ds003104_ReproVBM/sub-01/report/cat_sub-01_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
   <SPMpreprocessing>
      <Affine>[0.988813804849561 0.0662893734986113 0.0248480667478684 -4.66018880274919;-0.0373317883306704 0.965723078901027 0.233645673607962 -50.9129733945355;-0.012264377723061 -0.278118489772332 1.03947552638198 8.41025835372149;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>[73.3585655219576 109.845942898271 14.0525478779814 39.445921056378 36.9643727207815 9.70896870579335 20.8614928115029 131.812424594044 250.709136475744 220.027571900609 69.0470401386757 22.4838945219038 5.49030774953671]</mn>
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      <ll>-4.45304298400879</ll>
      <Affine_translation>[-4.66018880274919 -50.9129733945355 8.41025835372149]</Affine_translation>
      <Affine_rotation>[0.278930101153801 0.0223147796427918 0.0328600022249208]</Affine_rotation>
      <Affine_scaling>[0.989594269406389 1.00660791871747 1.06391903028842]</Affine_scaling>
      <Affine_shearing>[0.0336023028634042 0.00316469945177246 -0.0611070717337793]</Affine_shearing>
      <Affine0_translation>[-4.66018880274919 -50.9129733945355 8.41025835372149]</Affine0_translation>
      <Affine0_rotation>[0.278930101153801 0.0223147796427918 0.0328600022249208]</Affine0_rotation>
      <Affine0_scaling>[0.989594269406389 1.00660791871747 1.06391903028842]</Affine0_scaling>
      <Affine0_shearing>[0.0336023028634042 0.00316469945177246 -0.0611070717337793]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_20259/ds/sub-01</path>
      <file>sub-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_20259/ds/sub-01/sub-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_20259/ds/sub-01/sub-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_20259/ds/sub-01/mri/msub-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_20259/ds/sub-01/mri/p0sub-01_T1w.nii</Fp0>
      <fnames>..20259/ds/sub-01/sub-01_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>28</SurfaceEulerNumber>
      <SurfaceDefectArea>1.42052994686953</SurfaceDefectArea>
      <SurfaceDefectNumber>16</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0727588981389999</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0872767791152</SurfacePositionRMSE>
      <res_vx_vol>[1 1 1]</res_vx_vol>
      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>1</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[2.0239999294281 8.19250297546387 58.3431587219238 103.032943725586]</tissue_mn>
      <tissue_mnr>[0.0196442026644945 0.0795134305953979 0.566257357597351 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[2.11730490868946 18.5353486520109 13.2795360492031 7.78493341648275]</tissue_std>
      <tissue_stdr>[0.0209615584462881 0.183502063155174 0.131468921899796 0.0770717263221741]</tissue_stdr>
      <contrast>35.5305557250977</contrast>
      <contrastr>0.344846546649933</contrastr>
      <NCR>0.0843914151191711</NCR>
      <ICR>0.0670401751995087</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2 2 2]</res_vx_vol>
      <res_RMS>2</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.31805419921875 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>2.91063499450684</contrastr>
      <NCR>1.5425124168396</NCR>
      <ICR>0.626091718673706</ICR>
      <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
      <SurfaceDefectArea>1.35513248671738</SurfaceDefectArea>
      <SurfaceDefectNumber>1.8</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.45517802238464</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.74553561210632</SurfacePositionRMSE>
      <IQR>1.86125018439022</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>1980</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20220711-105948</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>28</SurfaceEulerNumber>
         <SurfaceDefectArea>1.42052994686953</SurfaceDefectArea>
         <SurfaceDefectNumber>16</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0727588981389999</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0872767791152</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>28</EC_abs>
      <defect_size>1.42052994686953</defect_size>
      <vol_abs_CGW>[344.735368627451 788.373894117647 633.04551372549 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.45033725490196</vol_abs_WMH>
      <vol_rel_WMH>0.000821183553233231</vol_rel_WMH>
      <surf_TSA>2285.29666032756</surf_TSA>
      <vol_TIV>1766.15477647059</vol_TIV>
