CORR_cat12.8.1/XHCUMS/sub-0026002/ses-3/report/cat_sub-0026002_ses-3_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   <filedata>
      <path>/var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3</path>
      <file>sub-0026002_ses-3_run-1_T1w</file>
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      <F>/var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/sub-0026002_ses-3_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/mri/msub-0026002_ses-3_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/mri/p0sub-0026002_ses-3_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0026002/ses-3/sub-0026002_ses-3_run-1_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
         </tpm>
         <ngaus>[1 1 2 3 4 2]</ngaus>
         <affreg>mni</affreg>
         <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
         <tol>0.0001</tol>
         <accstr>0.5</accstr>
         <biasstr>0.5</biasstr>
         <biasreg>0.001</biasreg>
         <biasfwhm>60</biasfwhm>
         <samp>3</samp>
         <redspmres>0</redspmres>
         <fwhm>1</fwhm>
         <biasacc>0</biasacc>
      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
         <BVCstr>0.5</BVCstr>
         <regstr>0.5</regstr>
         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
         <SLC>0</SLC>
         <mrf>1</mrf>
         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</nproc>
         <species>human</species>
         <APP>1070</APP>
         <setCOM>1</setCOM>
         <vox>1.5</vox>
         <bb>12</bb>
         <shootingsurf>Template_T1</shootingsurf>
         <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
         <darteltpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
         </darteltpm>
         <shootingtpm>
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         </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>
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         <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>
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            <tr>
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               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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               <td>[false]</td>
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            <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>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
               <td>0</td>
               <td>
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               <td>[false]</td>
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            <tr>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
               <td>1</td>
               <td>
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               <td>[false]</td>
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            <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>
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               <td>[false]</td>
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            <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>
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               <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>
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               <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>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
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               <td>
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               <td>[false]</td>
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            <tr>
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                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</item>
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               <td>[false]</td>
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         </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>
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            <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>
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            <tr>
               <td>Schaefer2018_100P_17N</td>
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               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_200P_17N</td>
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               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_400P_17N</td>
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               <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>
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         <LAB>
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            <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>
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         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
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               <regstr>0.5</regstr>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
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         <shootingtpms>
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      <ICR>1.67760229110718</ICR>
      <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
      <SurfaceDefectArea>1.20818572837586</SurfaceDefectArea>
      <SurfaceDefectNumber>1.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.26194369792938</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.32652449607849</SurfacePositionRMSE>
