CORR_cat12.8.1/SWU_4/sub-0025849/ses-1/report/cat_sub-0025849_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine0_shearing>[-0.00623670485248684 0.0157150732776998 0.0176478864493421]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1</path>
      <file>sub-0025849_ses-1_run-1_T1w</file>
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      <F>/var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/sub-0025849_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/mri/msub-0025849_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/mri/p0sub-0025849_ses-1_run-1_T1w.nii</Fp0>
      <fnames>..s/SWU_4/sub-0025849/ses-1/sub-0025849_ses-1_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>
            <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>
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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>
               </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>
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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>
                  <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/aal3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</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/mori.nii</td>
               <td>1</td>
               <td>
                  <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/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>
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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>
               <td>1</td>
               <td>
                  <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/Schaefer2018_600Parcels_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>/var/lib/condor/execute/dir_3038396/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</item>
               </td>
               <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>
            </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>
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         </satlas>
         <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>
         </LAB>
         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
         <regmethod>
            <shooting>
               <shootingtpm>
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               <regstr>0.5</regstr>
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         <restypes>
            <optimal>[1 0.3]</optimal>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
         <darteltpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
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         </darteltpms>
         <shootingtpms>
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            <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>
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         </shootingtpms>
         <templates>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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         <AMAPframing>1</AMAPframing>
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      <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
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      <res_vx_vol>[0.999999989767493 0.999999989767493 1]</res_vx_vol>
      <res_vx_voli>[0.999999989588703 0.999999989588703 1]</res_vx_voli>
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      <NCR>0.140747398138046</NCR>
      <ICR>0.290597975254059</ICR>
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      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
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      <NCR>2.35152745246887</NCR>
      <ICR>1.18055057525635</ICR>
      <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
      <SurfaceDefectArea>1.05051800381351</SurfaceDefectArea>
      <SurfaceDefectNumber>1.475</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.28361999988556</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.25269186496735</SurfacePositionRMSE>
      <SIQR>2.34390603790654</SIQR>
      <IQR>2.22258880475759</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>20231031-004628</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>12</SurfaceEulerNumber>
         <SurfaceDefectArea>0.20207201525404</SurfaceDefectArea>
         <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.064180999994278</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0626345947384834</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>12</EC_abs>
      <defect_size>0.20207201525404</defect_size>
      <vol_abs_CGW>[203.181187926103 613.237912720992 423.171873541405 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.0631882339783747</vol_abs_WMH>
      <vol_rel_WMH>5.09750678200452e-05</vol_rel_WMH>
      <surf_TSA>1712.47277775019</surf_TSA>
      <vol_TIV>1239.5909741885</vol_TIV>
      <vol_rel_CGW>[0.163909863944529 0.49470988857631 0.341380247479161 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.60393900983899 0.640745465349454]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.59384083747864 0.754871129524739 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.0038772290979 0.243034757597864 0.320526679927355;2.6339049184721 0.182368786789 0.400321427541872;3.31038393540116 0.270683514292871 0.279151892530773]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.945704099118864 0.360327870748506 0.54333441804968;4.232273586912 0.332904511180039 0.45666558195032]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.58904272233526</vol_TIV>
      <vol_rel_CGW>[0.79363979785433 6.73473219425843 3.98096708834701 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.005097506782</vol_rel_WMH>
      <surf_TSA>8.51722989652246</surf_TSA>
      <SQR>5.51762628805679</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3357639497 0.379784990616419]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00140222022309899 0.00120210112072527 0.0166112277656794]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[735.242792533475 380.560368546334 324.447146185345 529.520459562246 1028.40509231143 8978.97624048541]</SPMvols0>
      <SPMvols1>[652.167009949603 357.081302368563 196.088701799278 354.560259283802 740.257992429046 9234.20166262193]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[154.419998168945 279.907196044922 371.598907470703]</T3th>
            <Tth>
               <T3th>[-5.39416980743408 64.3611526489258 2.38516187667847 154.419998168945 279.907196044922 371.598907470703 480.188354492188 970.494140625]</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>[0.0230461359024048 0.078032098710537 0.0859740078449249 0 0]</dtc>
         <ll>[0.0828422738724396 0 0.0828422738724396 0;0.188689361242544 0.0102813635982958 0.19897072484084 2192.48022460938;0.188689361242544 0.0102813635982958 0.19897072484084 2192.48022460938]</ll>
         <rmsdtc>[0.0478468239307404 0.101324923336506 0.111251719295979]</rmsdtc>
         <rmsgdt>[0.034100279211998 0.0442710444331169 0.0542168766260147]</rmsgdt>
