ds003468_ReproVBM/sub-AL038/report/cat_sub-AL038_ses-7_acq-RARE_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.05784613445313 -0.034774307659133 0.0022308241477301 -86.401225672277;0.0613310919052601 0.971717390843567 0.117906629819875 -85.7496141713391;-0.0704250362855626 -0.0798842977139299 1.45849466049258 -94.0269696922037;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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      <vr>[3592662.94797162;852347.06623896;1169543.12767072;1047769.99557739;12664825.4032241;695517.360603844;2153695.45291769;2296449.20756022;42597141.1725897;5110536.25912414;116411.499608051;400597.645190617;133161.481616024]</vr>
      <ll>-9.00889587402344</ll>
      <Affine_translation>[-86.401225672277 -85.7496141713391 -94.0269696922037]</Affine_translation>
      <Affine_rotation>[0.0842170223232003 0.06138391719134 -0.063168376604556]</Affine_rotation>
      <Affine_scaling>[1.0619602783285 0.975247873611118 1.46062451289749]</Affine_scaling>
      <Affine_shearing>[0.0252150151572101 -0.0825737379068723 0.000348679271241549]</Affine_shearing>
      <Affine0_translation>[-86.401225672277 -85.7496141713391 -94.0269696922037]</Affine0_translation>
      <Affine0_rotation>[0.0842170223232003 0.06138391719134 -0.063168376604556]</Affine0_rotation>
      <Affine0_scaling>[1.0619602783285 0.975247873611118 1.46062451289749]</Affine0_scaling>
      <Affine0_shearing>[0.0252150151572101 -0.0825737379068723 0.000348679271241549]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_30228/ds/sub-AL038</path>
      <file>sub-AL038_ses-7_acq-RARE_T1w</file>
      <fname>/var/lib/condor/execute/dir_30228/ds/sub-AL038/sub-AL038_ses-7_acq-RARE_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_30228/ds/sub-AL038/sub-AL038_ses-7_acq-RARE_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_30228/ds/sub-AL038/mri/msub-AL038_ses-7_acq-RARE_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_30228/ds/sub-AL038/mri/p0sub-AL038_ses-7_acq-RARE_T1w.nii</Fp0>
      <fnames>..28/ds/sub-AL038/sub-AL038_ses-7_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>32</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>6</SurfaceEulerNumber>
      <SurfaceDefectArea>0.511410645275092</SurfaceDefectArea>
      <SurfaceDefectNumber>4</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.123732700943947</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.471393704414368</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>2612.25</res_BB>
      <tissue_mn>[781.148498535156 12659.7763671875 8324.4296875 12458.552734375]</tissue_mn>
      <tissue_mnr>[0.0626997798681259 1.01615142822266 0.668169856071472 0.999999940395355]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[984.959355028535 2530.13344211838 2791.74284064395 1853.69696182649]</tissue_std>
      <tissue_stdr>[0.0843474566936493 0.216669172048569 0.239072203636169 0.15874220430851]</tissue_stdr>
      <contrast>4410.67138671875</contrast>
      <contrastr>0.354027569293976</contrastr>
      <NCR>1.10404479503632</NCR>
      <ICR>0.343325316905975</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[3 9 3]</res_vx_vol>
      <res_RMS>5.74456264653803</res_RMS>
      <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>2.77291965484619</contrastr>
      <NCR>10.5</NCR>
      <ICR>1.3113226890564</ICR>
      <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
      <SurfaceDefectArea>1.12785266131877</SurfaceDefectArea>
      <SurfaceDefectNumber>1.2</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>2.47465419769287</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>9.4278736114502</SurfacePositionRMSE>
      <IQR>9.63816947112904</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>20220711-201654</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>[12625.15663 6603.69449 12361.50238 5619.47698 4856.51719 1469.41018]</data>
         </item>
         <item>
            <identifier>cat_main:skipLAS</identifier>
            <message>Skip LAS due to image contrast. Use global normalization.</message>
            <level>0</level>
         </item>
         <item>
            <identifier>cat_main_registration:Hydrocephalus</identifier>
            <message>Very large ventricles detected (1.00%% of TIV). Use seperate class and adapt schedule. &lt;/br&gt;</message>
            <level>1</level>
         </item>
      </cat_warnings>
   </software>
   <subjectmeasures>
      <software/>
      <qualitymeasures>
