CORR_cat12.8.1/UWM/sub-0027269/ses-2/report/cat_sub-0027269_ses-2_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine>[1.03388173955719 0.0792338169353001 0.0646934881051407 4.59665505148207;-0.0630897063723827 1.03458013367895 -0.00814182242829756 -42.6042709680246;-0.0766376842236001 0.0366814875557248 1.13205397547582 -23.4548012450623;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-7.51143789291382</ll>
      <Affine_translation>[4.59665505148207 -42.6042709680246 -23.4548012450623]</Affine_translation>
      <Affine_rotation>[-0.0409182352127981 0.0714460768234246 0.0637535559826262]</Affine_rotation>
      <Affine_scaling>[1.03863617166124 1.03817249460061 1.13317111638852]</Affine_scaling>
      <Affine_shearing>[0.012825642403135 -0.017945439597952 0.0356988147998888]</Affine_shearing>
      <Affine0_translation>[4.59665505148207 -42.6042709680246 -23.4548012450623]</Affine0_translation>
      <Affine0_rotation>[-0.0409182352127981 0.0714460768234246 0.0637535559826262]</Affine0_rotation>
      <Affine0_scaling>[1.03863617166124 1.03817249460061 1.13317111638852]</Affine0_scaling>
      <Affine0_shearing>[0.012825642403135 -0.017945439597952 0.0356988147998888]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2</path>
      <file>sub-0027269_ses-2_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/sub-0027269_ses-2_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/sub-0027269_ses-2_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/mri/msub-0027269_ses-2_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/mri/p0sub-0027269_ses-2_run-1_T1w.nii</Fp0>
      <fnames>../ds/UWM/sub-0027269/ses-2/sub-0027269_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_611862/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>
         </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>16</SurfaceEulerNumber>
      <SurfaceDefectArea>0.832067280806159</SurfaceDefectArea>
      <SurfaceDefectNumber>15</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.067968562245369</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.071462407708168</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>185.686660766602</res_BB>
      <tissue_mn>[157.856002807617 509.380004882812 1509.41003417969 2424.73901367188]</tissue_mn>
      <tissue_mnr>[0.0651022642850876 0.210076212882996 0.622504115104675 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.0292233526706696 0.117115452885628 0.116195067763329 0.0741190612316132]</tissue_stdr>
      <contrast>854.906555175781</contrast>
      <contrastr>0.352576732635498</contrastr>
      <res_ECR>0.397137761116028</res_ECR>
      <NCR>0.148517191410065</NCR>
      <ICR>0.251647025346756</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2 2 2]</res_vx_vol>
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      <res_ECR>2.92417216300964</res_ECR>
      <res_BB>10.5</res_BB>
      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>2.794682264328</contrastr>
      <NCR>2.46306610107422</NCR>
      <ICR>1.08394598960876</ICR>
      <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
      <SurfaceDefectArea>1.20801682020154</SurfaceDefectArea>
      <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.35937118530273</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.42924809455872</SurfacePositionRMSE>
      <SIQR>2.63426151617533</SIQR>
      <IQR>2.30804592435906</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>20231031-000026</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>16</SurfaceEulerNumber>
         <SurfaceDefectArea>0.832067280806159</SurfaceDefectArea>
         <SurfaceDefectNumber>15</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.067968562245369</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.071462407708168</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>16</EC_abs>
      <defect_size>0.832067280806159</defect_size>
      <vol_abs_CGW>[246.266490196078 710.3606 513.522364705882 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.325192156862745</vol_abs_WMH>
      <vol_rel_WMH>0.000221196665263146</vol_rel_WMH>
      <surf_TSA>1936.77225115102</surf_TSA>
      <vol_TIV>1470.14945490196</vol_TIV>
