ds003826_ReproVBM/sub-120/report/cat_sub-120_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.00263135406552 0.0214038036751282 -0.00817042848621995 2.53289431648352;-0.0270265128956887 1.0057535295666 0.173333413421644 6.56962692638669;0.0266326225982488 -0.230183080530093 1.05520683253301 28.6200023990741;0 0 0 1]</Affine>
      <Affine0>[1.00263135406552 0.0214038036751282 -0.00817042848621995 2.53289431648352;-0.0270265128956887 1.0057535295666 0.173333413421644 6.56962692638669;0.0266326225982488 -0.230183080530093 1.05520683253301 28.6200023990741;0 0 0 1]</Affine0>
      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[291.123766161977 402.578085568243 101.209635353335 187.966270592511 453.703948394375 46.4816083616705 134.343721909651 291.696584644893 554.958367373795 509.266743087993 277.893842567939 304.987168700201 105.782041662701]</mn>
      <vr>[2180.6740513902;313.045839709448;698.489743643026;2756.29947132883;5399.05470165789;351.081870156629;2846.98893543489;6291.92093789756;18713.7478213282;23066.2983919261;1528.35745301991;1107.22901179047;4771.754505971]</vr>
      <ll>-5.80153226852417</ll>
      <Affine_translation>[2.53289431648352 6.56962692638669 28.6200023990741]</Affine_translation>
      <Affine_rotation>[0.225403497950738 -0.0198636191645236 0.0321929951586517]</Affine_rotation>
      <Affine_scaling>[1.00334907242745 1.03191230036457 1.0672060272659]</Affine_scaling>
      <Affine_shearing>[-0.0117732740406788 0.0151249212654178 -0.0643810222898056]</Affine_shearing>
      <Affine0_translation>[2.53289431648352 6.56962692638669 28.6200023990741]</Affine0_translation>
      <Affine0_rotation>[0.225403497950738 -0.0198636191645236 0.0321929951586517]</Affine0_rotation>
      <Affine0_scaling>[1.00334907242745 1.03191230036457 1.0672060272659]</Affine0_scaling>
      <Affine0_shearing>[-0.0117732740406788 0.0151249212654178 -0.0643810222898056]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_1631/ds/sub-120</path>
      <file>sub-120_T1w</file>
      <fname>/var/lib/condor/execute/dir_1631/ds/sub-120/sub-120_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_1631/ds/sub-120/sub-120_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_1631/ds/sub-120/mri/msub-120_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_1631/ds/sub-120/mri/p0sub-120_T1w.nii</Fp0>
      <fnames>..1631/ds/sub-120/sub-120_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>42</SurfaceEulerNumber>
      <SurfaceDefectArea>1.67456453928847</SurfaceDefectArea>
      <SurfaceDefectNumber>22.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0670506730675697</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0727917775511742</SurfacePositionRMSE>
      <res_vx_vol>[1.10000197737154 1 1.00000001958861]</res_vx_vol>
      <res_vx_voli>[1.10000197759257 1 1.00000001920181]</res_vx_voli>
      <res_RMS>1.03440875051057</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[5.1399998664856 85.6149063110352 259.690734863281 403.331268310547]</tissue_mn>
      <tissue_mnr>[0.0127438670024276 0.212269455194473 0.643864631652832 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[4.19115815504836 50.8594386352004 43.5395536770682 25.0728161465253]</tissue_std>
      <tissue_stdr>[0.0105254901573062 0.127726152539253 0.109343320131302 0.0629667639732361]</tissue_stdr>
      <contrast>145.494705200195</contrast>
      <contrastr>0.360732525587082</contrastr>
      <NCR>0.157491400837898</NCR>
      <ICR>0.202398180961609</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.20000395474308 2 2.00000003917722]</res_vx_vol>
      <res_RMS>2.06881750102114</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>2.67234539985657</contrastr>
      <NCR>2.59189486503601</NCR>
      <ICR>0.961801052093506</ICR>
      <SurfaceEulerNumber>3.04081632653061</SurfaceEulerNumber>
      <SurfaceDefectArea>1.41864113482212</SurfaceDefectArea>
      <SurfaceDefectNumber>2.125</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.34101343154907</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.45583558082581</SurfacePositionRMSE>
      <IQR>2.42252323506449</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>20220703-104920</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>42</SurfaceEulerNumber>
         <SurfaceDefectArea>1.67456453928847</SurfaceDefectArea>
         <SurfaceDefectNumber>22.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0670506730675697</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0727917775511742</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>42</EC_abs>
