ds003721_ReproVBM/sub-13/report/cat_sub-13_acq-highres_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.07659053813325 -0.0172068938367196 0.00393996154302049 -0.151489054988773;0.00882765271336763 1.00727557558286 0.396773815564507 -6.17804950568618;-0.00126301888649878 -0.403306342579416 1.1010233479005 58.7071588633154;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-4.78274345397949</ll>
      <Affine_translation>[-0.151489054988773 -6.17804950568618 58.7071588633154]</Affine_translation>
      <Affine_rotation>[0.380814281785844 -0.00195848797186155 -0.00804808366213418]</Affine_rotation>
      <Affine_scaling>[1.0766274701433 1.08511951272137 1.16961012079733]</Affine_scaling>
      <Affine_shearing>[-0.00787102611399919 0.00548144860490033 -0.0377133761822024]</Affine_shearing>
      <Affine0_translation>[-0.151489054988773 -6.17804950568618 58.7071588633154]</Affine0_translation>
      <Affine0_rotation>[0.380814281785844 -0.00195848797186155 -0.00804808366213418]</Affine0_rotation>
      <Affine0_scaling>[1.0766274701433 1.08511951272137 1.16961012079733]</Affine0_scaling>
      <Affine0_shearing>[-0.00787102611399919 0.00548144860490033 -0.0377133761822024]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_26128/ds/sub-13</path>
      <file>sub-13_acq-highres_T1w</file>
      <fname>/var/lib/condor/execute/dir_26128/ds/sub-13/sub-13_acq-highres_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_26128/ds/sub-13/sub-13_acq-highres_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_26128/ds/sub-13/mri/msub-13_acq-highres_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_26128/ds/sub-13/mri/p0sub-13_acq-highres_T1w.nii</Fp0>
      <fnames>..26128/ds/sub-13/sub-13_acq-highres_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>24</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>0.849233093418438</SurfaceDefectArea>
      <SurfaceDefectNumber>13</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0687691122293472</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0756738558411598</SurfacePositionRMSE>
      <res_vx_vol>[1.00000001741718 0.999999766131934 1.0000002038512]</res_vx_vol>
      <res_vx_voli>[1.00000007700827 0.999999761579746 1.00000019939993]</res_vx_voli>
      <res_RMS>0.999999995800119</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[1.21000003814697 52.6531105041504 121.068740844727 171.403991699219]</tissue_mn>
      <tissue_mnr>[0.00705934595316648 0.30718719959259 0.706335604190826 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.00722421053797007 0.107527166604996 0.0934593081474304 0.0544348806142807]</tissue_stdr>
      <contrast>50.6931114196777</contrast>
      <contrastr>0.295752227306366</contrastr>
      <NCR>0.127543598413467</NCR>
      <ICR>0.178387001156807</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.00000003483436 1.99999953226387 2.00000040770239]</res_vx_vol>
      <res_RMS>1.99999999160024</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[5.41265916824341 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.62399909588845 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>3.64704990386963</contrastr>
      <NCR>2.16198110580444</NCR>
      <ICR>0.90224951505661</ICR>
      <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
      <SurfaceDefectArea>1.21230827335461</SurfaceDefectArea>
      <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.3753821849823</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.51347708702087</SurfacePositionRMSE>
      <IQR>2.09186373220825</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>1980</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20220712-144947</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>18</SurfaceEulerNumber>
         <SurfaceDefectArea>0.849233093418438</SurfaceDefectArea>
         <SurfaceDefectNumber>13</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0687691122293472</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0756738558411598</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>18</EC_abs>
      <defect_size>0.849233093418438</defect_size>
      <vol_abs_CGW>[252.144833107863 646.710004959309 470.327182572622 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.639517671352754</vol_abs_WMH>
      <vol_rel_WMH>0.000467080097249538</vol_rel_WMH>
      <surf_TSA>1850.93013191169</surf_TSA>
      <vol_TIV>1369.18202063979</vol_TIV>
