ds003468_ReproVBM/sub-AL034/report/cat_sub-AL034_ses-1_acq-RARE_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine>[1.09911098180999 -0.0198835369359425 0.0623612801351671 -112.957459849856;0.0216808834134411 0.880299687101627 0.189670843739302 -113.322987080212;-0.132211448358987 0.158994224209747 2.31377502242753 -274.51532945438;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>-9.1418285369873</ll>
      <Affine_translation>[-112.957459849856 -113.322987080212 -274.51532945438]</Affine_translation>
      <Affine_rotation>[-0.175978143148537 0.121286841668745 0.00162600335879582]</Affine_rotation>
      <Affine_scaling>[1.10724652996435 0.894505698331171 2.23588861007858]</Affine_scaling>
      <Affine_shearing>[-0.0194041557649742 -0.190256380160172 0.661231419701585]</Affine_shearing>
      <Affine0_translation>[-112.957459849856 -113.322987080212 -274.51532945438]</Affine0_translation>
      <Affine0_rotation>[-0.175978143148537 0.121286841668745 0.00162600335879582]</Affine0_rotation>
      <Affine0_scaling>[1.10724652996435 0.894505698331171 2.23588861007858]</Affine0_scaling>
      <Affine0_shearing>[-0.0194041557649742 -0.190256380160172 0.661231419701585]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_27041/ds/sub-AL034</path>
      <file>sub-AL034_ses-1_acq-RARE_T1w</file>
      <fname>/var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_27041/ds/sub-AL034/mri/msub-AL034_ses-1_acq-RARE_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_27041/ds/sub-AL034/mri/p0sub-AL034_ses-1_acq-RARE_T1w.nii</Fp0>
      <fnames>..41/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
         </tpm>
         <ngaus>[1 1 2 3 4 2]</ngaus>
         <affreg>mni</affreg>
         <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
         <tol>0.0001</tol>
         <accstr>0.5</accstr>
         <biasstr>0.5</biasstr>
         <biasreg>0.001</biasreg>
         <biasfwhm>60</biasfwhm>
         <samp>3</samp>
         <redspmres>0</redspmres>
         <fwhm>1</fwhm>
         <biasacc>0</biasacc>
      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
         <BVCstr>0.5</BVCstr>
         <regstr>0.5</regstr>
         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
         <SLC>0</SLC>
         <mrf>1</mrf>
         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>64</nproc>
         <species>human</species>
         <APP>1070</APP>
         <setCOM>1</setCOM>
         <vox>1.5</vox>
         <bb>12</bb>
         <shootingsurf>Template_T1</shootingsurf>
         <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
         <darteltpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
         </darteltpm>
         <shootingtpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
         </shootingtpm>
         <shootingT1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
         </shootingT1>
         <brainmask>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
         </brainmask>
         <T1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
         </T1>
         <cat12atlas>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
         </cat12atlas>
         <pbtres>0.5</pbtres>
         <SRP>22</SRP>
         <reduce_mesh>1</reduce_mesh>
         <vdist>2</vdist>
         <pbtlas>0</pbtlas>
         <thick_measure>1</thick_measure>
         <thick_limit>5</thick_limit>
         <close_parahipp>0</close_parahipp>
         <scale_cortex>0.7</scale_cortex>
         <add_parahipp>0.1</add_parahipp>
         <colormap>BCGWHw</colormap>
         <report/>
         <verb>2</verb>
         <ignoreErrors>1</ignoreErrors>
         <expertgui>1</expertgui>
         <subfolders>1</subfolders>
         <experimental>0</experimental>
         <print>2</print>
         <fontsize>10</fontsize>
         <send_info>1</send_info>
         <gifti_dat>1</gifti_dat>
         <atlas>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
         </atlas>
         <satlas>
            <tr>
               <td>Desikan</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <tr>
               <td>Destrieux</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <tr>
               <td>HCP</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_100P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_200P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_400P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_600P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
         </satlas>
         <LAB>
            <NB>0</NB>
            <CT>1</CT>
