ds003791_ReproVBM/sub-18/report/cat_sub-18_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[1.07618320005256 0.0308605013737525 0.0126984517957863 0.249695939930695;-0.0109641574357159 0.966966267437378 0.270406722404778 -15.131761280829;-0.00889561288549064 -0.257407333984107 1.12561772075472 6.67230795079204;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[167.307804785421 231.153062745931 49.4896120934279 98.9188737742772 60.0252637151821 17.8062212290224 35.528748465899 128.165092840281 219.80887959813 176.491390613053 108.539848337422 19.0801194777086 8.32079328732236]</mn>
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      <ll>-4.91442632675171</ll>
      <Affine_translation>[0.249695939930695 -15.131761280829 6.67230795079204]</Affine_translation>
      <Affine_rotation>[0.259840442585174 0.0106055818107036 0.0077216885988557]</Affine_rotation>
      <Affine_scaling>[1.07627581258349 1.00084936506076 1.15737604238834]</Affine_scaling>
      <Affine_shearing>[0.0214951930690996 0.000593954725328251 -0.0278436670826082]</Affine_shearing>
      <Affine0_translation>[0.249695939930695 -15.131761280829 6.67230795079204]</Affine0_translation>
      <Affine0_rotation>[0.259840442585174 0.0106055818107036 0.0077216885988557]</Affine0_rotation>
      <Affine0_scaling>[1.07627581258349 1.00084936506076 1.15737604238834]</Affine0_scaling>
      <Affine0_shearing>[0.0214951930690996 0.000593954725328251 -0.0278436670826082]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_31201/ds/sub-18</path>
      <file>sub-18_T1w</file>
      <fname>/var/lib/condor/execute/dir_31201/ds/sub-18/sub-18_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_31201/ds/sub-18/sub-18_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_31201/ds/sub-18/mri/msub-18_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_31201/ds/sub-18/mri/p0sub-18_T1w.nii</Fp0>
      <fnames>..31201/ds/sub-18/sub-18_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>14</SurfaceEulerNumber>
      <SurfaceDefectArea>0.67556875561993</SurfaceDefectArea>
      <SurfaceDefectNumber>5.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0618598163127899</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0692014843225479</SurfacePositionRMSE>
      <res_vx_vol>[0.940000002956685 0.937500024960718 0.937499980047605]</res_vx_vol>
      <res_vx_voli>[0.940000003131476 0.9375000235812 0.937499981023705]</res_vx_voli>
      <res_RMS>0.938334076071199</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[1.72699999809265 52.0017585754395 149.897064208984 231.756607055664]</tissue_mn>
      <tissue_mnr>[0.00745178293436766 0.224380910396576 0.646786570549011 0.999999940395355]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[1.31693605094127 24.0811442269752 24.9607761389572 14.5207516889437]</tissue_std>
      <tissue_stdr>[0.00572507176548243 0.10468714684248 0.10851114243269 0.0631255730986595]</tissue_stdr>
      <contrast>82.47412109375</contrast>
      <contrastr>0.355865240097046</contrastr>
      <NCR>0.108381375670433</NCR>
      <ICR>0.233324587345123</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[1.88000000591337 1.87500004992144 1.87499996009521]</res_vx_vol>
      <res_RMS>1.8766681521424</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[7.76655101776123 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.62399993039057 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>2.74535465240479</contrastr>
      <NCR>1.88689887523651</NCR>
      <ICR>1.03850340843201</ICR>
      <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
      <SurfaceDefectArea>1.16889218890498</SurfaceDefectArea>
      <SurfaceDefectNumber>1.275</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.2371963262558</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.38402962684631</SurfacePositionRMSE>
      <IQR>1.88183217903</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>20220712-150508</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>14</SurfaceEulerNumber>
         <SurfaceDefectArea>0.67556875561993</SurfaceDefectArea>
         <SurfaceDefectNumber>5.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0618598163127899</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0692014843225479</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>14</EC_abs>
      <defect_size>0.67556875561993</defect_size>
      <vol_abs_CGW>[279.676146055442 686.922879054025 529.858098485403 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.779679464147686</vol_abs_WMH>
      <vol_rel_WMH>0.000521016908439513</vol_rel_WMH>
      <surf_TSA>1985.42374148577</surf_TSA>
