ds003468_ReproVBM/sub-AL020/report/cat_sub-AL020_ses-3_acq-RARE_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.09870753856439 0.0843263057258892 0.0144811838086067 -112.205179238964;0.0380114585127627 0.936815263541036 -0.0766524708974533 -73.6167427484486;0.000998151148191405 0.292739825774111 2.14535771876427 -200.211103563736;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>-9.01549053192139</ll>
      <Affine_translation>[-112.205179238964 -73.6167427484486 -200.211103563736]</Affine_translation>
      <Affine_rotation>[-0.303684721686541 0.00947849579539512 -0.033271314307242]</Affine_rotation>
      <Affine_scaling>[1.09936532716937 0.978139607001603 2.07015479687874]</Affine_scaling>
      <Affine_shearing>[0.10636391066009 0.0125254453363572 0.580955626949612]</Affine_shearing>
      <Affine0_translation>[-112.205179238964 -73.6167427484486 -200.211103563736]</Affine0_translation>
      <Affine0_rotation>[-0.303684721686541 0.00947849579539512 -0.033271314307242]</Affine0_rotation>
      <Affine0_scaling>[1.09936532716937 0.978139607001603 2.07015479687874]</Affine0_scaling>
      <Affine0_shearing>[0.10636391066009 0.0125254453363572 0.580955626949612]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_28436/ds/sub-AL020</path>
      <file>sub-AL020_ses-3_acq-RARE_T1w</file>
      <fname>/var/lib/condor/execute/dir_28436/ds/sub-AL020/sub-AL020_ses-3_acq-RARE_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_28436/ds/sub-AL020/sub-AL020_ses-3_acq-RARE_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_28436/ds/sub-AL020/mri/msub-AL020_ses-3_acq-RARE_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_28436/ds/sub-AL020/mri/p0sub-AL020_ses-3_acq-RARE_T1w.nii</Fp0>
      <fnames>..36/ds/sub-AL020/sub-AL020_ses-3_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>8</SurfaceEulerNumber>
      <SurfaceDefectArea>1.65033788644713</SurfaceDefectArea>
      <SurfaceDefectNumber>5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.123707428574562</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.365684330463409</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>101.25</res_BB>
      <tissue_mn>[1566.19702148438 12787.3056640625 NaN 12563.3828125]</tissue_mn>
      <tissue_mnr>[0.124663643538952 1.0178234577179 NaN 1]</tissue_mnr>
      <tissue_std>[1946.78213642407 2262.43640731238 1837.97074753264 1364.01553260721]</tissue_std>
      <tissue_stdr>[0.177025482058525 0.205728679895401 0.167131006717682 0.124033145606518]</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 8.62400054931641 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>1.30612244897959</SurfaceEulerNumber>
      <SurfaceDefectArea>1.41258447161178</SurfaceDefectArea>
      <SurfaceDefectNumber>1.25</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>2.47414875030518</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>7.31368637084961</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>20220711-214255</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>[14128.57196 7366.15882 13810.89708 6568.73868 4261.13089 1223.75418]</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>8</SurfaceEulerNumber>
         <SurfaceDefectArea>1.65033788644713</SurfaceDefectArea>
         <SurfaceDefectNumber>5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.123707428574562</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.365684330463409</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>8</EC_abs>
      <defect_size>1.65033788644713</defect_size>
      <vol_abs_CGW>[236.14542745098 0.70958431372549 77.0512039215686 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>314.566694520451</surf_TSA>
