805052953089;3.10172835834261 0.25139360910369 0.296616978187975]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.863582041319119 0.316273266479178 0.584857921370183;4.00002311464212 0.36868297945165 0.415142078629817]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.22392995268805</vol_TIV>
      <vol_rel_CGW>[0.5 6.86570535656085 4.22519787828458 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.07015111496603</vol_rel_WMH>
      <surf_TSA>8.60653490366739</surf_TSA>
      <SQR>5.62884661337497</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.370433058057513 1 1 6226.8949849792 0.338455460988144]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0 0 0.155891999602318]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[783.574175680699 410.499050792407 281.579290967308 535.842252259308 2257.21643165241 6118.9802777084]</SPMvols0>
      <SPMvols1>[694.654615131573 384.009444303501 173.272479189411 403.960308340992 1225.33543765654 7009.69965957512]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[335.841094970703 742.560729980469 997.755981445312]</T3th>
            <Tth>
               <T3th>[0 0 15.2718849182129 335.841094970703 742.560729980469 997.755981445312 1328.71337890625 2329.87109375]</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>[0.0228404831141233 0.0729715079069138 0.0798535421490669 0 0]</dtc>
         <ll>[0.0820867592642526 0 0.0820867592642526 0;0.190219837935174 0.00924437386648995 0.199464211801664 1971.34423828125;0.190219837935174 0.00924437386648995 0.199464211801664 1971.34423828125]</ll>
         <rmsdtc>[0.0472592674195766 0.0941307097673416 0.102878607809544]</rmsdtc>
         <rmsgdt>[0.0333933383226395 0.0404528602957726 0.0496108308434486]</rmsgdt>
         <rmsdt>0.102878607809544</rmsdt>
         <dt>0.0798535421490669</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>[0.0105941230431199 0.0371844060719013 0.0505404435098171 0.0580258890986443 0.0640276670455933 0.0714578181505203]</dtc>
         <ll>[0.0828860452922863 0 0.0828860452922863 0;0.213731013431013 0.0133104223901099 0.227041435821123 6813.2724609375;0.193516490797708 0.0156387234798433 0.209155214277551 11255.376953125;0.174118954911191 0.017563241159814 0.191682196071005 18937.951171875;0.157713165953355 0.0202575587052756 0.177970724658631 35437.62109375;0.157713165953355 0.0202575587052756 0.177970724658631 35437.62109375]</ll>
         <rmsdtc>[0.0122181950137019 0.0422147698700428 0.0609540492296219 0.0843231827020645 0.106685124337673 0.112606056034565]</rmsdtc>
         <rmsgdt>[0.00333046703599393 0.0122659346088767 0.0267976950854063 0.0475092865526676 0.0657835975289345 0.0708396807312965]</rmsgdt>
         <rmsdt>0.112606056034565</rmsdt>
         <dt>0.0714578181505203</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-season108_ses-3_acq-MPrageHiRes_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 47s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 9s</item>
      <item>Estimate background 8s</item>
      <item>Initial correction 19s</item>
      <item>Refine background 5s</item>
      <item>Final correction 14s</item>
      <item>Final scaling 10s</item>
      <item>74s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 116s</item>
      <item>SPM preprocessing 1 (estimate 2): 109s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 24s</item>
      <item>Update Segmentation 26s</item>
      <item>Update Skull-Stripping 57s</item>
      <item>Update probability maps 12s</item>
      <item>118s</item>
      <item>Global intensity correction: 22s</item>
      <item>SANLM denoising after intensity normalization (medium): 14s</item>
      <item>Fast Optimized Shooting registration 46s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 6s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 19s</item>
      <item>Estimate local tissue thresholds (WM) 25s</item>
      <item>Estimate local tissue thresholds (GM) 34s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 32s</item>
      <item>124s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 12s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 23s</item>
      <item>Blood vessel detection 13s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 39s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 7s</item>
      <item>105s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 6s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>15s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0829 0.0000 0.0829 | 32.0000</item>
      <item>2 | 2.50 | 0.0799 0.0013 0.0812 | 29.4886</item>
