ds003146_ReproVBM/sub-429/report/cat_sub-429_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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      <Affine_rotation>[0.186772899306084 0.00172996341935352 -0.0285396389855132]</Affine_rotation>
      <Affine_scaling>[1.014037180175 0.984756953431636 1.14505321043318]</Affine_scaling>
      <Affine_shearing>[0.0124475952335257 0.00313148158035808 0.0335026202031415]</Affine_shearing>
      <Affine0_translation>[3.45821828457093 -11.5587179812101 48.883326219629]</Affine0_translation>
      <Affine0_rotation>[0.186772899306084 0.00172996341935352 -0.0285396389855132]</Affine0_rotation>
      <Affine0_scaling>[1.014037180175 0.984756953431636 1.14505321043318]</Affine0_scaling>
      <Affine0_shearing>[0.0124475952335257 0.00313148158035808 0.0335026202031415]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_13301/ds/sub-429</path>
      <file>sub-429_T1w</file>
      <fname>/var/lib/condor/execute/dir_13301/ds/sub-429/sub-429_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_13301/ds/sub-429/sub-429_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_13301/ds/sub-429/mri/msub-429_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_13301/ds/sub-429/mri/p0sub-429_T1w.nii</Fp0>
      <fnames>..3301/ds/sub-429/sub-429_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>64</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>24</SurfaceEulerNumber>
      <SurfaceDefectArea>0.689518241608231</SurfaceDefectArea>
      <SurfaceDefectNumber>14</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0670641288161278</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0673805475234985</SurfacePositionRMSE>
      <res_vx_vol>[1.09999847412109 1 1]</res_vx_vol>
      <res_vx_voli>[1.09999847412109 1 1]</res_vx_voli>
      <res_RMS>1.03440750240073</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[86.6009979248047 371.487274169922 1008.4765625 1466.58813476562]</tissue_mn>
      <tissue_mnr>[0.0590492933988571 0.253300338983536 0.687634468078613 0.999999940395355]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[66.990783451068 186.089746661039 181.828989842316 114.720950527529]</tissue_std>
      <tissue_stdr>[0.0485444962978363 0.134848892688751 0.131761357188225 0.0831318944692612]</tissue_stdr>
      <contrast>486.860321044922</contrast>
      <contrastr>0.331967979669571</contrastr>
      <NCR>0.13181272149086</NCR>
      <ICR>0.892478764057159</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.19999694824219 2 2]</res_vx_vol>
      <res_RMS>2.06881500480146</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>3.10381364822388</contrastr>
      <NCR>2.22326612472534</NCR>
      <ICR>2.67331027984619</ICR>
      <SurfaceEulerNumber>2.12244897959184</SurfaceEulerNumber>
      <SurfaceDefectArea>1.17237956040206</SurfaceDefectArea>
      <SurfaceDefectNumber>1.7</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.34128260612488</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.34761095046997</SurfacePositionRMSE>
      <IQR>2.15564662207976</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>20220711-130258</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>24</SurfaceEulerNumber>
         <SurfaceDefectArea>0.689518241608231</SurfaceDefectArea>
         <SurfaceDefectNumber>14</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0670641288161278</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0673805475234985</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>24</EC_abs>
      <defect_size>0.689518241608231</defect_size>
      <vol_abs_CGW>[342.924058425544 707.204811539564 574.645535421095 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.05323775467218</vol_abs_WMH>
      <vol_rel_WMH>0.000648236303563528</vol_rel_WMH>
      <surf_TSA>2028.19879396409</surf_TSA>
      <vol_TIV>1624.7744053862</vol_TIV>
      <vol_rel_CGW>[0.211059490652201 0.435263387455604 0.353677121892195 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.4992886706384 0.642535598103904]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.50561189651489 0.805644290656366 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.81179234043513 0.295925115125388 0.25670016239118;2.49481007431738 0.186236932282684 0.455073808622605;3.17311311798863 0.285487496497552 0.288226028986215]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.801058502090074 0.234050396124737 0.568045245669848;4.21387418948492 0.383086216735453 0.431954754330152]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.11350737931878</vol_TIV>
