ds003949_ReproVBM/sub-470/report/cat_sub-470_ses-20140807_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_rotation>[0.0715865681048292 -0.0458078165199174 -0.108533553089601]</Affine_rotation>
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      <Affine_shearing>[-0.0170519106484002 0.00557246447353281 0.00571885909806016]</Affine_shearing>
      <Affine0_translation>[-0.195057085249003 -14.654181756114 -23.9959944884417]</Affine0_translation>
      <Affine0_rotation>[0.0715865681048292 -0.0458078165199174 -0.108533553089601]</Affine0_rotation>
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      <Affine0_shearing>[-0.0170519106484002 0.00557246447353281 0.00571885909806016]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_4114/ds/sub-470</path>
      <file>sub-470_ses-20140807_T1w</file>
      <fname>/var/lib/condor/execute/dir_4114/ds/sub-470/sub-470_ses-20140807_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_4114/ds/sub-470/sub-470_ses-20140807_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_4114/ds/sub-470/mri/msub-470_ses-20140807_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_4114/ds/sub-470/mri/p0sub-470_ses-20140807_T1w.nii</Fp0>
      <fnames>..4114/ds/sub-470/sub-470_ses-20140807_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>
         <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>
         <inv_weighting>0</inv_weighting>
         <AMAPframing>1</AMAPframing>
      </extopts>
   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>278</SurfaceEulerNumber>
      <SurfaceDefectArea>7.66498955511618</SurfaceDefectArea>
      <SurfaceDefectNumber>151</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.102289468050003</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.140631347894669</SurfacePositionRMSE>
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      <res_vx_voli>[1.00000005215195 0.781249976392523 0.781250025056531]</res_vx_voli>
      <res_RMS>2.00920199511038</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[6.48449993133545 164.090316772461 331.9130859375 391.588470458984]</tissue_mn>
      <tissue_mnr>[0.0165594760328531 0.419037669897079 0.847606897354126 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.281857520341873 0.128819704055786 0.0652075633406639 0.0362758189439774]</tissue_stdr>
      <contrast>60.6802215576172</contrast>
      <contrastr>0.154959157109261</contrastr>
      <NCR>0.368270099163055</NCR>
      <ICR>0.22583532333374</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[6.59999237186949 1.56249998394833 1.56250004073349]</res_vx_vol>
      <res_RMS>4.01840399022075</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>5.75894594192505</contrastr>
      <NCR>5.61771583557129</NCR>
      <ICR>1.01992893218994</ICR>
      <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
      <SurfaceDefectArea>2.91624738877904</SurfaceDefectArea>
      <SurfaceDefectNumber>8.55</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>2.04578924179077</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>2.81262707710266</SurfacePositionRMSE>
      <IQR>5.19433455624043</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>
      <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>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>20220712-163032</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>278</SurfaceEulerNumber>
         <SurfaceDefectArea>7.66498955511618</SurfaceDefectArea>
         <SurfaceDefectNumber>151</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.102289468050003</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.140631347894669</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>278</EC_abs>
      <defect_size>7.66498955511618</defect_size>
      <vol_abs_CGW>[182.390172897938 567.465235820809 631.231122766434 0 0]</vol_abs_CGW>
      <vol_abs_WMH>9.6525309670737</vol_abs_WMH>
      <vol_rel_WMH>0.00698908485965296</vol_rel_WMH>
      <surf_TSA>1791.47256266713</surf_TSA>
      <vol_TIV>1381.08653148518</vol_TIV>
      <vol_rel_CGW>[0.132062813400838 0.410883187174791 0.457053999424371 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[1.92760632747328 0.581868200117613]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[1.9552698135376 0.549519175853557 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.36552912062295 0.215179589014233 0.276501944964702;1.94705779105212 0.159317769359128 0.41543005330644;2.49678558457325 0.209239018167044 0.308068001728858]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.661337190708682 0.18765507018129 0.595485175202156;3.24055731687748 0.292709776150525 0.404514824797844]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00851790026282</vol_TIV>