         <software/>
         <SurfaceEulerNumber>6</SurfaceEulerNumber>
         <SurfaceDefectArea>0.511410645275092</SurfaceDefectArea>
         <SurfaceDefectNumber>4</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.123732700943947</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.471393704414368</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>6</EC_abs>
      <defect_size>0.511410645275092</defect_size>
      <vol_abs_CGW>[207.316756862745 15.4034509803922 194.792866666667 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>430.394711901695</surf_TSA>
      <vol_TIV>417.513074509804</vol_TIV>
      <vol_rel_CGW>[0.496551532203279 0.0368933380073837 0.466555129789337 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[0.826410127108253 0.346041680515623]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[0.844511568546295 0.559505057236693 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[0.558990979639713 0.0721755153897607 0.421105382005241;0.916328595662388 0.0875042618112658 0.501599990339681;1.46391574812919 0.209349454266528 0.0772946276550783]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[2.08891611148596 0.501813662748604 0.791938352104327;3.43816871302468 0.746215191857822 0.208061647895673]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>8.25063566990614</vol_TIV>
      <vol_rel_CGW>[6.76780769043246 0.5 6.22907919880275 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>7.33641835378635</surf_TSA>
      <SQR>5.82945987941252</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 4976.64 0.554544175754647]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0823189488591781 0.0772136897217782 0.365074942727463]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[123.647870588235 151.359019607843 294.533015686274 1639.70380392157 525.325850980392 2240.8297254902]</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>[0.0378321073949337 0.359165668487549 0.534756064414978 0 0]</dtc>
         <ll>[0.206909106416004 0 0.206909106416004 0;0.125913170443959 0.0231581860038937 0.149071356447853 14815.310546875;0.286062343638627 0.0985060161760016 0.384568359814629 21006.2109375]</ll>
         <rmsdtc>[0.0833203122019768 0.737287878990173 1.17484557628632]</rmsdtc>
         <rmsgdt>[0.0592427290976048 0.459479182958603 0.714074313640594]</rmsgdt>
         <rmsdt>1.17484557628632</rmsdt>
         <dt>0.534756064414978</dt>
      </reginitp>
      <SPMvols1>[108.024521568627 220.807082352941 200.379560784314 1680.83265098039 529.368117647059 2237.23850196078]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[12625.15663 6603.69449 12361.50238]</T3th>
            <Tth>
               <T3th>[-3.29765367507935 828.093322753906 7897.5224609375 12412.2236328125 13122.2412109375 36424.47265625]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>
               <CGW>[0.563669262145136 0.627659204745336 0.979960040879563]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.69100778643541 1.88297761423601 2.93988012263869 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.563670615415998 0.627659493353199 0.979958880231682]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.69101184624799 1.8829784800596 2.93987664069505 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.295078082146545 0.472299124413942 0.999063875541267]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.885234246439635 1.41689737324183 2.9971916266238 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.295074983387904 0.472309610518864 0.999046642867521]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.885224950163713 1.41692883155659 2.99713992860256 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>[0.0216557513922453 0.108588390052319 0.228007569909096 0.315775096416473 0.479637891054153 0.766467273235321]</dtc>
         <ll>[0.299938524070583 0 0.299938524070583 0;0.256116809116809 0.0325933887871388 0.288710197903948 50051.22265625;0.18300495834908 0.141794709782061 0.324799668131141 306154.0625;0.135857060726174 0.180788374052805 0.31664543477898 584817.125;0.112937397426363 0.179761758109046 0.292699155535408 943400.3125;0.320608462099988 0.175087714572188 0.495696176672175 306290.21875]</ll>
         <rmsdtc>[0.031151108443737 0.164097443223 0.332268267869949 0.454170048236847 0.755034804344177 1.58160889148712]</rmsdtc>
         <rmsgdt>[0.0138056669384241 0.0717649608850479 0.142453476786613 0.171167925000191 0.275478720664978 0.714198470115662]</rmsgdt>