      <vol_rel_CGW>[1.64043625452947 5.66708669999289 4.20181612593741 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06482363035635</vol_rel_WMH>
      <surf_TSA>8.6223339034706</surf_TSA>
      <SQR>4.68528067472985</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.221329758806926 40 6 9205.96752980804 0.705521970106329]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.076114721596241 0.0702756196260452 0.249399915337563]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[903.693937016027 546.074929955187 528.881108315651 837.240622138887 1576.09713918409 8422.38731793922]</SPMvols0>
      <SPMvols1>[769.541880361909 507.608043707245 305.108953626416 817.25283888484 986.63012942086 8437.57938392415]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[414.248687744141 1046.55712890625 1466.67578125]</T3th>
            <Tth>
               <T3th>[0 0 97.0620422363281 414.248687744141 1046.55712890625 1466.67578125 1992.88940429688 4817.2490234375]</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>[0.0205171220004559 0.0715548768639565 0.0785671398043633 0 0]</dtc>
         <ll>[0.0837944186463648 0 0.0837944186463648 0;0.198435422753086 0.0104435718073851 0.208878994560471 2227.07080078125;0.198435422753086 0.0104435718073851 0.208878994560471 2227.07080078125]</ll>
         <rmsdtc>[0.045157253742218 0.0931475386023521 0.104613661766052]</rmsdtc>
         <rmsgdt>[0.0323011465370655 0.0477286651730537 0.0589578375220299]</rmsgdt>
         <rmsdt>0.104613661766052</rmsdt>
         <dt>0.0785671398043633</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>[0.0100781414657831 0.0406609959900379 0.0541589371860027 0.0642980262637138 0.0717490017414093 0.0817238241434097]</dtc>
         <ll>[0.0874064673900248 0 0.0874064673900248 0;0.224864010989011 0.017379014041514 0.242243025030525 8895.8828125;0.207456354937808 0.0193159457793534 0.226772300717162 13901.91796875;0.185470740453244 0.021525478091335 0.206996218544579 23210.3203125;0.167925888171227 0.0247723997815192 0.192698287952746 43335.671875;0.167925888171227 0.0247723997815192 0.192698287952746 43335.671875]</ll>
         <rmsdtc>[0.011514650657773 0.0420878492295742 0.0674352869391441 0.0961417034268379 0.124529547989368 0.133084148168564]</rmsdtc>
         <rmsgdt>[0.00357792316935956 0.0147709790617228 0.0323408506810665 0.0551863349974155 0.075991578400135 0.0821364969015121]</rmsgdt>
         <rmsdt>0.133084148168564</rmsdt>
         <dt>0.0817238241434097</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_13301/ds/sub-429/sub-429_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 93s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 13s</item>
      <item>Initial correction 11s</item>
      <item>Refine background 5s</item>
      <item>Final correction 9s</item>
      <item>Final scaling 11s</item>
      <item>65s</item>
      <item>Correct center-of-mass 15s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 105s</item>
      <item>SPM preprocessing 1 (estimate 2): 78s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 21s</item>
      <item>Update Segmentation 24s</item>
      <item>Update Skull-Stripping 50s</item>
      <item>Update probability maps 11s</item>
      <item>106s</item>
      <item>Global intensity correction: 19s</item>
      <item>SANLM denoising after intensity normalization (medium): 9s</item>
      <item>Fast Optimized Shooting registration 44s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 19s</item>
      <item>Estimate local tissue thresholds (WM) 28s</item>
      <item>Estimate local tissue thresholds (GM) 38s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 36s</item>
      <item>133s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 9s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 16s</item>
      <item>Blood vessel detection 13s</item>
      <item>WMH detection (WMHCstr=0.48 &gt; WMHCstr'=0.09) 33s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 6s</item>
      <item>86s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.24):</item>
      <item>Level 1 cleanup (ROI estimation) 5s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</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 | 0.0874 0.0000 0.0874 | 32.0000</item>
      <item>2 | 2.50 | 0.0846 0.0012 0.0858 | 29.4886</item>
      <item>3 | 2.50 | 0.0837 0.0019 0.0856 | 26.9772</item>
      <item>4 | 2.50 | 0.0833 0.0021 0.0854 | 24.6107</item>
      <item>5 | 2.50 | 0.0829 0.0023 0.0852 | 22.6548</item>