         <rmsdt>0.111251719295979</rmsdt>
         <dt>0.0859740078449249</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>[0.0110351340845227 0.0404046773910522 0.0555427484214306 0.0633391141891479 0.0693910121917725 0.0782639384269714]</dtc>
         <ll>[0.0842249805079082 0 0.0842249805079082 0;0.215331547619048 0.0151240499084249 0.230455597527473 7741.623046875;0.19260273553866 0.0172383786413871 0.209841114180047 12406.66796875;0.172344819999036 0.0185949356354426 0.190939755634478 20050.3984375;0.156095157038059 0.020940299963758 0.177035457001817 36631.9765625;0.156095157038059 0.020940299963758 0.177035457001817 36631.9765625]</ll>
         <rmsdtc>[0.0126774972304702 0.0457616858184338 0.0671830847859383 0.0920777320861816 0.115204453468323 0.122220665216446]</rmsdtc>
         <rmsgdt>[0.00352227524854243 0.0134685877710581 0.0288372337818146 0.0489690490067005 0.0664687976241112 0.071971207857132]</rmsgdt>
         <rmsdt>0.122220665216446</rmsdt>
         <dt>0.0782639384269714</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025849/ses-1/sub-0025849_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 32s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 4s</item>
      <item>Initial correction 4s</item>
      <item>Refine background 2s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 3s</item>
      <item>27s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 6s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 8s</item>
      <item>Use initial fine affine registration. 46s</item>
      <item>SPM preprocessing 1 (estimate 2): 38s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 13s</item>
      <item>Update Segmentation 13s</item>
      <item>Update Skull-Stripping 30s</item>
      <item>Update probability maps 7s</item>
      <item>62s</item>
      <item>Global intensity correction: 12s</item>
      <item>SANLM denoising after intensity normalization (medium): 16s</item>
      <item>Fast Optimized Shooting registration 26s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 2s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.12) 9s</item>
      <item>Estimate local tissue thresholds (WM) 14s</item>
      <item>Estimate local tissue thresholds (GM) 19s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 31s</item>
      <item>80s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 2s</item>
      <item>Ventricle detection 8s</item>
      <item>Blood vessel detection 6s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 13s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 2s</item>
      <item>Final corrections 4s</item>
      <item>42s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s</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) 3s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>8s</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 | 0.0842 0.0000 0.0842 | 32.0000</item>
      <item>2 | 2.50 | 0.0812 0.0013 0.0825 | 29.4886</item>
      <item>3 | 2.50 | 0.0802 0.0020 0.0823 | 26.9772</item>
      <item>4 | 2.50 | 0.0798 0.0023 0.0821 | 24.6107</item>
      <item>5 | 2.50 | 0.0794 0.0025 0.0819 | 22.6548</item>
      <item>6 | 2.50 | 0.0791 0.0026 0.0817 | 20.6989</item>
      <item>7 | 2.50 | 0.0788 0.0027 0.0815 | 18.9688</item>
      <item>8 | 2.50 | 0.0784 0.0028 0.0812 | 17.4455</item>
      <item>9 | 2.50 | 0.0781 0.0029 0.0810 | 15.9223</item>
      <item>10 | 2.50 | 0.0777 0.0030 0.0807 | 14.6627</item>
      <item>11 | 2.50 | 0.0773 0.0031 0.0804 | 13.4764</item>
      <item>12 | 2.50 | 0.0769 0.0032 0.0801 | 12.3015</item>
      <item>13 | 2.50 | 0.0765 0.0033 0.0799 | 11.3776</item>
      <item>14 | 2.50 | 0.0762 0.0034 0.0795 | 10.4537</item>
      <item>15 | 2.25 | 0.0751 0.0035 0.0785 | 9.5920</item>
      <item>16 | 2.25 | 0.0718 0.0050 0.0768 | 8.8725</item>
      <item>29 | 2.00 | 0.0724 0.0023 0.0747 | 3.3283</item>
      <item>30 | 2.00 | 0.0663 0.0048 0.0710 | 3.1221</item>
      <item>31 | 2.00 | 0.0642 0.0057 0.0699 | 2.9160</item>
      <item>43 | 1.75 | 0.0629 0.0033 0.0663 | 1.5785</item>
      <item>44 | 1.75 | 0.0588 0.0055 0.0643 | 1.5194</item>
      <item>45 | 1.75 | 0.0574 0.0062 0.0636 | 1.4626</item>
      <item>57 | 1.50 | 0.0558 0.0046 0.0604 | 1.0900</item>
      <item>58 | 1.50 | 0.0530 0.0064 0.0594 | 1.0730</item>
      <item>59 | 1.50 | 0.0520 0.0070 0.0590 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 145s</item>
      <item>Prepare output 7s</item>
      <item>152s</item>
      <item>Jacobian determinant (RMS): 0.013 0.046 0.067 0.092 0.115 | 0.122221</item>
      <item>Template Matching: 0.084 0.215 0.193 0.172 0.156 | 0.156095</item>
      <item>Write result maps: 34s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 19s</item>
      <item>CSF distance: 10s</item>
      <item>PBT2x thickness: 29s</item>
      <item>61s</item>
      <item>Create initial surface 54s</item>
      <item>Topology correction: 54s</item>
      <item>Surface refinement: 51s</item>
      <item>Reduction of surface collisions with optimization: 42s</item>
      <item>Spherical mapping with areal smoothing 62s</item>
      <item>Spherical registration 218s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 16s</item>
      <item>CSF distance: 9s</item>
      <item>PBT2x thickness: 28s</item>
      <item>58s</item>
      <item>Create initial surface 51s</item>
      <item>Topology correction: 53s</item>
      <item>Surface refinement: 47s</item>
      <item>Reduction of surface collisions with optimization: 40s</item>
      <item>Spherical mapping with areal smoothing 55s</item>
      <item>Spherical registration 218s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.6039 0.6405 mm</item>
      <item>Surface intensity / position RMSE: 0.0642 / 0.0626</item>
      <item>Euler number / defect number / defect size: 12.0 / 9.5 / 0.20%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/surf/lh.thickness.sub-0025849_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/surf/rh.thickness.sub-0025849_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/sub-0025849_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1133s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 28s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 12s</item>
      <item>ROI estimation of 'mori' atlas 17s</item>
      <item>ROI estimation of 'anatomy3' atlas 29s</item>
      <item>ROI estimation of 'julichbrain' atlas 35s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 56s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
      <item>Write results 8s</item>
      <item>356s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/report/catreport_sub-0025849_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 36 minute(s) and 24 second(s).</item>
      <item>Image Quality Rating (IQR): 82.77% (B-)</item>
      <item>GM volume (GMV): 49.47% (613.24 / 1239.59 ml)</item>
      <item>GM thickness (GMT): 2.60 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3038396/ds/SWU_4/sub-0025849/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>