      <item>3 | 2.50 | 0.0791 0.0019 0.0811 | 26.9772</item>
      <item>4 | 2.50 | 0.0787 0.0022 0.0809 | 24.6107</item>
      <item>5 | 2.50 | 0.0784 0.0023 0.0807 | 22.6548</item>
      <item>6 | 2.50 | 0.0781 0.0024 0.0805 | 20.6989</item>
      <item>7 | 2.50 | 0.0779 0.0025 0.0803 | 18.9688</item>
      <item>8 | 2.50 | 0.0776 0.0026 0.0801 | 17.4455</item>
      <item>9 | 2.50 | 0.0773 0.0026 0.0799 | 15.9223</item>
      <item>10 | 2.50 | 0.0770 0.0027 0.0797 | 14.6627</item>
      <item>11 | 2.50 | 0.0767 0.0028 0.0794 | 13.4764</item>
      <item>12 | 2.50 | 0.0763 0.0028 0.0792 | 12.3015</item>
      <item>13 | 2.50 | 0.0760 0.0029 0.0790 | 11.3776</item>
      <item>14 | 2.50 | 0.0757 0.0030 0.0787 | 10.4537</item>
      <item>15 | 2.25 | 0.0742 0.0031 0.0773 | 9.5920</item>
      <item>16 | 2.25 | 0.0712 0.0044 0.0757 | 8.8725</item>
      <item>29 | 2.00 | 0.0722 0.0020 0.0742 | 3.3283</item>
      <item>30 | 2.00 | 0.0664 0.0043 0.0707 | 3.1221</item>
      <item>31 | 2.00 | 0.0645 0.0052 0.0697 | 2.9160</item>
      <item>43 | 1.75 | 0.0635 0.0030 0.0665 | 1.5785</item>
      <item>44 | 1.75 | 0.0594 0.0051 0.0645 | 1.5194</item>
      <item>45 | 1.75 | 0.0580 0.0059 0.0639 | 1.4626</item>
      <item>57 | 1.50 | 0.0565 0.0043 0.0607 | 1.0900</item>
      <item>58 | 1.50 | 0.0535 0.0061 0.0597 | 1.0730</item>
      <item>59 | 1.50 | 0.0526 0.0068 0.0593 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 223s</item>
      <item>Prepare output 13s</item>
      <item>235s</item>
      <item>Jacobian determinant (RMS): 0.012 0.042 0.061 0.084 0.107 | 0.112606</item>
      <item>Template Matching: 0.083 0.214 0.194 0.174 0.158 | 0.157713</item>
      <item>Write result maps: 37s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 47s</item>
      <item>102s</item>
      <item>Create initial surface 80s</item>
      <item>Topology correction: 91s</item>
      <item>Surface refinement: 78s</item>
      <item>Reduction of surface collisions with optimization: 58s</item>
      <item>Spherical mapping with areal smoothing 85s</item>
      <item>Spherical registration 256s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 42s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 46s</item>
      <item>110s</item>
      <item>Create initial surface 78s</item>
      <item>Topology correction: 91s</item>
      <item>Surface refinement: 72s</item>
      <item>Reduction of surface collisions with optimization: 59s</item>
      <item>Spherical mapping with areal smoothing 87s</item>
      <item>Spherical registration 269s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4662 0.6091 mm</item>
      <item>Surface intensity / position RMSE: 0.0726 / 0.0763</item>
      <item>Euler number / defect number / defect size: 22.0 / 15.0 / 0.62%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_10175/ds/sub-season108/surf/lh.thickness.sub-season108_ses-3_acq-MPrageHiRes_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_10175/ds/sub-season108/surf/rh.thickness.sub-season108_ses-3_acq-MPrageHiRes_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_10175/ds/sub-season108/sub-season108_ses-3_acq-MPrageHiRes_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1618s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 18s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 65s</item>
      <item>ROI estimation of 'lpba40' atlas 19s</item>
      <item>ROI estimation of 'hammers' atlas 46s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 16s</item>
      <item>ROI estimation of 'aal3' atlas 27s</item>
      <item>ROI estimation of 'mori' atlas 40s</item>
      <item>ROI estimation of 'anatomy3' atlas 58s</item>
      <item>ROI estimation of 'julichbrain' atlas 77s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 185s</item>
      <item>Write results 186s</item>
      <item>747s</item>
      <item>Quality check: 7s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_10175/ds/sub-season108/report/catreport_sub-season108_ses-3_acq-MPrageHiRes_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 60 minute(s) and 51 second(s).</item>
      <item>Image Quality Rating (IQR): 84.92% (B)</item>
      <item>GM volume (GMV): 50.20% (653.77 / 1302.33 ml)</item>
      <item>GM thickness (GMT): 2.47 0.61 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_10175/ds/sub-season108/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_10175/ds/sub-season108/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_10175/ds/sub-season108/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>