ds003554_ReproVBM/sub-sc033/report/cat_sub-sc033_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <ll>-12.2505359649658</ll>
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      <Affine_rotation>[0.0477836564143878 0.0119473809713026 -0.0333491043178711]</Affine_rotation>
      <Affine_scaling>[1.10547900088223 0.999477549136644 1.13969788261887]</Affine_scaling>
      <Affine_shearing>[-0.00359453244111333 0.00150525387033199 0.0358058683444372]</Affine_shearing>
      <Affine0_translation>[-2.0081551646305 -24.6037037861539 -22.8132531494477]</Affine0_translation>
      <Affine0_rotation>[0.0477836564143878 0.0119473809713026 -0.0333491043178711]</Affine0_rotation>
      <Affine0_scaling>[1.10547900088223 0.999477549136644 1.13969788261887]</Affine0_scaling>
      <Affine0_shearing>[-0.00359453244111333 0.00150525387033199 0.0358058683444372]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_23543/ds/sub-sc033</path>
      <file>sub-sc033_T1w</file>
      <fname>/var/lib/condor/execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_23543/ds/sub-sc033/mri/msub-sc033_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_23543/ds/sub-sc033/mri/p0sub-sc033_T1w.nii</Fp0>
      <fnames>..43/ds/sub-sc033/sub-sc033_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>18</SurfaceEulerNumber>
      <SurfaceDefectArea>0.937548803795627</SurfaceDefectArea>
      <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0694435834884644</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0686726942658424</SurfacePositionRMSE>
      <res_vx_vol>[1.00000002497399 0.999999996645872 1.00000000022787]</res_vx_vol>
      <res_vx_voli>[1.00000002683223 0.999999996030489 0.99999999893217]</res_vx_voli>
      <res_RMS>1.00000000728258</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[0 36495.87109375 171197.890625 329258.3125]</tissue_mn>
      <tissue_mnr>[0 0.110842667520046 0.519950091838837 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.0125196883454919 0.0964059233665466 0.126094833016396 0.0948154479265213]</tissue_stdr>
      <contrast>111066.5234375</contrast>
      <contrastr>0.337323367595673</contrastr>
      <NCR>0.154352650046349</NCR>
      <ICR>0.285582333803177</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.00000004994798 1.99999999329174 2.00000000045575]</res_vx_vol>
      <res_RMS>2.00000001456516</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[1.89584374427795 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>3.02348279953003</contrastr>
      <NCR>2.54683685302734</NCR>
      <ICR>1.16811096668243</ICR>
      <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
      <SurfaceDefectArea>1.23438720094891</SurfaceDefectArea>
      <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.38887166976929</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.37345385551453</SurfacePositionRMSE>
      <IQR>2.37522679473888</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>20220711-184532</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>18</SurfaceEulerNumber>
         <SurfaceDefectArea>0.937548803795627</SurfaceDefectArea>
         <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0694435834884644</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0686726942658424</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>18</EC_abs>
      <defect_size>0.937548803795627</defect_size>
      <vol_abs_CGW>[205.080247606956 759.890040091132 460.20076689277 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.561972561267738</vol_abs_WMH>
      <vol_rel_WMH>0.000394319376230294</vol_rel_WMH>
      <surf_TSA>1986.02414413974</surf_TSA>
      <vol_TIV>1425.17105459086</vol_TIV>
      <vol_rel_CGW>[0.143898689877498 0.533192164998947 0.322909145123556 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.70300692538398 0.643046314373923]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.70350790023804 0.805484505661758 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.0788004671556 0.265835192867191 0.296937648555857;2.72363447170047 0.18575828033727 0.41764903603755;3.40115580514522 0.284910858653628 0.285413315406593]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.947168540528879 0.365942134277359 0.566041293485434;4.37775026920591 0.332929372909493 0.433958706514566]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.01508015703558</vol_TIV>
      <vol_rel_CGW>[0.5 7.42586503230867 3.64923033627075 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.03943193762303</vol_rel_WMH>
      <surf_TSA>8.62085025685729</surf_TSA>
      <SQR>6.07519369026438</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.709201783459596 2474 795 3684.99508050879 0.49043546529477]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0 0 0.204794749617577]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[903.340274590163 408.498259883567 319.33955205801 623.116892012137 1707.38917838883 9339.97465846569]</SPMvols0>
      <SPMvols1>[817.654217820684 384.791565249235 177.936470544773 846.338073347806 1358.05699430459 9087.25184119291]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[45371.16015625 193581.53125 335790.875]</T3th>
            <Tth>
               <T3th>[0 0 1096.703125 45371.16015625 193581.53125 335790.875 481000.75 714154.0625]</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>[0.020701976493001 0.0714291408658028 0.0789643079042435 0 0]</dtc>
         <ll>[0.0803044667574061 0 0.0803044667574061 0;0.190335185587907 0.00959899874866939 0.199934184336576 2046.96728515625;0.190335185587907 0.00959899874866939 0.199934184336576 2046.96728515625]</ll>
         <rmsdtc>[0.0438670888543129 0.0962721034884453 0.107347443699837]</rmsdtc>
         <rmsgdt>[0.0310346819460392 0.0460345074534416 0.05645552277565]</rmsgdt>
         <rmsdt>0.107347443699837</rmsdt>
         <dt>0.0789643079042435</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>[0.00992708466947079 0.0357244461774826 0.0498673282563686 0.0586083047091961 0.0655693411827087 0.0738477781414986]</dtc>