      <vol_TIV>313.906215686274</vol_TIV>
      <vol_rel_CGW>[0.752280189593282 0.00226049781197919 0.245459312594738 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[0.856557265021112 0.167227064005077]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[0.882045924663544 0.0465623953631616 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[0.83084897836778 0.0197807244820627 0.261995060857294;0.886291524417684 0.0164362569758685 0.408405362497795;0.946297018784761 0.0183419796924115 0.329599576644911]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.635388285358434 0.0982241111294573 0.599571625274109;1.07386127204249 0.0802986420114822 0.400428374725891]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>8.43289799237456</vol_TIV>
      <vol_rel_CGW>[10.5 0.5 2.2582491486124 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>8.10754579662941</surf_TSA>
      <SQR>8.58654197010597</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 4976.64 0.509926693856446]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0654188536700126 0.0554232864507909 0.344132191807723]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[42.1044039215686 72.9062823529412 359.55577254902 1515.95421960784 693.014780392157 2292.3518]</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>[0.0401974022388458 0.430615454912186 0.673457384109497 0 0]</dtc>
         <ll>[0.238871989225378 0 0.238871989225378 0;0.141608181358481 0.0287234278477016 0.170331609206182 18375.640625;0.301498449721686 0.126339641081042 0.427838090802727 26941.67578125]</ll>
         <rmsdtc>[0.0881874784827232 0.905674159526825 1.43832659721375]</rmsdtc>
         <rmsgdt>[0.0623753182590008 0.539890110492706 0.815501689910889]</rmsgdt>
         <rmsdt>1.43832659721375</rmsdt>
         <dt>0.673457384109497</dt>
      </reginitp>
      <SPMvols1>[32.9857803921569 105.38951372549 274.638078431373 1570.77934901961 703.525329411765 2289.40074509804]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[14128.57196 7366.15882 13810.89708]</T3th>
            <Tth>
               <T3th>[-2.73208832740784 758.384887695312 8188.93701171875 13749.5419921875 13771.814453125 25483.10546875]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>NaN</Tthm>
            <Tthmi>NaN</Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.418095370680376 0.994378473677966 0.660834346385831]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.25428611204113 1.98250303915749 2.9831354210339 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.418115139459976 0.994051930048185 0.66106222700377]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.25434541837993 1.98318668101131 2.98215579014456 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>[0.0232771690934896 0.119484595954418 0.341566354036331 0.391630381345749 0.409586399793625 1.14173269271851]</dtc>
         <ll>[0.262297761058196 0 0.262297761058196 0;0.261442368742369 0.0241632733007733 0.285605642043142 37105.7265625;0.166430229499207 0.0599133135603779 0.226343543059585 129360.9921875;0.221610320146494 0.218408278477045 0.440018598623538 235503.53125;0.197180918459568 0.225449155344862 0.422630073804429 394390.15625;0.197180918459568 0.225449155344862 0.422630073804429 394390.15625]</ll>
         <rmsdtc>[0.0317055433988571 0.175946742296219 0.527837216854095 1.20172131061554 2.44606995582581 2.20877885818481]</rmsdtc>
         <rmsgdt>[0.0128048621118069 0.074104867875576 0.23325178027153 0.477537840604782 1.85605120658875 0.897607445716858]</rmsgdt>
         <rmsdt>2.20877885818481</rmsdt>