      <defect_size>1.67456453928847</defect_size>
      <vol_abs_CGW>[336.546940136596 749.442715470375 636.527842459788 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.782795932151933</vol_abs_WMH>
      <vol_rel_WMH>0.000454448754819903</vol_rel_WMH>
      <surf_TSA>2281.28907672726</surf_TSA>
      <vol_TIV>1722.51749806676</vol_TIV>
      <vol_rel_CGW>[0.195380854194117 0.435085690747119 0.369533455058764 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.3651568978486 0.56691440418949]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.36450004577637 0.652135923966325 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.81249543125497 0.232009786119882 0.296889940252806;2.38032580124394 0.159551671832217 0.432280065661116;2.96110354395333 0.233436361817656 0.270829994086078]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.90925576292955 0.300244114601115 0.537645394530022;3.87573183038781 0.399279327120923 0.462354605469978]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>3.11575332564839</vol_TIV>
      <vol_rel_CGW>[1.35885154802652 5.66389530795832 4.48659222447494 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04544487548199</vol_rel_WMH>
      <surf_TSA>8.62397843356545</surf_TSA>
      <SQR>4.7159431627557</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.234991705662344 1 1 9402.94578699392 0.367897240910254]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0102689005434513 0.00692004803568125 0.0690603256225586]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[949.862738851241 565.220631325247 627.330807709468 2756.68337637215 2584.3176227897 5956.7172222381]</SPMvols0>
      <SPMvols1>[784.214054728676 529.350239089563 369.406320626731 3298.79038609188 2275.5043471631 5034.52214777693]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[108.361099243164 276.262084960938 402.697296142578]</T3th>
            <Tth>
               <T3th>[0 0 7.73550415039062 108.361099243164 276.262084960938 402.697296142578 549.865356445312 1203.33813476562]</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>[0.0198583118617535 0.0692702010273933 0.0758671909570694 0 0]</dtc>
         <ll>[0.086095326802596 0 0.086095326802596 0;0.207638524159664 0.00975335202440351 0.217391876184067 2079.8828125;0.207638524159664 0.00975335202440351 0.217391876184067 2079.8828125]</ll>
         <rmsdtc>[0.0438302494585514 0.0898304283618927 0.100453332066536]</rmsdtc>
         <rmsgdt>[0.0313952639698982 0.0448373109102249 0.055546585470438]</rmsgdt>
         <rmsdt>0.100453332066536</rmsdt>
         <dt>0.0758671909570694</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>[0.00846094079315662 0.0329360440373421 0.0426038987934589 0.051206324249506 0.0579508356750011 0.0643430128693581]</dtc>
         <ll>[0.0867562074728288 0 0.0867562074728288 0;0.224803159340659 0.0144509510454823 0.239254110386142 7397.08056640625;0.211361215493142 0.0161440118582155 0.227505227351357 11619.0390625;0.191553968989272 0.0188689453762594 0.210422914365531 20345.85546875;0.174578240498058 0.0223853319805951 0.196963572478654 39159.84765625;0.174578240498058 0.0223853319805951 0.196963572478654 39159.84765625]</ll>
         <rmsdtc>[0.00977927632629871 0.0344676375389099 0.052845261991024 0.0755126103758812 0.0994258970022202 0.105986341834068]</rmsdtc>
         <rmsgdt>[0.00318210548721254 0.0120894778519869 0.0266581028699875 0.046727005392313 0.0655264630913734 0.0709738507866859]</rmsgdt>
         <rmsdt>0.105986341834068</rmsdt>
         <dt>0.0643430128693581</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./execute/dir_1631/ds/sub-120/sub-120_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 24s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 8s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 4s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 9s</item>
      <item>47s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 10s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 72s</item>
      <item>SPM preprocessing 1 (estimate 2): 46s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 37s</item>
      <item>Update probability maps 8s</item>
      <item>78s</item>
      <item>Global intensity correction: 14s</item>
      <item>SANLM denoising after intensity normalization (medium): 8s</item>
      <item>Fast Optimized Shooting registration 29s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.13) 13s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 24s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 22s</item>