      <vol_rel_CGW>[0.184157277342892 0.472333112187022 0.343509610470087 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.44590835246046 0.594889082421531]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.47308564186096 0.712760075891834 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.88075330158703 0.238844186294725 0.285322898982789;2.48272497355171 0.165704248007397 0.426931942086594;3.07122769157134 0.248605357888629 0.287745158930617]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.836676959987043 0.31872857758082 0.606316597868868;3.95171787209175 0.345482928161106 0.393683402131132]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.02259419662567</vol_TIV>
      <vol_rel_CGW>[1.15727868791113 6.33285043439335 4.0192099581553 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04670800972495</vol_rel_WMH>
      <surf_TSA>8.60353211125016</surf_TSA>
      <SQR>5.19563390885996</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.46426248550415 1709 211 6741.13791506342 0.38964576676072]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00583770032972097 0 0.0826874151825905]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[757.04707189588 427.691137815714 424.458227888981 742.674200761649 2616.13200134213 8187.46328749509]</SPMvols0>
      <SPMvols1>[669.196178362531 402.234368221214 255.182856752683 1568.06082819478 2292.03214981458 7396.29929273455]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[59.7078018188477 125.452499389648 166.374603271484]</T3th>
            <Tth>
               <T3th>[0 0 1.67757773399353 59.7078018188477 125.452499389648 166.374603271484 219.7080078125 503.279693603516]</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>[0.0212158616632223 0.0750328823924065 0.0827040448784828 0 0]</dtc>
         <ll>[0.0836922598629296 0 0.0836922598629296 0;0.196499773004905 0.0103181687866797 0.206817941791585 2200.32885742188;0.196499773004905 0.0103181687866797 0.206817941791585 2200.32885742188]</ll>
         <rmsdtc>[0.0462044253945351 0.0984977409243584 0.108736351132393]</rmsdtc>
         <rmsgdt>[0.0328780598938465 0.0428403466939926 0.0526402555406094]</rmsgdt>
         <rmsdt>0.108736351132393</rmsdt>
         <dt>0.0827040448784828</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>[0.00984229799360037 0.0364514291286469 0.0511381477117538 0.0585636422038078 0.0633340626955032 0.0707990303635597]</dtc>
         <ll>[0.0838186688735065 0 0.0838186688735065 0;0.221208318070818 0.0132736797924298 0.234481997863248 6794.46484375;0.199858176777655 0.0165179922880611 0.216376169065717 11888.197265625;0.179850144490444 0.018456414667403 0.198306559157847 19901.03515625;0.166805134526879 0.0192302391584203 0.1860353736853 33640.4765625;0.166805134526879 0.0192302391584203 0.1860353736853 33640.4765625]</ll>
         <rmsdtc>[0.0115888668224216 0.0425585620105267 0.0626840516924858 0.0857350304722786 0.106807187199593 0.111351899802685]</rmsdtc>
         <rmsgdt>[0.0031801916193217 0.012530573643744 0.0271392855793238 0.0456569530069828 0.0634004697203636 0.0668830201029778]</rmsgdt>
         <rmsdt>0.111351899802685</rmsdt>
         <dt>0.0707990303635597</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_26128/ds/sub-13/sub-13_acq-highres_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 76s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 10s</item>
      <item>Estimate background 11s</item>
      <item>Initial correction 9s</item>
      <item>Refine background 5s</item>
      <item>Final correction 7s</item>
      <item>Final scaling 8s</item>
      <item>60s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 95s</item>
      <item>SPM preprocessing 1 (estimate 2): 113s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 26s</item>
      <item>Update Segmentation 26s</item>
      <item>Update Skull-Stripping 59s</item>
      <item>Update probability maps 13s</item>
      <item>123s</item>
      <item>Global intensity correction: 25s</item>
      <item>SANLM denoising after intensity normalization (medium): 19s</item>
      <item>Fast Optimized Shooting registration 53s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 6s</item>
      <item>Prepare partitions 4s</item>
      <item>Prepare segments (LASmod = 1.00) 19s</item>
      <item>Estimate local tissue thresholds (WM) 24s</item>
      <item>Estimate local tissue thresholds (GM) 31s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 29s</item>
      <item>116s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 11s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 19s</item>
      <item>Blood vessel detection 11s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.07) 30s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 6s</item>
      <item>88s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 49s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 5s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>14s</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 | 0.0812 0.0011 0.0824 | 29.4886</item>