      <item>6 | 2.50 | 0.0826 0.0024 0.0850 | 20.6989</item>
      <item>7 | 2.50 | 0.0823 0.0025 0.0848 | 18.9688</item>
      <item>8 | 2.50 | 0.0820 0.0026 0.0846 | 17.4455</item>
      <item>9 | 2.50 | 0.0816 0.0027 0.0844 | 15.9223</item>
      <item>10 | 2.50 | 0.0813 0.0029 0.0841 | 14.6627</item>
      <item>11 | 2.50 | 0.0809 0.0030 0.0839 | 13.4764</item>
      <item>12 | 2.50 | 0.0806 0.0030 0.0836 | 12.3015</item>
      <item>13 | 2.50 | 0.0802 0.0032 0.0833 | 11.3776</item>
      <item>14 | 2.50 | 0.0798 0.0032 0.0830 | 10.4537</item>
      <item>15 | 2.25 | 0.0804 0.0033 0.0837 | 9.5920</item>
      <item>16 | 2.25 | 0.0771 0.0049 0.0820 | 8.8725</item>
      <item>17 | 2.25 | 0.0758 0.0055 0.0813 | 8.1530</item>
      <item>18 | 2.25 | 0.0750 0.0058 0.0807 | 7.5234</item>
      <item>29 | 2.00 | 0.0770 0.0028 0.0798 | 3.3283</item>
      <item>30 | 2.00 | 0.0712 0.0054 0.0766 | 3.1221</item>
      <item>31 | 2.00 | 0.0692 0.0064 0.0756 | 2.9160</item>
      <item>43 | 1.75 | 0.0682 0.0037 0.0719 | 1.5785</item>
      <item>44 | 1.75 | 0.0635 0.0062 0.0697 | 1.5194</item>
      <item>45 | 1.75 | 0.0618 0.0072 0.0690 | 1.4626</item>
      <item>57 | 1.50 | 0.0606 0.0053 0.0658 | 1.0900</item>
      <item>58 | 1.50 | 0.0571 0.0075 0.0647 | 1.0730</item>
      <item>59 | 1.50 | 0.0560 0.0083 0.0642 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 222s</item>
      <item>Prepare output 14s</item>
      <item>236s</item>
      <item>Jacobian determinant (RMS): 0.012 0.042 0.067 0.096 0.125 | 0.133084</item>
      <item>Template Matching: 0.087 0.225 0.207 0.185 0.168 | 0.167926</item>
      <item>Write result maps: 35s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 61s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 60s</item>
      <item>150s</item>
      <item>Create initial surface 108s</item>
      <item>Topology correction: 149s</item>
      <item>Surface refinement: 90s</item>
      <item>Reduction of surface collisions with optimization: 88s</item>
      <item>Spherical mapping with areal smoothing 118s</item>
      <item>Spherical registration 346s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 53s</item>
      <item>CSF distance: 21s</item>
      <item>PBT2x thickness: 61s</item>
      <item>143s</item>
      <item>Create initial surface 113s</item>
      <item>Topology correction: 118s</item>
      <item>Surface refinement: 102s</item>
      <item>Reduction of surface collisions with optimization: 90s</item>
      <item>Spherical mapping with areal smoothing 122s</item>
      <item>Spherical registration 360s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4995 0.6423 mm</item>
      <item>Surface intensity / position RMSE: 0.0671 / 0.0674</item>
      <item>Euler number / defect number / defect size: 24.0 / 14.0 / 0.69%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_13301/ds/sub-429/surf/lh.thickness.sub-429_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_13301/ds/sub-429/surf/rh.thickness.sub-429_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_13301/ds/sub-429/sub-429_T1w.nii</item>
      <item>Surface ROI estimation: 46s</item>
      <item>Surface and thickness estimation takes: 2277s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 11s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 39s</item>
      <item>ROI estimation of 'lpba40' atlas 11s</item>
      <item>ROI estimation of 'hammers' atlas 27s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 10s</item>
      <item>ROI estimation of 'aal3' atlas 16s</item>
      <item>ROI estimation of 'mori' atlas 23s</item>
      <item>ROI estimation of 'anatomy3' atlas 33s</item>
      <item>ROI estimation of 'julichbrain' atlas 44s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 33s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 111s</item>
      <item>Write results 112s</item>
      <item>445s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_13301/ds/sub-429/report/catreport_sub-429_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 65 minute(s) and 30 second(s).</item>
      <item>Image Quality Rating (IQR): 83.44% (B)</item>
      <item>GM volume (GMV): 43.53% (707.20 / 1624.77 ml)</item>
      <item>GM thickness (GMT): 2.50 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_13301/ds/sub-429/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_13301/ds/sub-429/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_13301/ds/sub-429/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>