         <dt>1.14173269271851</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./ds/sub-AL020/sub-AL020_ses-3_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 3s</item>
      <item>22s</item>
      <item>Correct center-of-mass 10s</item>
      <item>Affine registration 57s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 14s</item>
      <item>Use initial fine affine registration. 37s</item>
      <item>SPM preprocessing 1 (estimate 2): 42s</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 7s</item>
      <item>Update segmentation 8s</item>
      <item>Update skull-stripping 6s</item>
      <item>Update probability maps 1s</item>
      <item>Update registration 29s</item>
      <item>51s</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>16s</item>
      <item>SANLM denoising after LAS (medium) 15s</item>
      <item>17s</item>
      <item>--- Update Ym and Ymi ---</item>
      <item>Update of intensities failed!</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 2s</item>
      <item>Major structures 1s</item>
      <item>Ventricle detection 4s</item>
      <item>Blood vessel detection 1s</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>11s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 11s</item>
      <item>AMAP peaks: [1.02 0.08,0.38 0.09,0.65 0.04]</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 | 0.2623 0.0000 0.2623 | 32.0000</item>
      <item>2 | 2.50 | 0.2457 0.0054 0.2512 | 29.4886</item>
      <item>3 | 2.50 | 0.2400 0.0091 0.2491 | 26.9772</item>
      <item>4 | 2.50 | 0.2368 0.0109 0.2477 | 24.6107</item>
      <item>5 | 2.50 | 0.2342 0.0123 0.2465 | 22.6548</item>
      <item>6 | 2.50 | 0.2319 0.0133 0.2452 | 20.6989</item>
      <item>7 | 2.50 | 0.2291 0.0144 0.2434 | 18.9688</item>
      <item>8 | 2.50 | 0.2265 0.0155 0.2420 | 17.4455</item>
      <item>9 | 2.50 | 0.2238 0.0164 0.2403 | 15.9223</item>
      <item>10 | 2.50 | 0.2209 0.0177 0.2387 | 14.6627</item>
      <item>11 | 2.50 | 0.2180 0.0189 0.2369 | 13.4764</item>
      <item>12 | 2.50 | 0.2150 0.0199 0.2350 | 12.3015</item>
      <item>13 | 2.50 | 0.2117 0.0215 0.2331 | 11.3776</item>
      <item>14 | 2.50 | 0.2085 0.0226 0.2311 | 10.4537</item>
      <item>15 | 2.25 | 0.2614 0.0242 0.2856 | 9.5920</item>
      <item>16 | 2.25 | 0.2435 0.0351 0.2786 | 8.8725</item>
      <item>17 | 2.25 | 0.2345 0.0396 0.2741 | 8.1530</item>
      <item>18 | 2.25 | 0.2273 0.0426 0.2700 | 7.5234</item>
      <item>19 | 2.25 | 0.2209 0.0450 0.2659 | 6.9630</item>
      <item>20 | 2.25 | 0.2148 0.0467 0.2615 | 6.4027</item>
      <item>21 | 2.25 | 0.2086 0.0489 0.2575 | 5.9447</item>
      <item>22 | 2.25 | 0.2027 0.0505 0.2533 | 5.5083</item>
      <item>23 | 2.25 | 0.1969 0.0518 0.2487 | 5.0803</item>
      <item>24 | 2.25 | 0.1896 0.0539 0.2435 | 4.7404</item>
      <item>25 | 2.25 | 0.1840 0.0549 0.2389 | 4.4005</item>
      <item>26 | 2.25 | 0.1782 0.0562 0.2344 | 4.0868</item>
      <item>27 | 2.25 | 0.1724 0.0577 0.2301 | 3.8221</item>
      <item>28 | 2.25 | 0.1668 0.0587 0.2255 | 3.5574</item>
      <item>29 | 2.00 | 0.1664 0.0599 0.2263 | 3.3283</item>
      <item>30 | 2.00 | 0.1590 0.0615 0.2205 | 3.1221</item>
      <item>31 | 2.00 | 0.1537 0.0620 0.2157 | 2.9160</item>
      <item>32 | 2.00 | 0.1472 0.0632 0.2105 | 2.7495</item>
      <item>33 | 2.00 | 0.1422 0.0639 0.2062 | 2.5890</item>
      <item>34 | 2.00 | 0.1372 0.0645 0.2017 | 2.4330</item>
      <item>35 | 2.00 | 0.1322 0.0657 0.1979 | 2.3080</item>
      <item>36 | 2.00 | 0.1275 0.0663 0.1938 | 2.1830</item>
      <item>37 | 2.00 | 0.1228 0.0670 0.1898 | 2.0688</item>
      <item>38 | 2.00 | 0.1183 0.0679 0.1863 | 1.9714</item>
      <item>39 | 2.00 | 0.1141 0.0684 0.1825 | 1.8740</item>