      <vol_rel_CGW>[0.195189783602293 0.446378711889057 0.358431504508649 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.36419799933192 0.615368030563662]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.36055707931519 0.724155490228346 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.77356651118884 0.24521699334817 0.304727777386251;2.3873319724639 0.174536319643375 0.42151542585776;3.03064070218119 0.256126886057469 0.273756796755989]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.795654432321122 0.288498507645809 0.554828660436137;3.97557801842439 0.389283223687082 0.445171339563863]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>3.60949586420133</vol_TIV>
      <vol_rel_CGW>[1.35541996412165 5.86671537157071 4.28720374476741 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.08211835532332</vol_rel_WMH>
      <surf_TSA>8.62398001346173</surf_TSA>
      <SQR>4.84472118962476</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.458880603313446 323 46 9078.477 0.60708184306481]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0 0 0.0631041526794434]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[1260.9039254902 289.619819607843 644.441701960784 635.29871372549 3366.80341568627 11441.1861333333]</SPMvols0>
      <SPMvols1>[1081.50056862745 292.653282352941 353.118552941176 693.174890196078 1557.98770588235 12799.7293921569]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[14.9485998153687 59.842601776123 109.844497680664]</T3th>
            <Tth>
               <T3th>[0 0 1.76381993293762 14.9485998153687 59.842601776123 109.844497680664 157.292449951172 265.906555175781]</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>[0.0188961401581764 0.082720972597599 0.0970985516905785 0 0]</dtc>
         <ll>[0.0942597986460209 0 0.0942597986460209 0;0.219983104325715 0.0149919422877794 0.234975046613494 3197.00170898438;0.219983104325715 0.0149919422877794 0.234975046613494 3197.00170898438]</ll>
         <rmsdtc>[0.0436942875385284 0.130298063158989 0.154712706804276]</rmsdtc>
         <rmsgdt>[0.031660620123148 0.0776141360402107 0.0985928177833557]</rmsgdt>
         <rmsdt>0.154712706804276</rmsdt>
         <dt>0.0970985516905785</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>[0.00816159322857857 0.0403502434492111 0.0419702380895615 0.052016980946064 0.0596282556653023 0.0665662959218025]</dtc>
         <ll>[0.0900145463413729 0 0.0900145463413729 0;0.224360958485958 0.0157297714438339 0.240090729929792 8051.6767578125;0.221075604721055 0.0167128347649824 0.237788439486037 12028.427734375;0.198466548213252 0.0201517831452778 0.21861833135853 21729.103515625;0.18043667430187 0.0241291173079419 0.204565791609812 42210.34375;0.18043667430187 0.0241291173079419 0.204565791609812 42210.34375]</ll>
         <rmsdtc>[0.00968340132385492 0.0346360802650452 0.0582598075270653 0.0789509788155556 0.106185115873814 0.113193094730377]</rmsdtc>
         <rmsgdt>[0.00309837772510946 0.0121511127799749 0.029097018763423 0.0496036261320114 0.0715557187795639 0.0777200013399124]</rmsgdt>
         <rmsdt>0.113193094730377</rmsdt>
         <dt>0.0665662959218025</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_20259/ds/sub-01/sub-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 75s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 9s</item>
      <item>Estimate background 9s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 5s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 7s</item>
      <item>52s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 10s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 78s</item>
      <item>SPM preprocessing 1 (estimate 2): 62s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 21s</item>
      <item>Update Segmentation 22s</item>
      <item>Update Skull-Stripping 57s</item>
      <item>Update probability maps 12s</item>
      <item>112s</item>
      <item>Global intensity correction: 22s</item>
      <item>SANLM denoising after intensity normalization (medium): 26s</item>
      <item>Fast Optimized Shooting registration 37s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 5s</item>
      <item>Prepare segments (LASmod = 1.07) 17s</item>
      <item>Estimate local tissue thresholds (WM) 23s</item>
      <item>Estimate local tissue thresholds (GM) 31s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 31s</item>
      <item>118s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 10s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 19s</item>
      <item>Blood vessel detection 12s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.09) 29s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 6s</item>
      <item>85s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 40s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.09,0.99 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) 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 | 0.0900 0.0000 0.0900 | 32.0000</item>
      <item>2 | 2.50 | 0.0869 0.0013 0.0882 | 29.4886</item>
      <item>3 | 2.50 | 0.0861 0.0019 0.0880 | 26.9772</item>
