CORR_cat12.8.1/UWM/sub-0027273/ses-2/report/cat_sub-0027273_ses-2_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_translation>[-2.33378974111914 -43.7093187882356 -25.6502426290293]</Affine_translation>
      <Affine_rotation>[0.0657986262975902 0.00583627321559659 -0.0057558207766063]</Affine_rotation>
      <Affine_scaling>[1.10689196625501 1.02265774766876 1.11755351556886]</Affine_scaling>
      <Affine_shearing>[0.0160590969627737 -0.00330296184202744 0.0146629639153704]</Affine_shearing>
      <Affine0_translation>[-2.33378974111914 -43.7093187882356 -25.6502426290293]</Affine0_translation>
      <Affine0_rotation>[0.0657986262975902 0.00583627321559659 -0.0057558207766063]</Affine0_rotation>
      <Affine0_scaling>[1.10689196625501 1.02265774766876 1.11755351556886]</Affine0_scaling>
      <Affine0_shearing>[0.0160590969627737 -0.00330296184202744 0.0146629639153704]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2</path>
      <file>sub-0027273_ses-2_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/sub-0027273_ses-2_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/sub-0027273_ses-2_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/mri/msub-0027273_ses-2_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/mri/p0sub-0027273_ses-2_run-1_T1w.nii</Fp0>
      <fnames>../ds/UWM/sub-0027273/ses-2/sub-0027273_ses-2_run-1_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_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</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>
            <tr>
               <td>/var/lib/condor/execute/dir_2615109/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</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>
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         <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>
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         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>14</SurfaceEulerNumber>
      <SurfaceDefectArea>0.522017604995716</SurfaceDefectArea>
      <SurfaceDefectNumber>10</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0668338239192963</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0623656138777733</SurfacePositionRMSE>
      <res_vx_vol>[1 1 1]</res_vx_vol>
      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>1</res_RMS>
      <res_BB>177.163864135742</res_BB>
      <tissue_mn>[152.350006103516 547.172973632812 1571.89501953125 2504.66088867188]</tissue_mn>
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      <tissue_weighting>T1</tissue_weighting>
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      <contrast>886.717529296875</contrast>
      <contrastr>0.354026973247528</contrastr>
      <res_ECR>0.391770005226135</res_ECR>
      <NCR>0.142552554607391</NCR>
      <ICR>0.28603783249855</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2 2 2]</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>2.7729287147522</contrastr>
      <NCR>2.37744140625</NCR>
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      <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
      <SurfaceDefectArea>1.13050440124893</SurfaceDefectArea>
      <SurfaceDefectNumber>1.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.33667647838593</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.24731230735779</SurfacePositionRMSE>
      <SIQR>2.59844674459922</SIQR>
      <IQR>2.2419731410866</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
         <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>2040</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>20231030-235856</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>14</SurfaceEulerNumber>
         <SurfaceDefectArea>0.522017604995716</SurfaceDefectArea>
         <SurfaceDefectNumber>10</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0668338239192963</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0623656138777733</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>14</EC_abs>
      <defect_size>0.522017604995716</defect_size>
      <vol_abs_CGW>[224.032749019608 714.128988235294 473.351498039216 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.479533333333333</vol_abs_WMH>
      <vol_rel_WMH>0.000339729958843363</vol_rel_WMH>
      <surf_TSA>1899.52659431681</surf_TSA>
      <vol_TIV>1411.51323529412</vol_TIV>