      <item>86s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 16s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.48 &gt; WMHCstr'=0.10) 24s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>68s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 30s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.24):</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 | 0.0868 0.0000 0.0868 | 32.0000</item>
      <item>2 | 2.50 | 0.0839 0.0013 0.0851 | 29.4886</item>
      <item>3 | 2.50 | 0.0831 0.0018 0.0849 | 26.9772</item>
      <item>4 | 2.50 | 0.0827 0.0021 0.0847 | 24.6107</item>
      <item>5 | 2.50 | 0.0824 0.0022 0.0846 | 22.6548</item>
      <item>6 | 2.50 | 0.0821 0.0023 0.0844 | 20.6989</item>
      <item>7 | 2.50 | 0.0819 0.0023 0.0842 | 18.9688</item>
      <item>8 | 2.50 | 0.0816 0.0024 0.0840 | 17.4455</item>
      <item>9 | 2.50 | 0.0813 0.0025 0.0838 | 15.9223</item>
      <item>10 | 2.50 | 0.0810 0.0026 0.0835 | 14.6627</item>
      <item>11 | 2.50 | 0.0807 0.0026 0.0833 | 13.4764</item>
      <item>12 | 2.50 | 0.0804 0.0027 0.0830 | 12.3015</item>
      <item>13 | 2.50 | 0.0801 0.0027 0.0828 | 11.3776</item>
      <item>14 | 2.50 | 0.0798 0.0028 0.0825 | 10.4537</item>
      <item>15 | 2.25 | 0.0793 0.0029 0.0822 | 9.5920</item>
      <item>16 | 2.25 | 0.0766 0.0042 0.0808 | 8.8725</item>
      <item>17 | 2.25 | 0.0756 0.0046 0.0802 | 8.1530</item>
      <item>18 | 2.25 | 0.0749 0.0048 0.0798 | 7.5234</item>
      <item>29 | 2.00 | 0.0774 0.0023 0.0797 | 3.3283</item>
      <item>30 | 2.00 | 0.0722 0.0045 0.0767 | 3.1221</item>
      <item>31 | 2.00 | 0.0705 0.0054 0.0758 | 2.9160</item>
      <item>43 | 1.75 | 0.0698 0.0030 0.0728 | 1.5785</item>
      <item>44 | 1.75 | 0.0653 0.0054 0.0708 | 1.5194</item>
      <item>45 | 1.75 | 0.0639 0.0063 0.0701 | 1.4626</item>
      <item>57 | 1.50 | 0.0627 0.0045 0.0672 | 1.0900</item>
      <item>58 | 1.50 | 0.0593 0.0068 0.0661 | 1.0730</item>
      <item>59 | 1.50 | 0.0582 0.0075 0.0657 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 149s</item>
      <item>Prepare output 9s</item>
      <item>158s</item>
      <item>Jacobian determinant (RMS): 0.010 0.034 0.053 0.076 0.099 | 0.105986</item>
      <item>Template Matching: 0.087 0.225 0.211 0.192 0.175 | 0.174578</item>
      <item>Write result maps: 20s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 45s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 47s</item>
      <item>114s</item>
      <item>Create initial surface 91s</item>
      <item>Topology correction: 101s</item>
      <item>Surface refinement: 94s</item>
      <item>Reduction of surface collisions with optimization: 81s</item>
      <item>Spherical mapping with areal smoothing 85s</item>
      <item>Spherical registration 273s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 38s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 47s</item>
      <item>109s</item>
      <item>Create initial surface 93s</item>
      <item>Topology correction: 106s</item>
      <item>Surface refinement: 93s</item>
      <item>Reduction of surface collisions with optimization: 79s</item>
      <item>Spherical mapping with areal smoothing 86s</item>
      <item>Spherical registration 277s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3651 0.5669 mm</item>
      <item>Surface intensity / position RMSE: 0.0671 / 0.0728</item>
      <item>Euler number / defect number / defect size: 42.0 / 22.5 / 1.67%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1631/ds/sub-120/surf/lh.thickness.sub-120_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1631/ds/sub-120/surf/rh.thickness.sub-120_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1631/ds/sub-120/sub-120_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1773s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 8s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 10s</item>
      <item>ROI estimation of 'mori' atlas 16s</item>
      <item>ROI estimation of 'anatomy3' atlas 22s</item>
      <item>ROI estimation of 'julichbrain' atlas 29s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s</item>
      <item>Write results 69s</item>
      <item>294s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_1631/ds/sub-120/report/catreport_sub-120_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 47 minute(s) and 35 second(s).</item>
      <item>Image Quality Rating (IQR): 80.77% (B-)</item>
      <item>GM volume (GMV): 43.51% (749.44 / 1722.52 ml)</item>
      <item>GM thickness (GMT): 2.37 0.57 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_1631/ds/sub-120/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>