ds003465_ReproVBM/sub-f5001ob/report/cat_sub-f5001ob_ses-wave1bas_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-6.59352731704712</ll>
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      <Affine_rotation>[0.459689570776267 -0.0250793945358759 -0.0612496714264071]</Affine_rotation>
      <Affine_scaling>[1.1102552578227 1.0343379194031 1.12086478163688]</Affine_scaling>
      <Affine_shearing>[0.00410521549991687 0.00419536479185294 -0.0391063765034041]</Affine_shearing>
      <Affine0_translation>[0.882571514417401 -3.47414802124656 44.1572599047596]</Affine0_translation>
      <Affine0_rotation>[0.459689570776267 -0.0250793945358759 -0.0612496714264071]</Affine0_rotation>
      <Affine0_scaling>[1.1102552578227 1.0343379194031 1.12086478163688]</Affine0_scaling>
      <Affine0_shearing>[0.00410521549991687 0.00419536479185294 -0.0391063765034041]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_15318/ds/sub-f5001ob</path>
      <file>sub-f5001ob_ses-wave1bas_T1w</file>
      <fname>/var/lib/condor/execute/dir_15318/ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_15318/ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_15318/ds/sub-f5001ob/mri/msub-f5001ob_ses-wave1bas_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_15318/ds/sub-f5001ob/mri/p0sub-f5001ob_ses-wave1bas_T1w.nii</Fp0>
      <fnames>../ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_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>
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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>
            <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>
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   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>14</SurfaceEulerNumber>
      <SurfaceDefectArea>0.579967039583145</SurfaceDefectArea>
      <SurfaceDefectNumber>12</SurfaceDefectNumber>
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      <SurfacePositionRMSE>0.066158153116703</SurfacePositionRMSE>
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      <res_RMS>0.800000629347425</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[22.3899993896484 287.873260498047 823.254577636719 1029.37170410156]</tissue_mn>
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      <tissue_weighting>T1</tissue_weighting>
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      <contrast>210.700103759766</contrast>
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      <NCR>0.115536265075207</NCR>
      <ICR>1.15176510810852</ICR>
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   <qualityratings>
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      <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>5.01301240921021</contrastr>
      <NCR>1.98961043357849</NCR>
      <ICR>3.31638169288635</ICR>
      <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
      <SurfaceDefectArea>1.14499175989579</SurfaceDefectArea>
      <SurfaceDefectNumber>1.6</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.31793200969696</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.32316303253174</SurfacePositionRMSE>
      <IQR>1.86161530799838</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>20220709-224605</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>14</SurfaceEulerNumber>
         <SurfaceDefectArea>0.579967039583145</SurfaceDefectArea>
         <SurfaceDefectNumber>12</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.065896600484848</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.066158153116703</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>14</EC_abs>
      <defect_size>0.579967039583145</defect_size>
      <vol_abs_CGW>[167.73761786728 602.692400910777 557.139965953598 0 0]</vol_abs_CGW>
      <vol_abs_WMH>2.17297532522059</vol_abs_WMH>
      <vol_rel_WMH>0.00163680660922733</vol_rel_WMH>
      <surf_TSA>1798.24033631012</surf_TSA>
      <vol_TIV>1327.56998473166</vol_TIV>
      <vol_rel_CGW>[0.126349359955728 0.453981641527246 0.419668998517027 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.48079374829963 0.626274033951893]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.50258183479309 0.791196638191587 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.82677407673847 0.275054965108575 0.263335268546183;2.48595506960068 0.178075662269761 0.432350150805001;3.11960788053194 0.273414024239297 0.304314580648816]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.76331805370242 0.310504129040366 0.57732818854938;4.11261946032026 0.370077524322591 0.42267181145062]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.12396954179805</vol_TIV>
