ds003468_ReproVBM/sub-AL011/report/cat_sub-AL011_ses-7_acq-RARE_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.34079016662704 0.090970111819239 -0.0761303141254697 -117.834612716817;-0.0454687322416574 0.848319827814984 -0.157410487257774 -52.5171616267352;0.0846894650785316 -0.0769888226823215 1.96868448722605 -178.31385970085;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>[1978673.63637758;932245.233323151;8371769.18084702;932189.425208317;8602807.2794439;578260.688879088;3072114.12307721;1246517.98131394;27017185.6351205;2916656.77134742;208989.082267024;336943.986693985;153570.099860793]</vr>
      <ll>-8.65899562835693</ll>
      <Affine_translation>[-117.834612716817 -52.5171616267352 -178.31385970085]</Affine_translation>
      <Affine_rotation>[0.0968703632861783 -0.0595174198155732 0.0397704817368853]</Affine_rotation>
      <Affine_scaling>[1.34423137220893 0.854738798116516 1.94531607279429]</Affine_scaling>
      <Affine_shearing>[0.042546458098377 0.0397404453126089 -0.403901823942718]</Affine_shearing>
      <Affine0_translation>[-117.834612716817 -52.5171616267352 -178.31385970085]</Affine0_translation>
      <Affine0_rotation>[0.0968703632861783 -0.0595174198155732 0.0397704817368853]</Affine0_rotation>
      <Affine0_scaling>[1.34423137220893 0.854738798116516 1.94531607279429]</Affine0_scaling>
      <Affine0_shearing>[0.042546458098377 0.0397404453126089 -0.403901823942718]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_12393/ds/sub-AL011</path>
      <file>sub-AL011_ses-7_acq-RARE_T1w</file>
      <fname>/var/lib/condor/execute/dir_12393/ds/sub-AL011/sub-AL011_ses-7_acq-RARE_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_12393/ds/sub-AL011/sub-AL011_ses-7_acq-RARE_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_12393/ds/sub-AL011/mri/msub-AL011_ses-7_acq-RARE_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_12393/ds/sub-AL011/mri/p0sub-AL011_ses-7_acq-RARE_T1w.nii</Fp0>
      <fnames>..93/ds/sub-AL011/sub-AL011_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>10</SurfaceEulerNumber>
      <SurfaceDefectArea>78.2480210703591</SurfaceDefectArea>
      <SurfaceDefectNumber>2.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.247814983129501</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.985225796699524</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>1377</res_BB>
      <tissue_mn>[2244.1279296875 10692.6103515625 NaN 11065.0966796875]</tissue_mn>
      <tissue_mnr>[0.202811419963837 0.966336846351624 NaN 1]</tissue_mnr>
      <tissue_std>[1599.21980540363 2308.17824468807 2312.8551050318 1468.91322141542]</tissue_std>
      <tissue_stdr>[0.181297525763512 0.261669486761093 0.26219967007637 0.166525155305862]</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>10.5</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>1.40816326530612</SurfaceEulerNumber>
      <SurfaceDefectArea>10.5</SurfaceDefectArea>
      <SurfaceDefectNumber>1.125</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>4.95629978179932</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>10.5</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>20220711-221918</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>[14338.64026 7268.7874 13785.57679 5309.76938 3671.26078 1336.59133]</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>10</SurfaceEulerNumber>
         <SurfaceDefectArea>78.2480210703591</SurfaceDefectArea>
         <SurfaceDefectNumber>2.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.247814983129501</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.985225796699524</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>10</EC_abs>
      <defect_size>78.2480210703591</defect_size>
      <vol_abs_CGW>[263.938266666667 3.77463529411765 67.3642196078431 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>434.848423956885</surf_TSA>
      <vol_TIV>335.077121568627</vol_TIV>