      <SIQR>2.19251509980289</SIQR>
      <IQR>2.23931887054481</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>2040</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20231031-022530</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>20</SurfaceEulerNumber>
         <SurfaceDefectArea>0.832742913503447</SurfaceDefectArea>
         <SurfaceDefectNumber>10</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0630971863865852</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0663262233138084</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>20</EC_abs>
      <defect_size>0.832742913503447</defect_size>
      <vol_abs_CGW>[260.236668294676 639.131416860333 522.460368124047 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.685745153997444</vol_abs_WMH>
      <vol_rel_WMH>0.000482298094693464</vol_rel_WMH>
      <surf_TSA>1897.29307258755</surf_TSA>
      <vol_TIV>1421.82845327906</vol_TIV>
      <vol_rel_CGW>[0.183029582573419 0.449513733802663 0.367456683623918 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.45450733777442 0.62735965225261]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.46148681640625 0.749961080199372 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.81238012141322 0.261205515009949 0.275559047424123;2.47259102895266 0.178905757383002 0.459346507067733;3.13375707561568 0.271674992521565 0.265094445508144]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.821324920828574 0.273452928134515 0.534315589353612;4.10448713515773 0.335704118976053 0.465684410646388]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.01134372118052</vol_TIV>
      <vol_rel_CGW>[1.13702554909158 5.92301964444437 4.44929388692382 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04822980946935</vol_rel_WMH>
      <surf_TSA>8.61291614307499</surf_TSA>
      <SQR>4.90246519870356</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3362865148 0.370629638147278]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00183162710163742 0.00129143171943724 0.320127844810486]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[784.30615027552 464.864630090782 473.759297483272 2026.49431830732 1294.80526644311 7281.81765695654]</SPMvols0>
      <SPMvols1>[656.882135955888 431.698537188281 292.908914098054 462.175935753732 1080.52140189828 8610.26040457591]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[155.744003295898 303.973388671875 396.935211181641]</T3th>
            <Tth>
               <T3th>[-6.62414979934692 -6.62415170669556 4.34219312667847 155.744003295898 303.973388671875 396.935211181641 517.530822753906 1202.91613769531]</T3th>
               <T3thx>[0 0.02 0.05 1 2 3 4 5]</T3thx>
            </Tth>
         </gintnorm>
      </tths>
      <reginitp>
         <opt>
            <nits>16</nits>
            <vxreg>1.5</vxreg>
            <rres>3</rres>
            <stepsize>0.5</stepsize>
            <resfac>[1 1 1 1 1]</resfac>
            <ll1th>0.015</ll1th>
            <ll3th>[0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03]</ll3th>
            <regstr>15</regstr>
         </opt>
         <fast>0</fast>
         <clsn>2</clsn>
         <regra>1</regra>
         <testfolder>Shooting_Template_0_GS_tr1.5_rr3.0-3.0_or1.5_regstr15.0</testfolder>
         <dtc>[0.0208614598959684 0.0761646926403046 0.0839199051260948 0 0]</dtc>
         <ll>[0.0847992700498168 0 0.0847992700498168 0;0.200815390853607 0.0106779993796835 0.211493390233291 2277.06201171875;0.200815390853607 0.0106779993796835 0.211493390233291 2277.06201171875]</ll>
         <rmsdtc>[0.0445991419255733 0.0986491963267326 0.109870590269566]</rmsdtc>
         <rmsgdt>[0.0318486243486404 0.0469847619533539 0.0581810101866722]</rmsgdt>
         <rmsdt>0.109870590269566</rmsdt>
         <dt>0.0839199051260948</dt>
      </reginitp>
      <reg>
         <opt>
            <nits>64</nits>
            <vxreg>1.5</vxreg>
            <rres>1.5</rres>
            <stepsize>0.25</stepsize>
            <resfac>[1.66666666666667 1.5 1.33333333333333 1.16666666666667 1]</resfac>
            <ll1th>0.051</ll1th>
            <ll3th>[0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501]</ll3th>
            <regstr>0.5</regstr>
         </opt>
         <fast>0</fast>
         <clsn>2</clsn>
         <regra>1</regra>
         <testfolder>Shooting_Template_0_GS_tr1.5_rr2.5-1.5_or1.5_regstr0.5</testfolder>
         <dtc>[0.00920608080923557 0.0330791883170605 0.0464895740151405 0.0540677942335606 0.0599054843187332 0.0665802583098412]</dtc>
         <ll>[0.0832847092237212 0 0.0832847092237212 0;0.221582997557998 0.0121497262286325 0.23373272378663 6219.14111328125;0.200565317272742 0.0160539218400034 0.216619239112746 11554.2001953125;0.179254109816447 0.0186168728617408 0.197870982678188 20074.052734375;0.161926795220862 0.0213870075286406 0.183313802749502 37413.42578125;0.161926795220862 0.0213870075286406 0.183313802749502 37413.42578125]</ll>
         <rmsdtc>[0.0106111848726869 0.0376101434230804 0.0554595366120338 0.0782064348459244 0.0997830480337143 0.106659501791]</rmsdtc>
         <rmsgdt>[0.00317532755434513 0.0122011601924896 0.0266162324696779 0.0462168790400028 0.0629337653517723 0.0680583789944649]</rmsgdt>
         <rmsdt>0.106659501791</rmsdt>
         <dt>0.0665802583098412</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0026002/ses-3/sub-0026002_ses-3_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 51s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 7s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 7s</item>