            <CB>3</CB>
            <BG>5</BG>
            <BV>7</BV>
            <TH>9</TH>
            <ON>11</ON>
            <MB>13</MB>
            <BS>13</BS>
            <VT>15</VT>
            <NV>17</NV>
            <HC>19</HC>
            <HD>21</HD>
            <HI>23</HI>
            <PH>25</PH>
            <LE>27</LE>
         </LAB>
         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
         <regmethod>
            <shooting>
               <shootingtpm>
                  <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
               </shootingtpm>
               <regstr>0.5</regstr>
            </shooting>
         </regmethod>
         <restypes>
            <optimal>[1 0.3]</optimal>
         </restypes>
         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
         <darteltpms>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
         </darteltpms>
         <shootingtpms>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
         </shootingtpms>
         <inv_weighting>[true]</inv_weighting>
         <histth>[0.96 0.9999]</histth>
         <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>
         <AMAPframing>1</AMAPframing>
      </extopts>
   </parameter>
   <qualitymeasures>
      <software/>
      <SurfaceEulerNumber>22</SurfaceEulerNumber>
      <SurfaceDefectArea>1.97242925460113</SurfaceDefectArea>
      <SurfaceDefectNumber>7</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0630294680595398</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.10944738984108</SurfacePositionRMSE>
      <res_vx_vol>[1.5 4.5 1.5]</res_vx_vol>
      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>2.87228132326901</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[5859.74853515625 NaN NaN 17423.400390625]</tissue_mn>
      <tissue_mnr>[0.336314857006073 NaN NaN 1]</tissue_mnr>
      <tissue_std>[2897.06963634106 3392.89992547749 2742.64116260078 2416.51634753725]</tissue_std>
      <tissue_stdr>[0.250532418489456 0.293410748243332 0.237177759408951 0.208975180983543]</tissue_stdr>
      <contrast>NaN</contrast>
      <contrastr>NaN</contrastr>
      <NCR>0</NCR>
      <ICR>NaN</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[3 9 3]</res_vx_vol>
      <res_RMS>5.74456264653803</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62400054931641 NaN NaN 8.62400054931641]</tissue_mn>
      <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
      <contrast>NaN</contrast>
      <contrastr>NaN</contrastr>
      <NCR>0.5</NCR>
      <ICR>NaN</ICR>
      <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
      <SurfaceDefectArea>1.49310731365028</SurfaceDefectArea>
      <SurfaceDefectNumber>1.35</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.2605893611908</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>2.1889476776123</SurfacePositionRMSE>
      <IQR>5.26778717548681</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>
      <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>20220711-215237</date>
      <cat_warnings>
         <item>
            <identifier>cat_run_job:failedBGD</identifier>
            <message>cat_run_job1639: Detection of background failed.</message>
            <level>1</level>
         </item>
         <item>
            <identifier>cat_run_job1639:nonT1contrast</identifier>
            <message>A non-T1 contrast was detected and the NEW EXPERIMENTAL &lt;/br&gt;PIPELINE is used! If it is was a high-resolution T1 image, &lt;/br&gt;the initial segmentation might have failed, probably due &lt;/br&gt;to alignment problems (please check the image orientation).</message>
            <level>1</level>
            <data>[15456.60634 9232.55033 15594.24065 8108.74399 3594.694 1410.03992]</data>
         </item>
         <item>
            <identifier>cat_main:skipLAS</identifier>
            <message>Skip LAS due to image contrast. Use global normalization.</message>
            <level>0</level>
         </item>
      </cat_warnings>
   </software>
   <subjectmeasures>
      <software/>
      <qualitymeasures>
         <software/>
         <SurfaceEulerNumber>22</SurfaceEulerNumber>
         <SurfaceDefectArea>1.97242925460113</SurfaceDefectArea>
         <SurfaceDefectNumber>7</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0630294680595398</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.10944738984108</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>22</EC_abs>
      <defect_size>1.97242925460113</defect_size>