      <vol_rel_CGW>[0.5 6.00326224007266 5.38701505957303 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.16368066092273</vol_rel_WMH>
      <surf_TSA>8.58438409912643</surf_TSA>
      <SQR>5.12942041968492</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.147906199919872 1 1 8711.50036753576 0.426519721603503]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0228851046413183 0.018102278932929 0.368009775876999]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[696.962239470909 534.592221488188 251.819674303432 983.926177190028 3174.02768005547 5125.69951299727]</SPMvols0>
      <SPMvols1>[604.326953749476 505.370294207815 160.396984151941 911.509124770367 2871.47851969224 5170.60299946426]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[371.154602050781 852.687683105469 1089.91052246094]</T3th>
            <Tth>
               <T3th>[0 2.82000732421875 21.6543426513672 371.154602050781 852.687683105469 1089.91052246094 1449.28845214844 3055.87719726562]</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>[0.024697070941329 0.0920482352375984 0.102006413042545 0 0]</dtc>
         <ll>[0.0852161115911208 0 0.0852161115911208 0;0.183734119868651 0.0126105259303428 0.196344645798993 2689.16943359375;0.183734119868651 0.0126105259303428 0.196344645798993 2689.16943359375]</ll>
         <rmsdtc>[0.0514902621507645 0.115552984178066 0.12705971300602]</rmsdtc>
         <rmsgdt>[0.0366240218281746 0.0520480684936047 0.0624798350036144]</rmsgdt>
         <rmsdt>0.12705971300602</rmsdt>
         <dt>0.102006413042545</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>[0.0120618129149079 0.0490657426416874 0.0660874620079994 0.0756154358386993 0.0819574669003487 0.093963161110878]</dtc>
         <ll>[0.0837761855651665 0 0.0837761855651665 0;0.203003632478632 0.020720012973138 0.22372364545177 10606.056640625;0.178554787800537 0.0206177088891112 0.199172496689648 14838.8125;0.157680746949749 0.0207458108465443 0.178426557796294 22369.626953125;0.14117395295575 0.0226027918428985 0.163776744798648 39540.26171875;0.14117395295575 0.0226027918428985 0.163776744798648 39540.26171875]</ll>
         <rmsdtc>[0.013993221335113 0.0525849685072899 0.0806971862912178 0.109253689646721 0.133843302726746 0.141636788845062]</rmsdtc>
         <rmsgdt>[0.00406933110207319 0.0164646729826927 0.0340538136661053 0.0550323650240898 0.0723099708557129 0.0777890235185623]</rmsgdt>
         <rmsdt>0.141636788845062</rmsdt>
         <dt>0.093963161110878</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 157s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 11s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 11s</item>
      <item>Refine background 5s</item>
      <item>Final correction 10s</item>
      <item>Final scaling 11s</item>
      <item>69s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 18s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 122s</item>
      <item>SPM preprocessing 1 (estimate 2): 44s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 26s</item>
      <item>Update Segmentation 31s</item>
      <item>Update Skull-Stripping 68s</item>
      <item>Update probability maps 15s</item>
      <item>141s</item>
      <item>Global intensity correction: 27s</item>
      <item>SANLM denoising after intensity normalization (medium): 35s</item>
      <item>Fast Optimized Shooting registration 41s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 7s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 24s</item>
      <item>Estimate local tissue thresholds (WM) 31s</item>
      <item>Estimate local tissue thresholds (GM) 40s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 69s</item>
      <item>182s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 13s</item>
      <item>Major structures 6s</item>
      <item>Ventricle detection 26s</item>
      <item>Blood vessel detection 17s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 58s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 3s</item>
      <item>Side alignment 7s</item>
      <item>Final corrections 7s</item>
      <item>137s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 50s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 8s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
      <item>19s</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 | 0.0838 0.0000 0.0838 | 32.0000</item>