      <vol_TIV>1496.45712359487</vol_TIV>
      <vol_rel_CGW>[0.186892187985706 0.459032783648262 0.354075028366031 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.49575395144423 0.610861243337066]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.49616527557373 0.777903272176691 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.94006350397935 0.251385837430977 0.307378204204844;2.53557537552167 0.17055760087484 0.428175082825525;3.17140126533767 0.270813370736124 0.264446712969632]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.816182971376099 0.344773502275393 0.591348890153671;4.16058033975939 0.379598315562297 0.408651109846329]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.2184757706166</vol_TIV>
      <vol_rel_CGW>[1.20639705434099 6.09397959138402 4.20896243473475 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.05210169084395</vol_rel_WMH>
      <surf_TSA>8.620822145091</surf_TSA>
      <SQR>5.01499688281761</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.296301755038175 5 1 6705.78270535363 0.353513457232246]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00780303683131933 0.00559792760759592 0.197096526622772]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[824.994535040531 466.133666342459 441.445933372408 613.472242855722 2261.18150620843 5503.44138985157]</SPMvols0>
      <SPMvols1>[734.43709962033 441.299244124875 269.501606058887 471.444227921162 1346.54817408248 6266.14906422241]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[55.7658996582031 160.255401611328 231.322601318359]</T3th>
            <Tth>
               <T3th>[0 0 3.63543677330017 55.7658996582031 160.255401611328 231.322601318359 319.100952148438 523.007507324219]</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>[0.0198580734431744 0.0731210857629776 0.0802749693393707 0 0]</dtc>
         <ll>[0.0843250691389837 0 0.0843250691389837 0;0.196794690776701 0.0109147544668502 0.207709445243552 2327.54956054688;0.196794690776701 0.0109147544668502 0.207709445243552 2327.54956054688]</ll>
         <rmsdtc>[0.0466080233454704 0.0945409312844276 0.10517043620348]</rmsdtc>
         <rmsgdt>[0.0338422954082489 0.0448063313961029 0.0552077516913414]</rmsgdt>
         <rmsdt>0.10517043620348</rmsdt>
         <dt>0.0802749693393707</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>[0.00917206238955259 0.0333061963319778 0.0479481890797615 0.0565859191119671 0.0627882108092308 0.0699652284383774]</dtc>
         <ll>[0.0845059504647313 0 0.0845059504647313 0;0.222210424297924 0.0136148628281441 0.235825287126068 6969.10791015625;0.198699488475946 0.0175734681893591 0.216272956665305 12647.8359375;0.177310041552595 0.0196956750447707 0.197005716597366 21237.294921875;0.15982453584268 0.0224133557342343 0.182237891576914 39208.87109375;0.15982453584268 0.0224133557342343 0.182237891576914 39208.87109375]</ll>
         <rmsdtc>[0.0106668835505843 0.0381587259471416 0.0576912015676498 0.082308903336525 0.104591526091099 0.111268125474453]</rmsdtc>
         <rmsgdt>[0.00324143865145743 0.0128076700493693 0.0281282160431147 0.0480840988457203 0.0655933171510696 0.0710633173584938]</rmsgdt>
         <rmsdt>0.111268125474453</rmsdt>
         <dt>0.0699652284383774</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_31201/ds/sub-18/sub-18_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 60s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 7s</item>
      <item>Initial correction 6s</item>
      <item>Refine background 3s</item>
      <item>Final correction 5s</item>
      <item>Final scaling 7s</item>
      <item>41s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 81s</item>
      <item>SPM preprocessing 1 (estimate 2): 69s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 16s</item>
      <item>Update Segmentation 20s</item>
      <item>Update Skull-Stripping 44s</item>
      <item>Update probability maps 9s</item>
      <item>89s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 13s</item>
      <item>Fast Optimized Shooting registration 31s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.04) 17s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 26s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 25s</item>
      <item>96s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 8s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 18s</item>
      <item>Blood vessel detection 11s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.08) 30s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 4s</item>