      <vol_rel_CGW>[0.16751119375989 0.483189377536702 0.349299428703408 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.53546405214496 0.642733183134951]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.53458881378174 0.78455562181803 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.90500869218979 0.271715645955211 0.29576073517978;2.55727491355004 0.186431257595818 0.430197432988771;3.24477478459916 0.278327426559305 0.274041831831449]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.845176301629896 0.285608675847568 0.574713758975354;4.23214710941876 0.372982795160011 0.425286241024646]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.11634467456548</vol_TIV>
      <vol_rel_CGW>[0.858318853446293 6.52782646438042 4.12319376263305 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.02211966652631</vol_rel_WMH>
      <surf_TSA>8.61758035056632</surf_TSA>
      <SQR>5.35495195261607</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 10223.616 0.432740725607977]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00166609743610024 0.00126854074187577 0.213820040225983]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[890.893643137255 445.232239215686 431.981682352941 431.210541176471 936.158250980392 7630.25]</SPMvols0>
      <SPMvols1>[770.486623529412 417.596258823529 246.886392156863 393.099509803922 730.751474509804 7664.82485882353]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[552.956726074219 1605.79516601562 2413.06372070312]</T3th>
            <Tth>
               <T3th>[-36.2405395507812 -36.240535736084 59.8415031433105 552.956726074219 1605.79516601562 2413.06372070312 3343.1171875 9341.224609375]</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>[0.0219789538532495 0.0755335837602615 0.0834907069802284 0 0]</dtc>
         <ll>[0.0862843062029499 0 0.0862843062029499 0;0.200469805842259 0.0107599237815243 0.211229729623783 2294.5322265625;0.200469805842259 0.0107599237815243 0.211229729623783 2294.5322265625]</ll>
         <rmsdtc>[0.0449957139790058 0.0994732975959778 0.110580615699291]</rmsdtc>
         <rmsgdt>[0.0317166410386562 0.0460298843681812 0.0569352507591248]</rmsgdt>
         <rmsdt>0.110580615699291</rmsdt>
         <dt>0.0834907069802284</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>[0.0102342963218689 0.0394214577972889 0.052807305008173 0.0612058639526367 0.0676441341638565 0.0758321583271027]</dtc>
         <ll>[0.0873574612489971 0 0.0873574612489971 0;0.22336130952381 0.0165889041514042 0.239950213675214 8491.4453125;0.203110237150416 0.0180677739845938 0.22117801113501 13003.59375;0.182250165078941 0.0195335395428983 0.201783704621839 21062.46875;0.16535441960542 0.0220762489581863 0.187430668563606 38619.15234375;0.16535441960542 0.0220762489581863 0.187430668563606 38619.15234375]</ll>
         <rmsdtc>[0.0117375813424587 0.0425629951059818 0.0641382783651352 0.087918259203434 0.110593140125275 0.117535665631294]</rmsdtc>
         <rmsgdt>[0.00323582137934864 0.0127675905823708 0.0282728914171457 0.0479244999587536 0.0658947601914406 0.0715550780296326]</rmsgdt>
         <rmsdt>0.117535665631294</rmsdt>
         <dt>0.0758321583271027</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0027269/ses-2/sub-0027269_ses-2_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 58s</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 5s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 78s</item>
      <item>SPM preprocessing 1 (estimate 2): 58s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 41s</item>
      <item>Update probability maps 9s</item>
      <item>83s</item>
      <item>Global intensity correction: 15s</item>
      <item>SANLM denoising after intensity normalization (medium): 28s</item>
      <item>Fast Optimized Shooting registration 31s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 14s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 26s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 37s</item>
      <item>104s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 13s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.04) 24s</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>66s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</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 | 0.0874 0.0000 0.0874 | 32.0000</item>
      <item>2 | 2.50 | 0.0844 0.0013 0.0857 | 29.4886</item>
      <item>3 | 2.50 | 0.0836 0.0019 0.0855 | 26.9772</item>