      <item>2 | 2.50 | 0.0800 0.0015 0.0815 | 29.4886</item>
      <item>3 | 2.50 | 0.0788 0.0024 0.0812 | 26.9772</item>
      <item>4 | 2.50 | 0.0783 0.0027 0.0809 | 24.6107</item>
      <item>5 | 2.50 | 0.0778 0.0029 0.0807 | 22.6548</item>
      <item>6 | 2.50 | 0.0774 0.0031 0.0805 | 20.6989</item>
      <item>7 | 2.50 | 0.0770 0.0032 0.0802 | 18.9688</item>
      <item>8 | 2.50 | 0.0766 0.0034 0.0799 | 17.4455</item>
      <item>9 | 2.50 | 0.0761 0.0035 0.0796 | 15.9223</item>
      <item>10 | 2.50 | 0.0757 0.0036 0.0793 | 14.6627</item>
      <item>11 | 2.50 | 0.0752 0.0038 0.0790 | 13.4764</item>
      <item>12 | 2.50 | 0.0748 0.0038 0.0786 | 12.3015</item>
      <item>13 | 2.50 | 0.0743 0.0040 0.0783 | 11.3776</item>
      <item>14 | 2.50 | 0.0738 0.0041 0.0779 | 10.4537</item>
      <item>15 | 2.25 | 0.0732 0.0042 0.0774 | 9.5920</item>
      <item>16 | 2.25 | 0.0693 0.0062 0.0755 | 8.8725</item>
      <item>17 | 2.25 | 0.0677 0.0069 0.0746 | 8.1530</item>
      <item>29 | 2.00 | 0.0681 0.0032 0.0713 | 3.3283</item>
      <item>30 | 2.00 | 0.0617 0.0059 0.0675 | 3.1221</item>
      <item>31 | 2.00 | 0.0595 0.0069 0.0664 | 2.9160</item>
      <item>43 | 1.75 | 0.0581 0.0040 0.0621 | 1.5785</item>
      <item>44 | 1.75 | 0.0539 0.0062 0.0601 | 1.5194</item>
      <item>45 | 1.75 | 0.0526 0.0069 0.0595 | 1.4626</item>
      <item>57 | 1.50 | 0.0508 0.0051 0.0559 | 1.0900</item>
      <item>58 | 1.50 | 0.0480 0.0069 0.0549 | 1.0730</item>
      <item>59 | 1.50 | 0.0471 0.0075 0.0546 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 158s</item>
      <item>Prepare output 14s</item>
      <item>172s</item>
      <item>Jacobian determinant (RMS): 0.014 0.053 0.081 0.109 0.134 | 0.141637</item>
      <item>Template Matching: 0.084 0.203 0.179 0.158 0.141 | 0.141174</item>
      <item>Write result maps: 36s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 39s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 39s</item>
      <item>96s</item>
      <item>Create initial surface 75s</item>
      <item>Topology correction: 73s</item>
      <item>Surface refinement: 77s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 82s</item>
      <item>Spherical registration 319s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 33s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 40s</item>
      <item>92s</item>
      <item>Create initial surface 75s</item>
      <item>Topology correction: 83s</item>
      <item>Surface refinement: 82s</item>
      <item>Reduction of surface collisions with optimization: 53s</item>
      <item>Spherical mapping with areal smoothing 67s</item>
      <item>Spherical registration 273s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4808 0.6262 mm</item>
      <item>Surface intensity / position RMSE: 0.0659 / 0.0662</item>
      <item>Euler number / defect number / defect size: 14.0 / 12.0 / 0.58%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/surf/lh.thickness.sub-f5001ob_ses-wave1bas_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/surf/rh.thickness.sub-f5001ob_ses-wave1bas_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/sub-f5001ob_ses-wave1bas_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1607s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 13s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 50s</item>
      <item>ROI estimation of 'lpba40' atlas 15s</item>
      <item>ROI estimation of 'hammers' atlas 35s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 12s</item>
      <item>ROI estimation of 'aal3' atlas 20s</item>
      <item>ROI estimation of 'mori' atlas 30s</item>
      <item>ROI estimation of 'anatomy3' atlas 42s</item>
      <item>ROI estimation of 'julichbrain' atlas 58s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 40s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 94s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 130s</item>
      <item>Write results 131s</item>
      <item>566s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_15318/ds/sub-f5001ob/report/catreport_sub-f5001ob_ses-wave1bas_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 60 minute(s) and 10 second(s).</item>
      <item>Image Quality Rating (IQR): 86.38% (B)</item>
      <item>GM volume (GMV): 45.40% (602.69 / 1327.57 ml)</item>
      <item>GM thickness (GMT): 2.48 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_15318/ds/sub-f5001ob/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>