      <vol_abs_CGW>[32.3583411764706 12.9342235294118 99.686462745098 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>249.267491762079</surf_TSA>
      <vol_TIV>144.97902745098</vol_TIV>
      <vol_rel_CGW>[0.223193255917042 0.0892144454051123 0.687592298677845 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[0.7420917509033 0.420368947236289]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[0.567666709423065 0.620113687500136 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[0.532079206751011 0.0649654541017424 0.675627624295459;0.840406283702592 0.120807924795545 0.232867212225907;1.45613963060555 0.188331193925918 0.0915051634786337]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.375746161744788 0.0499763703679095 0.175540571960009;2.17935538154097 0.291712408002683 0.824459428039991]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>8.56846914481617</vol_TIV>
      <vol_rel_CGW>[1.8583558893147 0.5 10.1988559388981 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>8.3400464690837</surf_TSA>
      <SQR>8.34027311965593</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 4976.64 0.515563150136068]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0872204813359605 0.0667394072051072 0.343850385766556]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[42.3634078431373 39.6758470588235 424.703976470588 1738.36661568627 1157.63332941176 1573.68630980392]</SPMvols0>
      <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>[0.0411871932446957 0.510926842689514 0.861334323883057 0 0]</dtc>
         <ll>[0.249532014954419 0 0.249532014954419 0;0.137718991405156 0.0339527290408351 0.171671720445991 21721.0546875;0.253375379692893 0.151823046112976 0.405198425805869 32375.9609375]</ll>
         <rmsdtc>[0.0894775316119194 1.21180057525635 2.03004193305969]</rmsdtc>
         <rmsgdt>[0.063137948513031 0.755503714084625 1.15925705432892]</rmsgdt>
         <rmsdt>2.03004193305969</rmsdt>
         <dt>0.861334323883057</dt>
      </reginitp>
      <SPMvols1>[23.0953254901961 104.303223529412 62.5117882352941 1934.05382352941 1199.35996862745 1653.366]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[15456.60634 9232.55033 15594.24065]</T3th>
            <Tth>
               <T3th>[-1.70161843299866 1052.31372070312 13559.0908203125 15868.771484375 16615.1171875 24622.69140625]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>
               <CGW>[0.614813089134864 0.617346147706653 0.86756636793683]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.84443926740459 1.85203844311996 2.60269910381049 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.614821129482046 0.61735034418183 0.867559975803558]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.84446338844614 1.85205103254549 2.60267992741067 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.308016775307319 0.301399865931127 0.939809603939654]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.90419959779338 0.924050325921957 2.81942881181896 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.308017941860945 0.301405907037158 0.939806242870167]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.904217721111475 0.924053825582836 2.8194187286105 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm2postamap>
      </tths>
      <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>[0.0228037312626839 0.118160769343376 0.341698855161667 0.382777482271194 0.407696515321732 1.14449417591095]</dtc>
         <ll>[0.259390700076248 0 0.259390700076248 0;0.261658221408221 0.023425055962556 0.285083277370777 35972.1015625;0.163450854878989 0.0607845568783069 0.224235411757295 131242.125;0.219100633351325 0.2176268487914 0.436727482142725 234660.9375;0.181965293025479 0.223491985322574 0.405457278348052 390966.375;0.181965293025479 0.223491985322574 0.405457278348052 390966.375]</ll>
         <rmsdtc>[0.0308313313871622 0.17324087023735 0.528151214122772 1.21057617664337 2.38769769668579 2.2737410068512]</rmsdtc>
         <rmsgdt>[0.0125624006614089 0.0734260976314545 0.227712631225586 0.475024104118347 1.72534370422363 0.900434911251068]</rmsgdt>
         <rmsdt>2.2737410068512</rmsdt>
         <dt>1.14449417591095</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 2s</item>
      <item>------------------------------------------------------------------------</item>
      <item>WARNING 01: cat_run_job:failedBGD</item>
      <item>cat_run_job1639: Detection of background failed.</item>
      <item>------------------------------------------------------------------------</item>