      <item>3 | 2.50 | 0.0804 0.0017 0.0822 | 26.9772</item>
      <item>4 | 2.50 | 0.0801 0.0020 0.0820 | 24.6107</item>
      <item>5 | 2.50 | 0.0798 0.0021 0.0819 | 22.6548</item>
      <item>6 | 2.50 | 0.0795 0.0022 0.0817 | 20.6989</item>
      <item>7 | 2.50 | 0.0792 0.0023 0.0815 | 18.9688</item>
      <item>8 | 2.50 | 0.0789 0.0024 0.0813 | 17.4455</item>
      <item>9 | 2.50 | 0.0787 0.0025 0.0811 | 15.9223</item>
      <item>10 | 2.50 | 0.0783 0.0026 0.0809 | 14.6627</item>
      <item>11 | 2.50 | 0.0780 0.0027 0.0807 | 13.4764</item>
      <item>12 | 2.50 | 0.0777 0.0027 0.0805 | 12.3015</item>
      <item>13 | 2.50 | 0.0774 0.0028 0.0802 | 11.3776</item>
      <item>14 | 2.50 | 0.0771 0.0029 0.0800 | 10.4537</item>
      <item>15 | 2.25 | 0.0766 0.0030 0.0796 | 9.5920</item>
      <item>16 | 2.25 | 0.0737 0.0044 0.0782 | 8.8725</item>
      <item>29 | 2.00 | 0.0749 0.0020 0.0769 | 3.3283</item>
      <item>30 | 2.00 | 0.0688 0.0045 0.0732 | 3.1221</item>
      <item>31 | 2.00 | 0.0666 0.0055 0.0721 | 2.9160</item>
      <item>43 | 1.75 | 0.0656 0.0032 0.0688 | 1.5785</item>
      <item>44 | 1.75 | 0.0614 0.0054 0.0667 | 1.5194</item>
      <item>45 | 1.75 | 0.0600 0.0062 0.0661 | 1.4626</item>
      <item>57 | 1.50 | 0.0586 0.0045 0.0630 | 1.0900</item>
      <item>58 | 1.50 | 0.0556 0.0064 0.0620 | 1.0730</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 225s</item>
      <item>Prepare output 13s</item>
      <item>238s</item>
      <item>Jacobian determinant (RMS): 0.012 0.043 0.063 0.086 0.107 | 0.111352</item>
      <item>Template Matching: 0.084 0.221 0.200 0.180 0.167 | 0.166805</item>
      <item>Write result maps: 38s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 49s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 58s</item>
      <item>134s</item>
      <item>Create initial surface 103s</item>
      <item>Topology correction: 124s</item>
      <item>Surface refinement: 121s</item>
      <item>Reduction of surface collisions with optimization: 84s</item>
      <item>Spherical mapping with areal smoothing 103s</item>
      <item>Spherical registration 284s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 48s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 58s</item>
      <item>133s</item>
      <item>Create initial surface 102s</item>
      <item>Topology correction: 118s</item>
      <item>Surface refinement: 108s</item>
      <item>Reduction of surface collisions with optimization: 86s</item>
      <item>Spherical mapping with areal smoothing 105s</item>
      <item>Spherical registration 300s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4459 0.5946 mm</item>
      <item>Surface intensity / position RMSE: 0.0688 / 0.0757</item>
      <item>Euler number / defect number / defect size: 18.0 / 13.0 / 0.85%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_26128/ds/sub-13/surf/lh.thickness.sub-13_acq-highres_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_26128/ds/sub-13/surf/rh.thickness.sub-13_acq-highres_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_26128/ds/sub-13/sub-13_acq-highres_T1w.nii</item>
      <item>Surface ROI estimation: 10s</item>
      <item>Surface and thickness estimation takes: 2020s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 21s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 69s</item>
      <item>ROI estimation of 'lpba40' atlas 20s</item>
      <item>ROI estimation of 'hammers' atlas 52s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 19s</item>
      <item>ROI estimation of 'aal3' atlas 32s</item>
      <item>ROI estimation of 'mori' atlas 47s</item>
      <item>ROI estimation of 'anatomy3' atlas 65s</item>
      <item>ROI estimation of 'julichbrain' atlas 85s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 45s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 138s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 190s</item>
      <item>Write results 192s</item>
      <item>816s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_26128/ds/sub-13/report/catreport_sub-13_acq-highres_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 68 minute(s) and 13 second(s).</item>
      <item>Image Quality Rating (IQR): 84.08% (B)</item>
      <item>GM volume (GMV): 47.23% (646.71 / 1369.18 ml)</item>
      <item>GM thickness (GMT): 2.45 0.59 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_26128/ds/sub-13/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_26128/ds/sub-13/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_26128/ds/sub-13/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>