      <item>Refine background 4s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 5s</item>
      <item>41s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 12s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 76s</item>
      <item>SPM preprocessing 1 (estimate 2): 66s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 18s</item>
      <item>Update Segmentation 20s</item>
      <item>Update Skull-Stripping 42s</item>
      <item>Update probability maps 9s</item>
      <item>89s</item>
      <item>Global intensity correction: 18s</item>
      <item>SANLM denoising after intensity normalization (medium): 24s</item>
      <item>Fast Optimized Shooting registration 40s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.14) 14s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 26s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 42s</item>
      <item>111s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 9s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 12s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.11) 24s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 5s</item>
      <item>68s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0833 0.0000 0.0833 | 32.0000</item>
      <item>2 | 2.50 | 0.0812 0.0011 0.0822 | 29.4886</item>
      <item>3 | 2.50 | 0.0805 0.0016 0.0821 | 26.9772</item>
      <item>4 | 2.50 | 0.0802 0.0018 0.0820 | 24.6107</item>
      <item>5 | 2.50 | 0.0799 0.0019 0.0819 | 22.6548</item>
      <item>6 | 2.50 | 0.0797 0.0020 0.0817 | 20.6989</item>
      <item>7 | 2.50 | 0.0794 0.0021 0.0816 | 18.9688</item>
      <item>8 | 2.50 | 0.0792 0.0022 0.0814 | 17.4455</item>
      <item>9 | 2.50 | 0.0789 0.0023 0.0812 | 15.9223</item>
      <item>10 | 2.50 | 0.0787 0.0024 0.0810 | 14.6627</item>
      <item>11 | 2.50 | 0.0784 0.0024 0.0809 | 13.4764</item>
      <item>12 | 2.50 | 0.0781 0.0025 0.0806 | 12.3015</item>
      <item>13 | 2.50 | 0.0779 0.0026 0.0805 | 11.3776</item>
      <item>14 | 2.50 | 0.0776 0.0027 0.0802 | 10.4537</item>
      <item>15 | 2.25 | 0.0765 0.0027 0.0793 | 9.5920</item>
      <item>16 | 2.25 | 0.0739 0.0040 0.0779 | 8.8725</item>
      <item>29 | 2.00 | 0.0754 0.0018 0.0772 | 3.3283</item>
      <item>30 | 2.00 | 0.0690 0.0043 0.0733 | 3.1221</item>
      <item>31 | 2.00 | 0.0669 0.0054 0.0722 | 2.9160</item>
      <item>43 | 1.75 | 0.0656 0.0031 0.0687 | 1.5785</item>
      <item>44 | 1.75 | 0.0612 0.0054 0.0666 | 1.5194</item>
      <item>45 | 1.75 | 0.0598 0.0062 0.0660 | 1.4626</item>
      <item>57 | 1.50 | 0.0581 0.0045 0.0626 | 1.0900</item>
      <item>58 | 1.50 | 0.0550 0.0065 0.0615 | 1.0730</item>
      <item>59 | 1.50 | 0.0540 0.0071 0.0611 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 207s</item>
      <item>Prepare output 10s</item>
      <item>218s</item>
      <item>Jacobian determinant (RMS): 0.011 0.038 0.055 0.078 0.100 | 0.106660</item>
      <item>Template Matching: 0.083 0.222 0.201 0.179 0.162 | 0.161927</item>
      <item>Write result maps: 46s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 56s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 48s</item>
      <item>127s</item>
      <item>Create initial surface 80s</item>
      <item>Topology correction: 90s</item>
      <item>Surface refinement: 98s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 82s</item>
      <item>Spherical registration 250s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 37s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 48s</item>
      <item>107s</item>
      <item>Create initial surface 78s</item>
      <item>Topology correction: 89s</item>
      <item>Surface refinement: 79s</item>
      <item>Reduction of surface collisions with optimization: 58s</item>
      <item>Spherical mapping with areal smoothing 82s</item>
      <item>Spherical registration 244s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4545 0.6273 mm</item>
      <item>Surface intensity / position RMSE: 0.0631 / 0.0663</item>
      <item>Euler number / defect number / defect size: 20.0 / 10.0 / 0.83%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/surf/lh.thickness.sub-0026002_ses-3_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/surf/rh.thickness.sub-0026002_ses-3_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/sub-0026002_ses-3_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1620s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 14s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 52s</item>
      <item>ROI estimation of 'lpba40' atlas 15s</item>
      <item>ROI estimation of 'hammers' atlas 37s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 13s</item>
      <item>ROI estimation of 'aal3' atlas 22s</item>
      <item>ROI estimation of 'mori' atlas 32s</item>
      <item>ROI estimation of 'anatomy3' atlas 46s</item>
      <item>ROI estimation of 'julichbrain' atlas 61s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 101s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 152s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s</item>
      <item>Write results 12s</item>
      <item>613s</item>
      <item>Quality check: 13s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/report/catreport_sub-0026002_ses-3_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 55 minute(s) and 10 second(s).</item>
      <item>Image Quality Rating (IQR): 82.61% (B-)</item>
      <item>GM volume (GMV): 44.95% (639.13 / 1421.83 ml)</item>
      <item>GM thickness (GMT): 2.45 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2737911/ds/XHCUMS/sub-0026002/ses-3/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>