      <item>40 | 2.00 | 0.1089 0.0691 0.1780 | 1.7907</item>
      <item>41 | 2.00 | 0.1051 0.0695 0.1746 | 1.7148</item>
      <item>42 | 2.00 | 0.1015 0.0697 0.1712 | 1.6390</item>
      <item>43 | 1.75 | 0.0982 0.0704 0.1686 | 1.5785</item>
      <item>44 | 1.75 | 0.0939 0.0717 0.1656 | 1.5194</item>
      <item>45 | 1.75 | 0.0908 0.0720 0.1627 | 1.4626</item>
      <item>46 | 1.75 | 0.0879 0.0724 0.1603 | 1.4166</item>
      <item>47 | 1.75 | 0.0854 0.0725 0.1578 | 1.3706</item>
      <item>48 | 1.75 | 0.0829 0.0726 0.1555 | 1.3290</item>
      <item>49 | 1.75 | 0.0796 0.0728 0.1524 | 1.2932</item>
      <item>50 | 1.75 | 0.0776 0.0727 0.1503 | 1.2574</item>
      <item>51 | 1.75 | 0.0757 0.0727 0.1484 | 1.2271</item>
      <item>52 | 1.75 | 0.0739 0.0728 0.1467 | 1.1992</item>
      <item>57 | 1.50 | 0.0753 0.0691 0.1445 | 1.0900</item>
      <item>Problem with Shooting (dets: 0.00344788 .. 3.36079)</item>
      <item>58 | 1.50 | 0.0687 0.0737 0.1425 | 1.0730</item>
      <item>59 | 1.50 | 0.0657 0.0751 0.1409 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 305s</item>
      <item>Prepare output 7s</item>
      <item>312s</item>
      <item>Jacobian determinant (RMS): 0.032 0.176 0.528 1.202 2.446 | 2.208779</item>
      <item>Template Matching: 0.262 0.261 0.166 0.222 0.197 | 0.197181</item>
      <item>Write result maps: 15s</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: 6s</item>
      <item>12s</item>
      <item>Create initial surface 19s</item>
      <item>Topology correction: 18s</item>
      <item>Surface refinement: 39s</item>
      <item>Reduction of surface collisions with optimization: 18s</item>
      <item>Spherical mapping with areal smoothing 32s</item>
      <item>Spherical registration 301s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 3s</item>
      <item>CSF distance: 2s</item>
      <item>PBT2x thickness: 6s</item>
      <item>13s</item>
      <item>Create initial surface 19s</item>
      <item>Topology correction: 20s</item>
      <item>Surface refinement: 50s</item>
      <item>Reduction of surface collisions with optimization: 20s</item>
      <item>Spherical mapping with areal smoothing 33s</item>
      <item>Spherical registration 308s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 0.8546 0.1474 mm</item>
      <item>Surface intensity / position RMSE: 0.1237 / 0.3657</item>
      <item>Euler number / defect number / defect size: 8.0 / 5.0 / 1.65%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28436/ds/sub-AL020/surf/lh.thickness.sub-AL020_ses-3_acq-RARE_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28436/ds/sub-AL020/surf/rh.thickness.sub-AL020_ses-3_acq-RARE_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_28436/ds/sub-AL020/sub-AL020_ses-3_acq-RARE_T1w.nii</item>
      <item>Surface ROI estimation: 1327s</item>
      <item>Surface and thickness estimation takes: 1295s</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 11s</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>140s</item>
      <item>Quality check: 2s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_28436/ds/sub-AL020/report/catreport_sub-AL020_ses-3_acq-RARE_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 29 minute(s) and 11 second(s).</item>
      <item>Image Quality Rating (IQR): 52.32% (E-)</item>
      <item>GM volume (GMV): 0.23% ( 0.71 / 313.91 ml)</item>
      <item>GM thickness (GMT): 0.86 0.17 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_28436/ds/sub-AL020/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_28436/ds/sub-AL020/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_28436/ds/sub-AL020/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>