      <vol_rel_CGW>[0.158718135556785 0.505931485712559 0.335350378730656 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.57432203847254 0.610791181060832]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.56140065193176 0.717270875086433 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.99047204389547 0.247820874071086 0.30443540552094;2.58899283191016 0.17435827707995 0.426098164436442;3.24492370783008 0.260291589816701 0.269466430042618]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.976109130807512 0.343646438392511 0.546408470857579;4.15673854709549 0.333873362755943 0.453591529142421]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00315745902665</vol_TIV>
      <vol_rel_CGW>[0.700397549511224 6.93626949914797 3.87267203180057 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.03397299588434</vol_rel_WMH>
      <surf_TSA>8.61324707588755</surf_TSA>
      <SQR>5.6789088312602</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 10223.616 0.485915743600467]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00182388408575207 0.00137618649750948 0.222320467233658]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[877.403603921569 412.588588235294 394.433247058824 405.162423529412 983.840639215686 7694.40081568627]</SPMvols0>
      <SPMvols1>[761.870611764706 386.351062745098 227.612666666667 363.775682352941 767.040501960784 7717.00284705882]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[614.262023925781 1685.79321289062 2499.49438476562]</T3th>
            <Tth>
               <T3th>[-33.9913291931152 -33.991325378418 59.2198677062988 614.262023925781 1685.79321289062 2499.49438476562 3442.11059570312 9785.8271484375]</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>[0.0216031037271023 0.0758927166461945 0.0844867900013924 0 0]</dtc>
         <ll>[0.0857370719283807 0 0.0857370719283807 0;0.202820044033238 0.0103001680408492 0.213120212074087 2196.490234375;0.202820044033238 0.0103001680408492 0.213120212074087 2196.490234375]</ll>
         <rmsdtc>[0.0451136454939842 0.10271367430687 0.114925369620323]</rmsdtc>
         <rmsgdt>[0.0318122692406178 0.0470861084759235 0.0585180297493935]</rmsgdt>
         <rmsdt>0.114925369620323</rmsdt>
         <dt>0.0844867900013924</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>[0.0103004472330213 0.0374493710696697 0.0529529452323914 0.061907734721899 0.069017767906189 0.0780616700649261]</dtc>
         <ll>[0.0858689182862535 0 0.0858689182862535 0;0.224290216727717 0.0138310897435897 0.238121306471306 7079.7890625;0.203397048923736 0.0164035042185277 0.219800553142264 11805.798828125;0.183560754498865 0.0185567162088972 0.202117470707762 20009.1875;0.16680224059981 0.0216608833380113 0.188463123937822 37892.53125;0.16680224059981 0.0216608833380113 0.188463123937822 37892.53125]</ll>
         <rmsdtc>[0.0120813362300396 0.0436982288956642 0.0653245225548744 0.0922578126192093 0.117014728486538 0.124039493501186]</rmsdtc>
         <rmsgdt>[0.0032951373141259 0.0128770899027586 0.0284834820777178 0.0496120192110538 0.0682915076613426 0.0741516202688217]</rmsgdt>
         <rmsdt>0.124039493501186</rmsdt>
         <dt>0.0780616700649261</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0027273/ses-2/sub-0027273_ses-2_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 55s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 5s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 3s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 4s</item>
      <item>33s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 75s</item>
      <item>SPM preprocessing 1 (estimate 2): 51s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 38s</item>
      <item>Update probability maps 8s</item>
      <item>79s</item>
      <item>Global intensity correction: 15s</item>
      <item>SANLM denoising after intensity normalization (medium): 27s</item>
      <item>Fast Optimized Shooting registration 31s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 13s</item>
      <item>Estimate local tissue thresholds (WM) 16s</item>
      <item>Estimate local tissue thresholds (GM) 25s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 36s</item>