      <item>Internal resampling (1.50x4.50x1.50mm &gt; 1.00x1.00x1.00mm): 1s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 3s</item>
      <item>Estimate background 4s</item>
      <item>Initial correction 4s</item>
      <item>Refine background 2s</item>
      <item>Final correction 3s</item>
      <item>Final scaling 4s</item>
      <item>23s</item>
      <item>Correct center-of-mass 17s</item>
      <item>Affine registration 5s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 20s</item>
      <item>Use initial fine affine registration. 44s</item>
      <item>SPM preprocessing 1 (estimate 2): 48s</item>
      <item>----------------------------------------------------------------------------</item>
      <item>WARNING 02: cat_run_job1639:nonT1contrast</item>
      <item>A non-T1 contrast was detected and the NEW EXPERIMENTAL</item>
      <item>PIPELINE is used! If it is was a high-resolution T1 image,</item>
      <item>the initial segmentation might have failed, probably due</item>
      <item>to alignment problems (please check the image orientation).</item>
      <item>----------------------------------------------------------------------------</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 8s</item>
      <item>Update segmentation 9s</item>
      <item>Update skull-stripping 7s</item>
      <item>Update probability maps 5s</item>
      <item>Update registration 31s</item>
      <item>60s</item>
      <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 1s</item>
      <item>------------------------------------------------------------------------</item>
      <item>NOTE 01: cat_main:skipLAS</item>
      <item>Skip LAS due to image contrast. Use global normalization.</item>
      <item>------------------------------------------------------------------------</item>
      <item>14s</item>
      <item>SANLM denoising after LAS (medium) 16s</item>
      <item>18s</item>
      <item>--- Update Ym and Ymi ---</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 2s</item>
      <item>Major structures 0s</item>
      <item>Ventricle detection 2s</item>
      <item>Blood vessel detection 0s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 0s</item>
      <item>Side alignment 1s</item>
      <item>Final corrections 2s</item>
      <item>8s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 36s</item>
      <item>AMAP peaks: [0.99 0.08,0.31 0.06,0.72 0.09]</item>
      <item>--- Update Ym and Ymi ---</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 | 0.2594 0.0000 0.2594 | 32.0000</item>
      <item>2 | 2.50 | 0.2438 0.0051 0.2489 | 29.4886</item>
      <item>3 | 2.50 | 0.2384 0.0086 0.2470 | 26.9772</item>
      <item>4 | 2.50 | 0.2354 0.0104 0.2458 | 24.6107</item>
      <item>5 | 2.50 | 0.2330 0.0117 0.2447 | 22.6548</item>
      <item>6 | 2.50 | 0.2308 0.0127 0.2435 | 20.6989</item>
      <item>7 | 2.50 | 0.2281 0.0137 0.2418 | 18.9688</item>
      <item>8 | 2.50 | 0.2257 0.0148 0.2405 | 17.4455</item>
      <item>9 | 2.50 | 0.2232 0.0157 0.2389 | 15.9223</item>
      <item>10 | 2.50 | 0.2204 0.0170 0.2374 | 14.6627</item>
      <item>11 | 2.50 | 0.2175 0.0182 0.2357 | 13.4764</item>
      <item>12 | 2.50 | 0.2146 0.0192 0.2338 | 12.3015</item>
      <item>13 | 2.50 | 0.2113 0.0208 0.2320 | 11.3776</item>
      <item>14 | 2.50 | 0.2081 0.0220 0.2300 | 10.4537</item>
      <item>15 | 2.25 | 0.2617 0.0234 0.2851 | 9.5920</item>
      <item>16 | 2.25 | 0.2445 0.0339 0.2785 | 8.8725</item>
      <item>17 | 2.25 | 0.2355 0.0387 0.2742 | 8.1530</item>
      <item>18 | 2.25 | 0.2282 0.0419 0.2701 | 7.5234</item>
      <item>19 | 2.25 | 0.2216 0.0444 0.2660 | 6.9630</item>
      <item>20 | 2.25 | 0.2153 0.0463 0.2616 | 6.4027</item>
      <item>21 | 2.25 | 0.2089 0.0486 0.2576 | 5.9447</item>
      <item>22 | 2.25 | 0.2028 0.0505 0.2533 | 5.5083</item>
      <item>23 | 2.25 | 0.1966 0.0520 0.2486 | 5.0803</item>
      <item>24 | 2.25 | 0.1891 0.0542 0.2433 | 4.7404</item>
      <item>25 | 2.25 | 0.1832 0.0554 0.2386 | 4.4005</item>
      <item>26 | 2.25 | 0.1772 0.0568 0.2339 | 4.0868</item>
      <item>27 | 2.25 | 0.1711 0.0585 0.2295 | 3.8221</item>
      <item>28 | 2.25 | 0.1652 0.0595 0.2247 | 3.5574</item>
      <item>29 | 2.00 | 0.1635 0.0608 0.2242 | 3.3283</item>
      <item>30 | 2.00 | 0.1561 0.0621 0.2181 | 3.1221</item>
      <item>31 | 2.00 | 0.1507 0.0625 0.2132 | 2.9160</item>
      <item>32 | 2.00 | 0.1441 0.0637 0.2078 | 2.7495</item>
      <item>33 | 2.00 | 0.1390 0.0643 0.2034 | 2.5890</item>
      <item>34 | 2.00 | 0.1339 0.0649 0.1988 | 2.4330</item>