      <vol_rel_CGW>[0.5 5.22922390759323 6.05844108161586 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.6989084859653</vol_rel_WMH>
      <surf_TSA>8.5809990032738</surf_TSA>
      <SQR>5.12350748376839</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.258549518845229 1 1 5959.25663428728 0.47560217019926]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00862439814954996 0.00578710436820984 0.423316150903702]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[736.507021719504 665.628652580627 306.430678218284 816.764034325982 1897.34878075928 4333.94023291305]</SPMvols0>
      <SPMvols1>[544.499258688181 590.141884755365 197.952276411497 766.051624456349 1347.01558764527 4597.4900781629]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[208.909896850586 323.783905029297 370.195587158203]</T3th>
            <Tth>
               <T3th>[-136.452270507812 127.030944824219 6.12667417526245 208.909896850586 323.783905029297 370.195587158203 450.838439941406 1255.07653808594]</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>[0.0217864960432053 0.0804411023855209 0.0888258442282677 0 0]</dtc>
         <ll>[0.0856587935467156 0 0.0856587935467156 0;0.201138389926283 0.011051814524638 0.212190204450921 2356.77734375;0.201138389926283 0.011051814524638 0.212190204450921 2356.77734375]</ll>
         <rmsdtc>[0.0471744425594807 0.102760314941406 0.115306280553341]</rmsdtc>
         <rmsgdt>[0.0336503535509109 0.0529112592339516 0.0654221475124359]</rmsgdt>
         <rmsdt>0.115306280553341</rmsdt>
         <dt>0.0888258442282677</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>[0.0103734396398067 0.0549586713314056 0.0559803135693073 0.0677090361714363 0.0771274268627167 0.0894100740551949]</dtc>
         <ll>[0.0906915201590337 0 0.0906915201590337 0;0.224996962759463 0.017619639041514 0.242616601800977 9019.052734375;0.222176261997855 0.0183134478834937 0.240489709881348 13180.408203125;0.200920778801638 0.0205009764755553 0.221421755277194 22105.62890625;0.186174134808698 0.0243572507592807 0.210531385567979 42609.4296875;0.186174134808698 0.0243572507592807 0.210531385567979 42609.4296875]</ll>
         <rmsdtc>[0.0118793491274118 0.0441896542906761 0.0762609168887138 0.0996516719460487 0.135109841823578 0.147027999162674]</rmsdtc>
         <rmsgdt>[0.00371703435666859 0.0148697663098574 0.0358571596443653 0.0607161484658718 0.0888635963201523 0.0975231379270554]</rmsgdt>
         <rmsdt>0.147027999162674</rmsdt>
         <dt>0.0894100740551949</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_4114/ds/sub-470/sub-470_ses-20140807_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 16s</item>
      <item>Internal resampling (3.30x0.78x0.78mm &gt; 1.00x0.78x0.78mm): 1s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 7s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 12s</item>
      <item>Refine background 4s</item>
      <item>Final correction 10s</item>
      <item>Final scaling 9s</item>
      <item>59s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 14s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 102s</item>
      <item>SPM preprocessing 1 (estimate 2): 59s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 19s</item>
      <item>Update Segmentation 26s</item>
      <item>Update Skull-Stripping 51s</item>
      <item>Update probability maps 11s</item>
      <item>107s</item>
      <item>Global intensity correction: 19s</item>
      <item>SANLM denoising after intensity normalization (medium): 14s</item>
      <item>Fast Optimized Shooting registration 32s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.32) 20s</item>
      <item>Estimate local tissue thresholds (WM) 23s</item>
      <item>Estimate local tissue thresholds (GM) 29s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 39s</item>
      <item>123s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 9s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 19s</item>
      <item>Blood vessel detection 14s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.02) 55s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 3s</item>
      <item>Side alignment 6s</item>
      <item>Final corrections 5s</item>
      <item>115s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.97 0.06]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 6s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>15s</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 | 0.0907 0.0000 0.0907 | 32.0000</item>
      <item>2 | 2.50 | 0.0877 0.0013 0.0889 | 29.4886</item>
      <item>3 | 2.50 | 0.0868 0.0019 0.0887 | 26.9772</item>
      <item>4 | 2.50 | 0.0863 0.0022 0.0885 | 24.6107</item>
      <item>5 | 2.50 | 0.0860 0.0024 0.0884 | 22.6548</item>
      <item>6 | 2.50 | 0.0857 0.0025 0.0881 | 20.6989</item>
      <item>7 | 2.50 | 0.0854 0.0026 0.0879 | 18.9688</item>