      <item>101s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 17s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.03) 23s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>68s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</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 | 0.0859 0.0000 0.0859 | 32.0000</item>
      <item>2 | 2.50 | 0.0831 0.0012 0.0843 | 29.4886</item>
      <item>3 | 2.50 | 0.0823 0.0019 0.0841 | 26.9772</item>
      <item>4 | 2.50 | 0.0819 0.0021 0.0840 | 24.6107</item>
      <item>5 | 2.50 | 0.0815 0.0023 0.0838 | 22.6548</item>
      <item>6 | 2.50 | 0.0813 0.0024 0.0836 | 20.6989</item>
      <item>7 | 2.50 | 0.0810 0.0025 0.0834 | 18.9688</item>
      <item>8 | 2.50 | 0.0806 0.0026 0.0832 | 17.4455</item>
      <item>9 | 2.50 | 0.0803 0.0026 0.0830 | 15.9223</item>
      <item>10 | 2.50 | 0.0800 0.0028 0.0828 | 14.6627</item>
      <item>11 | 2.50 | 0.0797 0.0029 0.0825 | 13.4764</item>
      <item>12 | 2.50 | 0.0794 0.0029 0.0823 | 12.3015</item>
      <item>13 | 2.50 | 0.0790 0.0030 0.0820 | 11.3776</item>
      <item>14 | 2.50 | 0.0787 0.0031 0.0818 | 10.4537</item>
      <item>15 | 2.25 | 0.0776 0.0032 0.0808 | 9.5920</item>
      <item>16 | 2.25 | 0.0748 0.0046 0.0794 | 8.8725</item>
      <item>29 | 2.00 | 0.0758 0.0021 0.0779 | 3.3283</item>
      <item>30 | 2.00 | 0.0698 0.0045 0.0743 | 3.1221</item>
      <item>31 | 2.00 | 0.0678 0.0055 0.0733 | 2.9160</item>
      <item>43 | 1.75 | 0.0668 0.0032 0.0700 | 1.5785</item>
      <item>44 | 1.75 | 0.0626 0.0054 0.0680 | 1.5194</item>
      <item>45 | 1.75 | 0.0612 0.0062 0.0674 | 1.4626</item>
      <item>57 | 1.50 | 0.0598 0.0045 0.0643 | 1.0900</item>
      <item>58 | 1.50 | 0.0567 0.0066 0.0632 | 1.0730</item>
      <item>59 | 1.50 | 0.0556 0.0072 0.0628 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 169s</item>
      <item>Prepare output 10s</item>
      <item>179s</item>
      <item>Jacobian determinant (RMS): 0.012 0.044 0.065 0.092 0.117 | 0.124039</item>
      <item>Template Matching: 0.086 0.224 0.203 0.184 0.167 | 0.166802</item>
      <item>Write result maps: 35s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 36s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 46s</item>
      <item>104s</item>
      <item>Create initial surface 85s</item>
      <item>Topology correction: 90s</item>
      <item>Surface refinement: 79s</item>
      <item>Reduction of surface collisions with optimization: 66s</item>
      <item>Spherical mapping with areal smoothing 84s</item>
      <item>Spherical registration 293s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 27s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 43s</item>
      <item>91s</item>
      <item>Create initial surface 82s</item>
      <item>Topology correction: 89s</item>
      <item>Surface refinement: 91s</item>
      <item>Reduction of surface collisions with optimization: 68s</item>
      <item>Spherical mapping with areal smoothing 85s</item>
      <item>Spherical registration 285s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5743 0.6107 mm</item>
      <item>Surface intensity / position RMSE: 0.0668 / 0.0624</item>
      <item>Euler number / defect number / defect size: 14.0 / 10.0 / 0.52%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/surf/lh.thickness.sub-0027273_ses-2_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/surf/rh.thickness.sub-0027273_ses-2_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/sub-0027273_ses-2_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1687s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 20s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 11s</item>
      <item>ROI estimation of 'mori' atlas 18s</item>
      <item>ROI estimation of 'anatomy3' atlas 26s</item>
      <item>ROI estimation of 'julichbrain' atlas 36s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 93s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
      <item>Write results 9s</item>
      <item>368s</item>
      <item>Quality check: 11s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/report/catreport_sub-0027273_ses-2_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 49 minute(s) and 7 second(s).</item>
      <item>Image Quality Rating (IQR): 82.58% (B-)</item>
      <item>GM volume (GMV): 50.59% (714.13 / 1411.51 ml)</item>
      <item>GM thickness (GMT): 2.57 0.61 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2615109/ds/UWM/sub-0027273/ses-2/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>