         <ll>[0.0812980114444161 0 0.0812980114444161 0;0.215318086080586 0.0121590621184371 0.227477148199023 6223.919921875;0.196140739281824 0.0153564694649561 0.21149720874678 11052.2353515625;0.176250896109701 0.0177036767218754 0.193954572831577 19089.37890625;0.159627695210744 0.0207620152993707 0.180389710510114 36320.09375;0.159627695210744 0.0207620152993707 0.180389710510114 36320.09375]</ll>
         <rmsdtc>[0.0114507023245096 0.0412513464689255 0.0618059895932674 0.0874534249305725 0.111586131155491 0.11849258095026]</rmsdtc>
         <rmsgdt>[0.00322762341238558 0.0129529992118478 0.0287194848060608 0.0491204038262367 0.0677889883518219 0.0734498426318169]</rmsgdt>
         <rmsdt>0.11849258095026</rmsdt>
         <dt>0.0738477781414986</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 24s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 7s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 6s</item>
      <item>Refine background 3s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 5s</item>
      <item>39s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 9s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 88s</item>
      <item>SPM preprocessing 1 (estimate 2): 49s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 17s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 40s</item>
      <item>Update probability maps 9s</item>
      <item>83s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 8s</item>
      <item>Fast Optimized Shooting registration 32s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.05) 14s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 23s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 13s</item>
      <item>77s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 13s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 25s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 5s</item>
      <item>68s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0813 0.0000 0.0813 | 32.0000</item>
      <item>2 | 2.50 | 0.0791 0.0010 0.0802 | 29.4886</item>
      <item>3 | 2.50 | 0.0785 0.0016 0.0800 | 26.9772</item>
      <item>4 | 2.50 | 0.0782 0.0018 0.0799 | 24.6107</item>
      <item>5 | 2.50 | 0.0779 0.0019 0.0798 | 22.6548</item>
      <item>6 | 2.50 | 0.0777 0.0020 0.0796 | 20.6989</item>
      <item>7 | 2.50 | 0.0774 0.0021 0.0795 | 18.9688</item>
      <item>8 | 2.50 | 0.0772 0.0022 0.0793 | 17.4455</item>
      <item>9 | 2.50 | 0.0769 0.0022 0.0791 | 15.9223</item>
      <item>10 | 2.50 | 0.0766 0.0023 0.0790 | 14.6627</item>
      <item>11 | 2.50 | 0.0764 0.0024 0.0788 | 13.4764</item>
      <item>12 | 2.50 | 0.0761 0.0025 0.0786 | 12.3015</item>
      <item>13 | 2.50 | 0.0758 0.0026 0.0784 | 11.3776</item>
      <item>14 | 2.50 | 0.0755 0.0026 0.0781 | 10.4537</item>
      <item>15 | 2.25 | 0.0744 0.0027 0.0771 | 9.5920</item>
      <item>16 | 2.25 | 0.0718 0.0041 0.0758 | 8.8725</item>
      <item>29 | 2.00 | 0.0731 0.0018 0.0749 | 3.3283</item>
      <item>30 | 2.00 | 0.0674 0.0042 0.0716 | 3.1221</item>
      <item>31 | 2.00 | 0.0654 0.0051 0.0705 | 2.9160</item>
      <item>43 | 1.75 | 0.0644 0.0029 0.0673 | 1.5785</item>
      <item>44 | 1.75 | 0.0602 0.0051 0.0653 | 1.5194</item>
      <item>45 | 1.75 | 0.0588 0.0059 0.0647 | 1.4626</item>
      <item>57 | 1.50 | 0.0573 0.0043 0.0616 | 1.0900</item>
      <item>58 | 1.50 | 0.0542 0.0063 0.0605 | 1.0730</item>
      <item>59 | 1.50 | 0.0532 0.0069 0.0601 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 173s</item>
      <item>Prepare output 10s</item>
      <item>183s</item>
      <item>Jacobian determinant (RMS): 0.011 0.041 0.062 0.087 0.112 | 0.118493</item>
      <item>Template Matching: 0.081 0.215 0.196 0.176 0.160 | 0.159628</item>
      <item>Write result maps: 26s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 45s</item>
      <item>94s</item>
      <item>Create initial surface 84s</item>
      <item>Topology correction: 91s</item>
      <item>Surface refinement: 81s</item>
      <item>Reduction of surface collisions with optimization: 77s</item>
      <item>Spherical mapping with areal smoothing 84s</item>
      <item>Spherical registration 298s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 45s</item>
      <item>98s</item>
      <item>Create initial surface 86s</item>
      <item>Topology correction: 97s</item>
      <item>Surface refinement: 89s</item>
      <item>Reduction of surface collisions with optimization: 73s</item>
      <item>Spherical mapping with areal smoothing 82s</item>
      <item>Spherical registration 315s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.7030 0.6430 mm</item>
      <item>Surface intensity / position RMSE: 0.0694 / 0.0687</item>
      <item>Euler number / defect number / defect size: 18.0 / 15.5 / 0.94%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_23543/ds/sub-sc033/surf/lh.thickness.sub-sc033_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_23543/ds/sub-sc033/surf/rh.thickness.sub-sc033_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_23543/ds/sub-sc033/sub-sc033_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1748s</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 9s</item>
      <item>ROI estimation of 'hammers' atlas 23s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 9s</item>
      <item>ROI estimation of 'aal3' atlas 14s</item>
      <item>ROI estimation of 'mori' atlas 20s</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 57s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s</item>
      <item>Write results 89s</item>
      <item>372s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_23543/ds/sub-sc033/report/catreport_sub-sc033_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 49 minute(s) and 23 second(s).</item>
      <item>Image Quality Rating (IQR): 81.25% (B-)</item>
      <item>GM volume (GMV): 53.32% (759.89 / 1425.17 ml)</item>
      <item>GM thickness (GMT): 2.70 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_23543/ds/sub-sc033/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>