      <vol_rel_CGW>[0.787694084964882 0.01126497469134 0.201040940343778 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[0.506601438965568 0.483543132245373]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[0.366287916898727 0.482647458107936 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[0.13018145086326 0.083465001391059 0.534722563221213;0.578178962833708 0.124022803506503 0.346587282101645;1.1012226308099 0.150799616068779 0.118690154677142]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[1.53153148682133 0.0837527592896744 0.593976698175423;1.86062186809572 0.152467835460441 0.406023301824577]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>8.40367215488022</vol_TIV>
      <vol_rel_CGW>[10.5 0.5 1.4605053941052 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>7.2954003310629</surf_TSA>
      <SQR>8.58653720704046</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 4976.64 0.542404044958696]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0783705306648803 0.0661933738811321 0.330798569087094]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[44.9296156862745 60.0752745098039 401.099678431373 1325.6246627451 819.673666666667 2324.25079607843]</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>[0.0401935242116451 0.432831466197968 0.681703686714172 0 0]</dtc>
         <ll>[0.242546041854242 0 0.242546041854242 0;0.144392632541298 0.0292080149931066 0.173600647534404 18685.65234375;0.30481671428337 0.130836587564713 0.435653301848083 27900.640625]</ll>
         <rmsdtc>[0.0876788720488548 0.888962924480438 1.42826724052429]</rmsdtc>
         <rmsgdt>[0.0619283057749271 0.531653642654419 0.815412282943726]</rmsgdt>
         <rmsdt>1.42826724052429</rmsdt>
         <dt>0.681703686714172</dt>
      </reginitp>
      <SPMvols1>[33.9299725490196 92.5955921568627 303.181160784314 1360.01525882353 864.995392156863 2321.97802352941]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[14338.64026 7268.7874 13785.57679]</T3th>
            <Tth>
               <T3th>[-0.845198392868042 934.318725585938 7488.67626953125 13852.6953125 14950.740234375 25046.482421875]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>
               <CGW>[0.333868084984497 0.656570244581199 0.723315242865162]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.00160425495349 1.9697107337436 2.16994572859549 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.333868144876872 0.656570247695865 0.723316285242575]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.00160443463062 1.9697107430876 2.16994885572772 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.345496480167537 0.980949087673602 0.69569576419577]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.03648944050261 2.08708729258731 2.94284726302081 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.345496488322691 0.980946637910127 0.695700353054298]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.03648946496807 2.08710105916289 2.94283991373038 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>[0.0235182419419289 0.12008099257946 0.34332937002182 0.395501017570496 0.411729842424393 1.15917325019836]</dtc>
         <ll>[0.265811940706008 0 0.265811940706008 0;0.264645767195767 0.0243642857142857 0.289010052910053 37414.40625;0.169435685153691 0.0602610293249244 0.229696714478616 130111.7578125;0.224382507382182 0.219129774305556 0.443512281687737 236281.5;0.202024387730778 0.229293987548539 0.431318375279318 401116.125;0.202024387730778 0.229293987548539 0.431318375279318 401116.125]</ll>
         <rmsdtc>[0.0319829694926739 0.176600441336632 0.530346810817719 1.20485270023346 2.47963380813599 2.23216223716736]</rmsdtc>
         <rmsgdt>[0.0127588929608464 0.0744070187211037 0.235600888729095 0.479053914546967 1.85845565795898 0.903569042682648]</rmsgdt>
         <rmsdt>2.23216223716736</rmsdt>
         <dt>1.15917325019836</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./ds/sub-AL011/sub-AL011_ses-7_acq-RARE_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 1s</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 2s</item>