      <item>4 | 2.50 | 0.0831 0.0022 0.0853 | 24.6107</item>
      <item>5 | 2.50 | 0.0828 0.0024 0.0852 | 22.6548</item>
      <item>6 | 2.50 | 0.0825 0.0025 0.0849 | 20.6989</item>
      <item>7 | 2.50 | 0.0822 0.0026 0.0847 | 18.9688</item>
      <item>8 | 2.50 | 0.0818 0.0027 0.0845 | 17.4455</item>
      <item>9 | 2.50 | 0.0815 0.0028 0.0843 | 15.9223</item>
      <item>10 | 2.50 | 0.0812 0.0029 0.0840 | 14.6627</item>
      <item>11 | 2.50 | 0.0808 0.0030 0.0838 | 13.4764</item>
      <item>12 | 2.50 | 0.0804 0.0030 0.0835 | 12.3015</item>
      <item>13 | 2.50 | 0.0801 0.0032 0.0832 | 11.3776</item>
      <item>14 | 2.50 | 0.0797 0.0032 0.0829 | 10.4537</item>
      <item>15 | 2.25 | 0.0792 0.0033 0.0825 | 9.5920</item>
      <item>16 | 2.25 | 0.0759 0.0049 0.0808 | 8.8725</item>
      <item>17 | 2.25 | 0.0745 0.0055 0.0800 | 8.1530</item>
      <item>29 | 2.00 | 0.0758 0.0025 0.0783 | 3.3283</item>
      <item>30 | 2.00 | 0.0698 0.0050 0.0748 | 3.1221</item>
      <item>31 | 2.00 | 0.0677 0.0060 0.0737 | 2.9160</item>
      <item>43 | 1.75 | 0.0665 0.0035 0.0700 | 1.5785</item>
      <item>44 | 1.75 | 0.0622 0.0057 0.0679 | 1.5194</item>
      <item>45 | 1.75 | 0.0608 0.0065 0.0673 | 1.4626</item>
      <item>57 | 1.50 | 0.0591 0.0048 0.0639 | 1.0900</item>
      <item>58 | 1.50 | 0.0561 0.0067 0.0628 | 1.0730</item>
      <item>59 | 1.50 | 0.0551 0.0074 0.0625 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 176s</item>
      <item>Prepare output 10s</item>
      <item>186s</item>
      <item>Jacobian determinant (RMS): 0.012 0.043 0.064 0.088 0.111 | 0.117536</item>
      <item>Template Matching: 0.087 0.223 0.203 0.182 0.165 | 0.165354</item>
      <item>Write result maps: 52s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 56s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 47s</item>
      <item>126s</item>
      <item>Create initial surface 93s</item>
      <item>Topology correction: 92s</item>
      <item>Surface refinement: 76s</item>
      <item>Reduction of surface collisions with optimization: 71s</item>
      <item>Spherical mapping with areal smoothing 80s</item>
      <item>Spherical registration 267s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 35s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 45s</item>
      <item>101s</item>
      <item>Create initial surface 88s</item>
      <item>Topology correction: 91s</item>
      <item>Surface refinement: 80s</item>
      <item>Reduction of surface collisions with optimization: 68s</item>
      <item>Spherical mapping with areal smoothing 78s</item>
      <item>Spherical registration 285s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5356 0.6425 mm</item>
      <item>Surface intensity / position RMSE: 0.0680 / 0.0715</item>
      <item>Euler number / defect number / defect size: 16.0 / 15.0 / 0.83%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/surf/lh.thickness.sub-0027269_ses-2_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/surf/rh.thickness.sub-0027269_ses-2_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/sub-0027269_ses-2_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1694s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 8s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 28s</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 8s</item>
      <item>ROI estimation of 'aal3' atlas 12s</item>
      <item>ROI estimation of 'mori' atlas 18s</item>
      <item>ROI estimation of 'anatomy3' atlas 28s</item>
      <item>ROI estimation of 'julichbrain' atlas 47s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 71s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 99s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
      <item>Write results 9s</item>
      <item>410s</item>
      <item>Quality check: 13s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/report/catreport_sub-0027269_ses-2_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 50 minute(s) and 52 second(s).</item>
      <item>Image Quality Rating (IQR): 81.92% (B-)</item>
      <item>GM volume (GMV): 48.32% (710.36 / 1470.15 ml)</item>
      <item>GM thickness (GMT): 2.54 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_611862/ds/UWM/sub-0027269/ses-2/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>