      <item>4 | 2.50 | 0.0856 0.0022 0.0878 | 24.6107</item>
      <item>5 | 2.50 | 0.0853 0.0023 0.0876 | 22.6548</item>
      <item>6 | 2.50 | 0.0850 0.0024 0.0874 | 20.6989</item>
      <item>7 | 2.50 | 0.0847 0.0025 0.0872 | 18.9688</item>
      <item>8 | 2.50 | 0.0844 0.0026 0.0870 | 17.4455</item>
      <item>9 | 2.50 | 0.0841 0.0026 0.0867 | 15.9223</item>
      <item>10 | 2.50 | 0.0838 0.0027 0.0865 | 14.6627</item>
      <item>11 | 2.50 | 0.0835 0.0028 0.0862 | 13.4764</item>
      <item>12 | 2.50 | 0.0831 0.0028 0.0859 | 12.3015</item>
      <item>13 | 2.50 | 0.0828 0.0029 0.0857 | 11.3776</item>
      <item>14 | 2.50 | 0.0825 0.0029 0.0854 | 10.4537</item>
      <item>15 | 2.25 | 0.0828 0.0030 0.0858 | 9.5920</item>
      <item>16 | 2.25 | 0.0797 0.0045 0.0842 | 8.8725</item>
      <item>17 | 2.25 | 0.0786 0.0050 0.0836 | 8.1530</item>
      <item>18 | 2.25 | 0.0779 0.0052 0.0831 | 7.5234</item>
      <item>19 | 2.25 | 0.0774 0.0053 0.0826 | 6.9630</item>
      <item>20 | 2.25 | 0.0769 0.0053 0.0821 | 6.4027</item>
      <item>21 | 2.25 | 0.0764 0.0053 0.0817 | 5.9447</item>
      <item>22 | 2.25 | 0.0760 0.0053 0.0813 | 5.5083</item>
      <item>23 | 2.25 | 0.0756 0.0052 0.0808 | 5.0803</item>
      <item>24 | 2.25 | 0.0752 0.0053 0.0804 | 4.7404</item>
      <item>25 | 2.25 | 0.0748 0.0052 0.0800 | 4.4005</item>
      <item>29 | 2.00 | 0.0769 0.0041 0.0810 | 3.3283</item>
      <item>30 | 2.00 | 0.0737 0.0056 0.0793 | 3.1221</item>
      <item>43 | 1.75 | 0.0730 0.0031 0.0760 | 1.5785</item>
      <item>44 | 1.75 | 0.0678 0.0058 0.0736 | 1.5194</item>
      <item>45 | 1.75 | 0.0662 0.0067 0.0729 | 1.4626</item>
      <item>57 | 1.50 | 0.0650 0.0049 0.0698 | 1.0900</item>
      <item>58 | 1.50 | 0.0613 0.0073 0.0686 | 1.0730</item>
      <item>59 | 1.50 | 0.0601 0.0080 0.0682 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 180s</item>
      <item>Prepare output 12s</item>
      <item>192s</item>
      <item>Jacobian determinant (RMS): 0.010 0.035 0.058 0.079 0.106 | 0.113193</item>
      <item>Template Matching: 0.090 0.224 0.221 0.198 0.180 | 0.180437</item>
      <item>Write result maps: 33s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 51s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 54s</item>
      <item>131s</item>
      <item>Create initial surface 102s</item>
      <item>Topology correction: 115s</item>
      <item>Surface refinement: 106s</item>
      <item>Reduction of surface collisions with optimization: 88s</item>
      <item>Spherical mapping with areal smoothing 93s</item>
      <item>Spherical registration 290s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 53s</item>
      <item>111s</item>
      <item>Create initial surface 104s</item>
      <item>Topology correction: 121s</item>
      <item>Surface refinement: 109s</item>
      <item>Reduction of surface collisions with optimization: 91s</item>
      <item>Spherical mapping with areal smoothing 123s</item>
      <item>Spherical registration 329s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3639 0.6132 mm</item>
      <item>Surface intensity / position RMSE: 0.0728 / 0.0873</item>
      <item>Euler number / defect number / defect size: 28.0 / 16.0 / 1.42%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_20259/ds/sub-01/surf/lh.thickness.sub-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_20259/ds/sub-01/surf/rh.thickness.sub-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_20259/ds/sub-01/sub-01_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 2029s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 12s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 43s</item>
      <item>ROI estimation of 'lpba40' atlas 12s</item>
      <item>ROI estimation of 'hammers' atlas 30s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 11s</item>
      <item>ROI estimation of 'aal3' atlas 19s</item>
      <item>ROI estimation of 'mori' atlas 26s</item>
      <item>ROI estimation of 'anatomy3' atlas 38s</item>
      <item>ROI estimation of 'julichbrain' atlas 49s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 115s</item>
      <item>Write results 116s</item>
      <item>493s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_20259/ds/sub-01/report/catreport_sub-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 59 minute(s) and 53 second(s).</item>
      <item>Image Quality Rating (IQR): 86.39% (B)</item>
      <item>GM volume (GMV): 44.64% (788.37 / 1766.15 ml)</item>
      <item>GM thickness (GMT): 2.36 0.62 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_20259/ds/sub-01/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_20259/ds/sub-01/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_20259/ds/sub-01/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>