         <rmsdt>1.58160889148712</rmsdt>
         <dt>0.766467273235321</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./ds/sub-AL038/sub-AL038_ses-7_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 2s</item>
      <item>Final scaling 3s</item>
      <item>20s</item>
      <item>Correct center-of-mass 9s</item>
      <item>Affine registration 5s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 13s</item>
      <item>Use initial fine affine registration. 38s</item>
      <item>SPM preprocessing 1 (estimate 2): 41s</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 10s</item>
      <item>Update skull-stripping 8s</item>
      <item>Update probability maps 1s</item>
      <item>Update registration 29s</item>
      <item>55s</item>
      <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 4s</item>
      <item>------------------------------------------------------------------------</item>
      <item>NOTE 01: cat_main:skipLAS</item>
      <item>Skip LAS due to image contrast. Use global normalization.</item>
      <item>------------------------------------------------------------------------</item>
      <item>20s</item>
      <item>SANLM denoising after LAS (medium) 17s</item>
      <item>21s</item>
      <item>--- Update Ym and Ymi ---</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 3s</item>
      <item>Major structures 1s</item>
      <item>Ventricle detection 5s</item>
      <item>Blood vessel detection 1s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 1s</item>
      <item>Final corrections 2s</item>
      <item>13s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 17s</item>
      <item>AMAP peaks: [0.86 0.13,0.25 0.09,0.64 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>------------------------------------------------------------------------------------------------------</item>
      <item>WARNING 03: cat_main_registration:Hydrocephalus</item>
      <item>Very large ventricles detected (1.00</item>
      <item>1 | 2.50 | 0.2999 0.0000 0.2999 | 32.0000</item>
      <item>2 | 2.50 | 0.2692 0.0088 0.2779 | 29.4886</item>
      <item>3 | 2.50 | 0.2501 0.0189 0.2689 | 26.9772</item>
      <item>4 | 2.50 | 0.2405 0.0242 0.2647 | 24.6107</item>
      <item>5 | 2.50 | 0.2373 0.0249 0.2622 | 22.6548</item>
      <item>6 | 2.50 | 0.2345 0.0253 0.2598 | 20.6989</item>
      <item>7 | 2.50 | 0.2308 0.0260 0.2568 | 18.9688</item>
      <item>8 | 2.50 | 0.2271 0.0272 0.2543 | 17.4455</item>
      <item>9 | 2.50 | 0.2245 0.0271 0.2516 | 15.9223</item>
      <item>10 | 2.50 | 0.2209 0.0283 0.2491 | 14.6627</item>
      <item>11 | 2.50 | 0.2182 0.0284 0.2466 | 13.4764</item>
      <item>12 | 2.50 | 0.2145 0.0293 0.2438 | 12.3015</item>
      <item>13 | 2.50 | 0.2114 0.0299 0.2413 | 11.3776</item>
      <item>14 | 2.50 | 0.2078 0.0309 0.2386 | 10.4537</item>
      <item>15 | 2.25 | 0.2561 0.0326 0.2887 | 10.0000</item>
      <item>16 | 2.25 | 0.2394 0.0427 0.2821 | 9.2366</item>
      <item>17 | 2.25 | 0.2324 0.0445 0.2769 | 8.4743</item>
      <item>18 | 2.25 | 0.2256 0.0469 0.2725 | 7.8084</item>
      <item>19 | 2.25 | 0.2197 0.0485 0.2682 | 7.2165</item>
      <item>20 | 2.25 | 0.2140 0.0497 0.2636 | 6.6255</item>
      <item>21 | 2.25 | 0.2081 0.0514 0.2595 | 6.1431</item>
      <item>22 | 2.25 | 0.2026 0.0527 0.2553 | 5.6842</item>
      <item>23 | 2.25 | 0.1971 0.0537 0.2508 | 5.2347</item>
      <item>24 | 2.25 | 0.1902 0.0557 0.2459 | 4.8782</item>
      <item>25 | 2.25 | 0.1848 0.0566 0.2413 | 4.5223</item>
      <item>26 | 2.25 | 0.1790 0.0577 0.2367 | 4.1941</item>
      <item>27 | 2.25 | 0.1732 0.0589 0.2322 | 3.9176</item>
      <item>28 | 2.25 | 0.1677 0.0598 0.2275 | 3.6415</item>
      <item>29 | 2.00 | 0.1830 0.1418 0.3248 | 8.0000</item>
      <item>30 | 2.00 | 0.1965 0.0943 0.2908 | 7.1626</item>
      <item>31 | 2.00 | 0.2008 0.0721 0.2730 | 6.3645</item>
      <item>32 | 2.00 | 0.1990 0.0657 0.2647 | 5.7493</item>
      <item>33 | 2.00 | 0.1948 0.0626 0.2575 | 5.1811</item>
      <item>34 | 2.00 | 0.1917 0.0593 0.2510 | 4.6535</item>
      <item>35 | 2.00 | 0.1831 0.0618 0.2449 | 4.2477</item>
      <item>36 | 2.00 | 0.1783 0.0603 0.2386 | 3.8576</item>
      <item>37 | 2.00 | 0.1705 0.0615 0.2320 | 3.5153</item>
      <item>38 | 2.00 | 0.1634 0.0641 0.2275 | 3.2341</item>
      <item>39 | 2.00 | 0.1569 0.0627 0.2196 | 2.9628</item>
      <item>40 | 2.00 | 0.1490 0.0642 0.2132 | 2.7387</item>
      <item>41 | 2.00 | 0.1428 0.0657 0.2085 | 2.5412</item>