      <item>Estimate background 3s</item>
      <item>Initial correction 3s</item>
      <item>Refine background 1s</item>
      <item>Final correction 2s</item>
      <item>Final scaling 3s</item>
      <item>17s</item>
      <item>Correct center-of-mass 10s</item>
      <item>Affine registration 45s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 11s</item>
      <item>Use initial fine affine registration. 28s</item>
      <item>SPM preprocessing 1 (estimate 2): 29s</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 6s</item>
      <item>Update segmentation 7s</item>
      <item>Update skull-stripping 5s</item>
      <item>Update probability maps 1s</item>
      <item>Update registration 23s</item>
      <item>41s</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>13s</item>
      <item>SANLM denoising after LAS (medium) 12s</item>
      <item>14s</item>
      <item>--- Update Ym and Ymi ---</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 1s</item>
      <item>10s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 9s</item>
      <item>AMAP peaks: [1.09 0.12,0.36 0.10,0.66 0.05]</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 | 0.2658 0.0000 0.2658 | 32.0000</item>
      <item>2 | 2.50 | 0.2487 0.0056 0.2543 | 29.4886</item>
      <item>3 | 2.50 | 0.2428 0.0093 0.2521 | 26.9772</item>
      <item>4 | 2.50 | 0.2395 0.0112 0.2507 | 24.6107</item>
      <item>5 | 2.50 | 0.2368 0.0126 0.2495 | 22.6548</item>
      <item>6 | 2.50 | 0.2345 0.0136 0.2481 | 20.6989</item>
      <item>7 | 2.50 | 0.2316 0.0147 0.2463 | 18.9688</item>
      <item>8 | 2.50 | 0.2291 0.0158 0.2449 | 17.4455</item>
      <item>9 | 2.50 | 0.2265 0.0167 0.2432 | 15.9223</item>
      <item>10 | 2.50 | 0.2236 0.0180 0.2416 | 14.6627</item>
      <item>11 | 2.50 | 0.2207 0.0191 0.2398 | 13.4764</item>
      <item>12 | 2.50 | 0.2177 0.0202 0.2378 | 12.3015</item>
      <item>13 | 2.50 | 0.2143 0.0217 0.2360 | 11.3776</item>
      <item>14 | 2.50 | 0.2111 0.0228 0.2339 | 10.4537</item>
      <item>15 | 2.25 | 0.2646 0.0244 0.2890 | 9.5920</item>
      <item>16 | 2.25 | 0.2469 0.0351 0.2820 | 8.8725</item>
      <item>17 | 2.25 | 0.2380 0.0396 0.2776 | 8.1530</item>
      <item>18 | 2.25 | 0.2309 0.0426 0.2736 | 7.5234</item>
      <item>19 | 2.25 | 0.2245 0.0450 0.2696 | 6.9630</item>
      <item>20 | 2.25 | 0.2185 0.0467 0.2652 | 6.4027</item>
      <item>21 | 2.25 | 0.2123 0.0489 0.2612 | 5.9447</item>
      <item>22 | 2.25 | 0.2064 0.0506 0.2570 | 5.5083</item>
      <item>23 | 2.25 | 0.2005 0.0519 0.2525 | 5.0803</item>
      <item>24 | 2.25 | 0.1932 0.0540 0.2472 | 4.7404</item>
      <item>25 | 2.25 | 0.1875 0.0551 0.2427 | 4.4005</item>
      <item>26 | 2.25 | 0.1817 0.0564 0.2381 | 4.0868</item>
      <item>27 | 2.25 | 0.1758 0.0580 0.2338 | 3.8221</item>
      <item>28 | 2.25 | 0.1702 0.0590 0.2292 | 3.5574</item>
      <item>29 | 2.00 | 0.1694 0.0603 0.2297 | 3.3283</item>
      <item>30 | 2.00 | 0.1621 0.0618 0.2239 | 3.1221</item>
      <item>31 | 2.00 | 0.1567 0.0623 0.2191 | 2.9160</item>
      <item>32 | 2.00 | 0.1502 0.0636 0.2138 | 2.7495</item>
      <item>33 | 2.00 | 0.1452 0.0643 0.2095 | 2.5890</item>
      <item>34 | 2.00 | 0.1401 0.0649 0.2050 | 2.4330</item>
      <item>35 | 2.00 | 0.1351 0.0660 0.2012 | 2.3080</item>
      <item>36 | 2.00 | 0.1304 0.0667 0.1971 | 2.1830</item>
      <item>37 | 2.00 | 0.1257 0.0674 0.1931 | 2.0688</item>
      <item>38 | 2.00 | 0.1212 0.0683 0.1895 | 1.9714</item>
      <item>39 | 2.00 | 0.1169 0.0688 0.1857 | 1.8740</item>
      <item>40 | 2.00 | 0.1117 0.0695 0.1811 | 1.7907</item>
      <item>41 | 2.00 | 0.1079 0.0699 0.1778 | 1.7148</item>
      <item>42 | 2.00 | 0.1043 0.0700 0.1743 | 1.6390</item>
      <item>43 | 1.75 | 0.1009 0.0708 0.1716 | 1.5785</item>
      <item>44 | 1.75 | 0.0967 0.0720 0.1686 | 1.5194</item>
      <item>45 | 1.75 | 0.0935 0.0723 0.1658 | 1.4626</item>