      <item>81s</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 0.05,0.67 0.08,0.98 0.04]</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) 4s</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 | 0.0845 0.0000 0.0845 | 32.0000</item>
      <item>2 | 2.50 | 0.0819 0.0012 0.0830 | 29.4886</item>
      <item>3 | 2.50 | 0.0811 0.0018 0.0829 | 26.9772</item>
      <item>4 | 2.50 | 0.0807 0.0020 0.0827 | 24.6107</item>
      <item>5 | 2.50 | 0.0804 0.0021 0.0826 | 22.6548</item>
      <item>6 | 2.50 | 0.0802 0.0022 0.0824 | 20.6989</item>
      <item>7 | 2.50 | 0.0799 0.0023 0.0822 | 18.9688</item>
      <item>8 | 2.50 | 0.0796 0.0024 0.0820 | 17.4455</item>
      <item>9 | 2.50 | 0.0793 0.0025 0.0818 | 15.9223</item>
      <item>10 | 2.50 | 0.0790 0.0026 0.0816 | 14.6627</item>
      <item>11 | 2.50 | 0.0787 0.0027 0.0814 | 13.4764</item>
      <item>12 | 2.50 | 0.0784 0.0027 0.0811 | 12.3015</item>
      <item>13 | 2.50 | 0.0781 0.0029 0.0809 | 11.3776</item>
      <item>14 | 2.50 | 0.0778 0.0029 0.0807 | 10.4537</item>
      <item>15 | 2.25 | 0.0772 0.0030 0.0802 | 9.5920</item>
      <item>16 | 2.25 | 0.0741 0.0045 0.0786 | 8.8725</item>
      <item>29 | 2.00 | 0.0752 0.0021 0.0773 | 3.3283</item>
      <item>30 | 2.00 | 0.0685 0.0048 0.0733 | 3.1221</item>
      <item>31 | 2.00 | 0.0662 0.0059 0.0721 | 2.9160</item>
      <item>43 | 1.75 | 0.0650 0.0034 0.0684 | 1.5785</item>
      <item>44 | 1.75 | 0.0605 0.0058 0.0663 | 1.5194</item>
      <item>45 | 1.75 | 0.0591 0.0066 0.0657 | 1.4626</item>
      <item>57 | 1.50 | 0.0574 0.0048 0.0622 | 1.0900</item>
      <item>58 | 1.50 | 0.0543 0.0068 0.0611 | 1.0730</item>
      <item>59 | 1.50 | 0.0533 0.0075 0.0607 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 163s</item>
      <item>Prepare output 11s</item>
      <item>174s</item>
      <item>Jacobian determinant (RMS): 0.011 0.038 0.058 0.082 0.105 | 0.111268</item>
      <item>Template Matching: 0.085 0.222 0.199 0.177 0.160 | 0.159825</item>
      <item>Write result maps: 26s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 40s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 45s</item>
      <item>106s</item>
      <item>Create initial surface 84s</item>
      <item>Topology correction: 97s</item>
      <item>Surface refinement: 108s</item>
      <item>Reduction of surface collisions with optimization: 74s</item>
      <item>Spherical mapping with areal smoothing 88s</item>
      <item>Spherical registration 285s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 44s</item>
      <item>97s</item>
      <item>Create initial surface 85s</item>
      <item>Topology correction: 95s</item>
      <item>Surface refinement: 98s</item>
      <item>Reduction of surface collisions with optimization: 70s</item>
      <item>Spherical mapping with areal smoothing 85s</item>
      <item>Spherical registration 306s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4959 0.6097 mm</item>
      <item>Surface intensity / position RMSE: 0.0619 / 0.0692</item>
      <item>Euler number / defect number / defect size: 14.0 / 5.5 / 0.68%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_31201/ds/sub-18/surf/lh.thickness.sub-18_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_31201/ds/sub-18/surf/rh.thickness.sub-18_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_31201/ds/sub-18/sub-18_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1772s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 9s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 32s</item>
      <item>ROI estimation of 'lpba40' atlas 9s</item>
      <item>ROI estimation of 'hammers' atlas 22s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 8s</item>
      <item>ROI estimation of 'aal3' atlas 12s</item>
      <item>ROI estimation of 'mori' atlas 19s</item>
      <item>ROI estimation of 'anatomy3' atlas 26s</item>
      <item>ROI estimation of 'julichbrain' atlas 34s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s</item>
      <item>Write results 82s</item>
      <item>346s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_31201/ds/sub-18/report/catreport_sub-18_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 51 minute(s) and 3 second(s).</item>
      <item>Image Quality Rating (IQR): 86.18% (B)</item>
      <item>GM volume (GMV): 45.90% (686.92 / 1496.46 ml)</item>
      <item>GM thickness (GMT): 2.50 0.61 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_31201/ds/sub-18/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_31201/ds/sub-18/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_31201/ds/sub-18/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>