      <item>42 | 2.00 | 0.1369 0.0652 0.2022 | 2.3500</item>
      <item>43 | 1.75 | 0.1359 0.1808 0.3166 | 6.0000</item>
      <item>44 | 1.75 | 0.1646 0.1021 0.2666 | 5.1658</item>
      <item>45 | 1.75 | 0.1732 0.0756 0.2488 | 4.4483</item>
      <item>46 | 1.75 | 0.1712 0.0670 0.2382 | 3.9240</item>
      <item>47 | 1.75 | 0.1677 0.0617 0.2293 | 3.4471</item>
      <item>48 | 1.75 | 0.1616 0.0596 0.2212 | 3.0545</item>
      <item>49 | 1.75 | 0.1537 0.0598 0.2135 | 2.7438</item>
      <item>50 | 1.75 | 0.1469 0.0591 0.2060 | 2.4574</item>
      <item>51 | 1.75 | 0.1392 0.0600 0.1992 | 2.2329</item>
      <item>52 | 1.75 | 0.1323 0.0609 0.1932 | 2.0402</item>
      <item>53 | 1.75 | 0.1255 0.0608 0.1863 | 1.8601</item>
      <item>54 | 1.75 | 0.1191 0.0623 0.1814 | 1.7267</item>
      <item>55 | 1.75 | 0.1131 0.0626 0.1757 | 1.6021</item>
      <item>56 | 1.75 | 0.1086 0.0621 0.1708 | 1.4898</item>
      <item>57 | 1.50 | 0.1129 0.1798 0.2927 | 4.0000</item>
      <item>58 | 1.50 | 0.1337 0.1072 0.2409 | 3.1096</item>
      <item>59 | 1.50 | 0.1376 0.0806 0.2182 | 2.4742</item>
      <item>60 | 1.50 | 0.1331 0.0709 0.2041 | 2.0222</item>
      <item>61 | 1.50 | 0.1243 0.0629 0.1873 | 1.6486</item>
      <item>62 | 1.50 | 0.1158 0.0601 0.1759 | 1.3868</item>
      <item>63 | 1.50 | 0.1069 0.0584 0.1652 | 1.1786</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 523s</item>
      <item>Prepare output 7s</item>
      <item>530s</item>
      <item>Jacobian determinant (RMS): 0.031 0.164 0.332 0.454 0.755 | 1.581609</item>
      <item>Template Matching: 0.300 0.256 0.183 0.136 0.113 | 0.320608</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: 7s</item>
      <item>CSF distance: 2s</item>
      <item>PBT2x thickness: 8s</item>
      <item>20s</item>
      <item>Create initial surface 27s</item>
      <item>Topology correction: 22s</item>
      <item>Surface refinement: 37s</item>
      <item>Reduction of surface collisions with optimization: 20s</item>
      <item>Spherical mapping with areal smoothing 31s</item>
      <item>Spherical registration 313s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 7s</item>
      <item>CSF distance: 3s</item>
      <item>PBT2x thickness: 8s</item>
      <item>19s</item>
      <item>Create initial surface 25s</item>
      <item>Topology correction: 23s</item>
      <item>Surface refinement: 30s</item>
      <item>Reduction of surface collisions with optimization: 15s</item>
      <item>Spherical mapping with areal smoothing 31s</item>
      <item>Spherical registration 340s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 0.8272 0.2915 mm</item>
      <item>Surface intensity / position RMSE: 0.1237 / 0.4714</item>
      <item>Euler number / defect number / defect size: 6.0 / 4.0 / 0.51%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_30228/ds/sub-AL038/surf/lh.thickness.sub-AL038_ses-7_acq-RARE_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_30228/ds/sub-AL038/surf/rh.thickness.sub-AL038_ses-7_acq-RARE_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_30228/ds/sub-AL038/sub-AL038_ses-7_acq-RARE_T1w.nii</item>
      <item>Surface ROI estimation: 1617s</item>
      <item>Surface and thickness estimation takes: 1578s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 4s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 13s</item>
      <item>ROI estimation of 'lpba40' atlas 4s</item>
      <item>ROI estimation of 'hammers' atlas 9s</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 15s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 6s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 11s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 24s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 36s</item>
      <item>Write results 36s</item>
      <item>148s</item>
      <item>Quality check: 2s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_30228/ds/sub-AL038/report/catreport_sub-AL038_ses-7_acq-RARE_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 33 minute(s) and 33 second(s).</item>
      <item>Image Quality Rating (IQR): 8.62% (F)</item>
      <item>GM volume (GMV): 3.69% (15.40 / 417.51 ml)</item>
      <item>GM thickness (GMT): 0.83 0.35 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_30228/ds/sub-AL038/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_30228/ds/sub-AL038/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_30228/ds/sub-AL038/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>