      <item>46 | 1.75 | 0.0907 0.0727 0.1634 | 1.4166</item>
      <item>47 | 1.75 | 0.0881 0.0727 0.1609 | 1.3706</item>
      <item>48 | 1.75 | 0.0856 0.0729 0.1585 | 1.3290</item>
      <item>49 | 1.75 | 0.0823 0.0731 0.1554 | 1.2932</item>
      <item>50 | 1.75 | 0.0803 0.0730 0.1533 | 1.2574</item>
      <item>51 | 1.75 | 0.0784 0.0730 0.1514 | 1.2271</item>
      <item>52 | 1.75 | 0.0765 0.0731 0.1496 | 1.1992</item>
      <item>53 | 1.75 | 0.0748 0.0730 0.1478 | 1.1713</item>
      <item>57 | 1.50 | 0.0762 0.0711 0.1473 | 1.0900</item>
      <item>Problem with Shooting (dets: 0.00294326 .. 3.19305)</item>
      <item>58 | 1.50 | 0.0701 0.0751 0.1452 | 1.0730</item>
      <item>59 | 1.50 | 0.0673 0.0764 0.1438 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 259s</item>
      <item>Prepare output 5s</item>
      <item>264s</item>
      <item>Jacobian determinant (RMS): 0.032 0.177 0.530 1.205 2.480 | 2.232162</item>
      <item>Template Matching: 0.266 0.265 0.169 0.224 0.202 | 0.202024</item>
      <item>Write result maps: 12s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 4s</item>
      <item>CSF distance: 1s</item>
      <item>PBT2x thickness: 5s</item>
      <item>12s</item>
      <item>Create initial surface 18s</item>
      <item>Topology correction: 503s</item>
      <item>Surface refinement: 123s</item>
      <item>Reduction of surface collisions with optimization: 94s</item>
      <item>Spherical mapping with areal smoothing 58s</item>
      <item>Spherical registration 269s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 4s</item>
      <item>CSF distance: 2s</item>
      <item>PBT2x thickness: 5s</item>
      <item>12s</item>
      <item>Create initial surface 18s</item>
      <item>Topology correction: 888s</item>
      <item>Surface refinement: 188s</item>
      <item>Reduction of surface collisions with optimization: 192s</item>
      <item>Spherical mapping with areal smoothing 153s</item>
      <item>Spherical registration 265s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 0.4933 0.4310 mm</item>
      <item>Surface intensity / position RMSE: 0.2478 / 0.9852</item>
      <item>Euler number / defect number / defect size: 10.0 / 2.5 / 78.25%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_12393/ds/sub-AL011/surf/lh.thickness.sub-AL011_ses-7_acq-RARE_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_12393/ds/sub-AL011/surf/rh.thickness.sub-AL011_ses-7_acq-RARE_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_12393/ds/sub-AL011/sub-AL011_ses-7_acq-RARE_T1w.nii</item>
      <item>Surface ROI estimation: 3179s</item>
      <item>Surface and thickness estimation takes: 3153s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 3s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 11s</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 4s</item>
      <item>ROI estimation of 'mori' atlas 7s</item>
      <item>ROI estimation of 'anatomy3' atlas 9s</item>
      <item>ROI estimation of 'julichbrain' atlas 12s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 5s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 9s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 20s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 30s</item>
      <item>Write results 31s</item>
      <item>125s</item>
      <item>Quality check: 1s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_12393/ds/sub-AL011/report/catreport_sub-AL011_ses-7_acq-RARE_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 58 minute(s) and 55 second(s).</item>
      <item>Image Quality Rating (IQR): 52.32% (E-)</item>
      <item>GM volume (GMV): 1.13% ( 3.77 / 335.08 ml)</item>
      <item>GM thickness (GMT): 0.51 0.48 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_12393/ds/sub-AL011/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_12393/ds/sub-AL011/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_12393/ds/sub-AL011/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>