      <item>35 | 2.00 | 0.1289 0.0660 0.1949 | 2.3080</item>
      <item>36 | 2.00 | 0.1241 0.0667 0.1907 | 2.1830</item>
      <item>37 | 2.00 | 0.1193 0.0673 0.1867 | 2.0688</item>
      <item>38 | 2.00 | 0.1148 0.0682 0.1830 | 1.9714</item>
      <item>39 | 2.00 | 0.1104 0.0686 0.1791 | 1.8740</item>
      <item>40 | 2.00 | 0.1051 0.0693 0.1744 | 1.7907</item>
      <item>41 | 2.00 | 0.1013 0.0697 0.1710 | 1.7148</item>
      <item>42 | 2.00 | 0.0976 0.0698 0.1675 | 1.6390</item>
      <item>43 | 1.75 | 0.0939 0.0707 0.1646 | 1.5785</item>
      <item>44 | 1.75 | 0.0896 0.0718 0.1614 | 1.5194</item>
      <item>45 | 1.75 | 0.0864 0.0721 0.1585 | 1.4626</item>
      <item>46 | 1.75 | 0.0835 0.0724 0.1560 | 1.4166</item>
      <item>47 | 1.75 | 0.0809 0.0725 0.1534 | 1.3706</item>
      <item>48 | 1.75 | 0.0784 0.0726 0.1509 | 1.3290</item>
      <item>49 | 1.75 | 0.0751 0.0728 0.1478 | 1.2932</item>
      <item>50 | 1.75 | 0.0730 0.0725 0.1456 | 1.2574</item>
      <item>57 | 1.50 | 0.0742 0.0661 0.1403 | 1.0900</item>
      <item>Problem with Shooting (dets: 0.00337295 .. 2.14688)</item>
      <item>58 | 1.50 | 0.0667 0.0713 0.1380 | 1.0730</item>
      <item>59 | 1.50 | 0.0631 0.0733 0.1363 | 1.0579</item>
      <item>60 | 1.50 | 0.0607 0.0745 0.1352 | 1.0447</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 320s</item>
      <item>Prepare output 7s</item>
      <item>327s</item>
      <item>Jacobian determinant (RMS): 0.031 0.173 0.528 1.211 2.388 | 2.273741</item>
      <item>Template Matching: 0.259 0.262 0.163 0.219 0.182 | 0.181965</item>
      <item>Write result maps: 16s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 3s</item>
      <item>CSF distance: 2s</item>
      <item>PBT2x thickness: 4s</item>
      <item>10s</item>
      <item>Create initial surface 14s</item>
      <item>Topology correction: 17s</item>
      <item>Surface refinement: 37s</item>
      <item>Reduction of surface collisions with optimization: 17s</item>
      <item>Spherical mapping with areal smoothing 31s</item>
      <item>Spherical registration 335s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 3s</item>
      <item>CSF distance: 2s</item>
      <item>PBT2x thickness: 4s</item>
      <item>10s</item>
      <item>Create initial surface 12s</item>
      <item>Topology correction: 16s</item>
      <item>Surface refinement: 37s</item>
      <item>Reduction of surface collisions with optimization: 18s</item>
      <item>Spherical mapping with areal smoothing 31s</item>
      <item>Spherical registration 326s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 0.7421 0.4194 mm</item>
      <item>Surface intensity / position RMSE: 0.0630 / 0.1094</item>
      <item>Euler number / defect number / defect size: 22.0 / 7.0 / 1.97%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_27041/ds/sub-AL034/surf/lh.thickness.sub-AL034_ses-1_acq-RARE_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_27041/ds/sub-AL034/surf/rh.thickness.sub-AL034_ses-1_acq-RARE_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_27041/ds/sub-AL034/sub-AL034_ses-1_acq-RARE_T1w.nii</item>
      <item>Surface ROI estimation: 1368s</item>
      <item>Surface and thickness estimation takes: 1336s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 3s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 12s</item>
      <item>ROI estimation of 'lpba40' atlas 3s</item>
      <item>ROI estimation of 'hammers' atlas 8s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 3s</item>
      <item>ROI estimation of 'aal3' atlas 5s</item>
      <item>ROI estimation of 'mori' atlas 7s</item>
      <item>ROI estimation of 'anatomy3' atlas 10s</item>
      <item>ROI estimation of 'julichbrain' atlas 14s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 6s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 10s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 22s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 33s</item>
      <item>Write results 34s</item>
      <item>138s</item>
      <item>Quality check: 1s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_27041/ds/sub-AL034/report/catreport_sub-AL034_ses-1_acq-RARE_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 29 minute(s) and 36 second(s).</item>
      <item>Image Quality Rating (IQR): 52.32% (E-)</item>
      <item>GM volume (GMV): 8.92% (12.93 / 144.98 ml)</item>
      <item>GM thickness (GMT): 0.74 0.42 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_27041/ds/sub-AL034/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>