      <item>8 | 2.50 | 0.0850 0.0027 0.0877 | 17.4455</item>
      <item>9 | 2.50 | 0.0847 0.0028 0.0875 | 15.9223</item>
      <item>10 | 2.50 | 0.0844 0.0029 0.0872 | 14.6627</item>
      <item>11 | 2.50 | 0.0840 0.0030 0.0870 | 13.4764</item>
      <item>12 | 2.50 | 0.0837 0.0030 0.0867 | 12.3015</item>
      <item>13 | 2.50 | 0.0833 0.0032 0.0864 | 11.3776</item>
      <item>14 | 2.50 | 0.0829 0.0032 0.0862 | 10.4537</item>
      <item>15 | 2.25 | 0.0845 0.0033 0.0878 | 9.5920</item>
      <item>16 | 2.25 | 0.0812 0.0049 0.0861 | 8.8725</item>
      <item>17 | 2.25 | 0.0799 0.0055 0.0854 | 8.1530</item>
      <item>18 | 2.25 | 0.0790 0.0058 0.0848 | 7.5234</item>
      <item>19 | 2.25 | 0.0783 0.0059 0.0843 | 6.9630</item>
      <item>20 | 2.25 | 0.0778 0.0059 0.0837 | 6.4027</item>
      <item>21 | 2.25 | 0.0772 0.0060 0.0832 | 5.9447</item>
      <item>22 | 2.25 | 0.0768 0.0060 0.0827 | 5.5083</item>
      <item>23 | 2.25 | 0.0763 0.0059 0.0822 | 5.0803</item>
      <item>24 | 2.25 | 0.0758 0.0060 0.0818 | 4.7404</item>
      <item>25 | 2.25 | 0.0754 0.0059 0.0813 | 4.4005</item>
      <item>26 | 2.25 | 0.0750 0.0059 0.0809 | 4.0868</item>
      <item>29 | 2.00 | 0.0767 0.0049 0.0817 | 3.3283</item>
      <item>30 | 2.00 | 0.0741 0.0061 0.0802 | 3.1221</item>
      <item>43 | 1.75 | 0.0733 0.0033 0.0767 | 1.5785</item>
      <item>44 | 1.75 | 0.0686 0.0059 0.0744 | 1.5194</item>
      <item>45 | 1.75 | 0.0670 0.0068 0.0738 | 1.4626</item>
      <item>57 | 1.50 | 0.0666 0.0050 0.0717 | 1.0900</item>
      <item>58 | 1.50 | 0.0632 0.0074 0.0705 | 1.0730</item>
      <item>59 | 1.50 | 0.0621 0.0081 0.0702 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 196s</item>
      <item>Prepare output 12s</item>
      <item>208s</item>
      <item>Jacobian determinant (RMS): 0.012 0.044 0.076 0.100 0.135 | 0.147028</item>
      <item>Template Matching: 0.091 0.225 0.222 0.201 0.186 | 0.186174</item>
      <item>Write result maps: 48s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 26s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 39s</item>
      <item>85s</item>
      <item>Create initial surface 81s</item>
      <item>Topology correction: 98s</item>
      <item>Surface refinement: 92s</item>
      <item>Reduction of surface collisions with optimization: 53s</item>
      <item>Spherical mapping with areal smoothing 81s</item>
      <item>Spherical registration 317s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 25s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 41s</item>
      <item>87s</item>
      <item>Create initial surface 83s</item>
      <item>Topology correction: 101s</item>
      <item>Surface refinement: 105s</item>
      <item>Reduction of surface collisions with optimization: 109s</item>
      <item>Spherical mapping with areal smoothing 75s</item>
      <item>Spherical registration 297s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 1.9280 0.5809 mm</item>
      <item>Surface intensity / position RMSE: 0.1023 / 0.1406</item>
      <item>Euler number / defect number / defect size: 278.0 / 151.0 / 7.66%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_4114/ds/sub-470/surf/lh.thickness.sub-470_ses-20140807_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_4114/ds/sub-470/surf/rh.thickness.sub-470_ses-20140807_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4114/ds/sub-470/sub-470_ses-20140807_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1757s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 9s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 34s</item>
      <item>ROI estimation of 'lpba40' atlas 10s</item>
      <item>ROI estimation of 'hammers' atlas 23s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 8s</item>
      <item>ROI estimation of 'aal3' atlas 14s</item>
      <item>ROI estimation of 'mori' atlas 19s</item>
      <item>ROI estimation of 'anatomy3' atlas 28s</item>
      <item>ROI estimation of 'julichbrain' atlas 36s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 86s</item>
      <item>Write results 87s</item>
      <item>369s</item>
      <item>Quality check: 4s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_4114/ds/sub-470/report/catreport_sub-470_ses-20140807_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 53 minute(s) and 15 second(s).</item>
      <item>Image Quality Rating (IQR): 53.06% (E-)</item>
      <item>GM volume (GMV): 41.09% (567.47 / 1381.09 ml)</item>
      <item>GM thickness (GMT): 1.93 0.58 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_4114/ds/sub-470/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_4114/ds/sub-470/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_4114/ds/sub-470/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>