ds003717_ReproVBM/sub-45/report/cat_sub-45_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <Affine_rotation>[0.181665418449697 -0.019188036262384 -0.040512881074555]</Affine_rotation>
      <Affine_scaling>[1.08224270913409 1.04236802812545 1.13420614303748]</Affine_scaling>
      <Affine_shearing>[0.0200833717073186 0.00075278229726137 -0.0115103905072078]</Affine_shearing>
      <Affine0_translation>[4.6218426038668 -24.7823491139854 2.07387786344827]</Affine0_translation>
      <Affine0_rotation>[0.181665418449697 -0.019188036262384 -0.040512881074555]</Affine0_rotation>
      <Affine0_scaling>[1.08224270913409 1.04236802812545 1.13420614303748]</Affine0_scaling>
      <Affine0_shearing>[0.0200833717073186 0.00075278229726137 -0.0115103905072078]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_28835/ds/sub-45</path>
      <file>sub-45_T1w</file>
      <fname>/var/lib/condor/execute/dir_28835/ds/sub-45/sub-45_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_28835/ds/sub-45/sub-45_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_28835/ds/sub-45/mri/msub-45_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_28835/ds/sub-45/mri/p0sub-45_T1w.nii</Fp0>
      <fnames>..28835/ds/sub-45/sub-45_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>
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            <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>
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   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>28</SurfaceEulerNumber>
      <SurfaceDefectArea>0.81426374630363</SurfaceDefectArea>
      <SurfaceDefectNumber>15</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0715722292661667</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0711714625358582</SurfacePositionRMSE>
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      <res_vx_voli>[0.799999955802358 0.800000028373785 0.799999966697779]</res_vx_voli>
      <res_RMS>0.799999983617636</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[22.8549995422363 291.323303222656 772.22509765625 1033.33410644531]</tissue_mn>
      <tissue_mnr>[0.0221177227795124 0.281925559043884 0.747314035892487 0.999999940395355]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.033454317599535 0.126364722847939 0.0896544009447098 0.0440389402210712]</tissue_stdr>
      <contrast>267.014770507812</contrast>
      <contrastr>0.258401185274124</contrastr>
      <NCR>0.111997678875923</NCR>
      <ICR>0.126518219709396</ICR>
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      <res_vx_vol>[1.59999991159708 1.60000005674757 1.59999993336117]</res_vx_vol>
      <res_RMS>1.59999996723527</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>4.20731544494629</contrastr>
      <NCR>1.93881249427795</NCR>
      <ICR>0.773606657981873</ICR>
      <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
      <SurfaceDefectArea>1.20356593657591</SurfaceDefectArea>
      <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.43144464492798</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.42342925071716</SurfacePositionRMSE>
      <IQR>1.82173117746165</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>20220709-214413</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>28</SurfaceEulerNumber>
         <SurfaceDefectArea>0.81426374630363</SurfaceDefectArea>
         <SurfaceDefectNumber>15</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0715722292661667</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0711714625358582</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>28</EC_abs>
      <defect_size>0.81426374630363</defect_size>
      <vol_abs_CGW>[230.53380858857 684.701886863903 475.885508659365 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.369342722417588</vol_abs_WMH>
      <vol_rel_WMH>0.00026550003071328</vol_rel_WMH>
      <surf_TSA>1943.46306318775</surf_TSA>
      <vol_TIV>1391.12120411184</vol_TIV>
      <vol_rel_CGW>[0.165717989135069 0.49219427095215 0.342087739912781 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.49782780444921 0.577808137413491]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.50186467170715 0.693389223390351 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.95140421363083 0.231720955562178 0.291182136658126;2.5232870197492 0.162722450805682 0.441637049140721;3.13015285087916 0.24815203767499 0.267180814201153]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.874681293494285 0.392916204459427 0.563048994729651;3.98338162438369 0.308526185041945 0.436951005270349]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.00187796528544</vol_TIV>
      <vol_rel_CGW>[0.826113310615464 6.68955228003143 3.99367348981288 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.02655000307133</vol_rel_WMH>
      <surf_TSA>8.61816055573236</surf_TSA>
      <SQR>5.48144171476751</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.0802021233974359 15 13975 9403.65971029679 0.30008230160128]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.026075666770339 0.0267862044274807 0.146996363997459]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[789.105794240945 440.669857676776 344.541221070001 568.051048662445 1606.91514800555 7009.64369592322]</SPMvols0>
      <SPMvols1>[703.777242806256 416.019261794431 224.928820446484 465.435302179518 1334.36225895413 7079.14144525553]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[336.796295166016 767.836975097656 1018.29962158203]</T3th>
            <Tth>
               <T3th>[0 0 28.2766017913818 336.796295166016 767.836975097656 1018.29962158203 1359.05126953125 2043.84362792969]</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>[0.0244179181754589 0.085069939494133 0.0942409187555313 0 0]</dtc>
         <ll>[0.0859446317589536 0 0.0859446317589536 0;0.192554652476225 0.0116257684714511 0.204180420947676 2479.171875;0.192554652476225 0.0116257684714511 0.204180420947676 2479.171875]</ll>
         <rmsdtc>[0.0519540756940842 0.109662845730782 0.120615147054195]</rmsdtc>
         <rmsgdt>[0.0369420759379864 0.0468660891056061 0.0576371438801289]</rmsgdt>
         <rmsdt>0.120615147054195</rmsdt>
         <dt>0.0942409187555313</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>[0.0119901411235332 0.0450840443372726 0.0625731274485588 0.0706959441304207 0.0771269351243973 0.0870979353785515]</dtc>
         <ll>[0.0853202999495605 0 0.0853202999495605 0;0.21784304029304 0.0167983001373626 0.234641340430403 8598.6298828125;0.194005227959239 0.0186712923016429 0.212676520260882 13437.953125;0.174019519193673 0.0199198274530916 0.193939346646764 21478.9921875;0.157103779940355 0.0228101787846707 0.179913958725026 39903.0546875;0.157103779940355 0.0228101787846707 0.179913958725026 39903.0546875]</ll>
         <rmsdtc>[0.0137055907398462 0.0504926182329655 0.0737802684307098 0.0994182676076889 0.121558383107185 0.128531411290169]</rmsdtc>
         <rmsgdt>[0.00352695793844759 0.0136070372536778 0.0293200518935919 0.0497360229492188 0.0674427524209023 0.0726691335439682]</rmsgdt>
         <rmsdt>0.128531411290169</rmsdt>
         <dt>0.0870979353785515</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_28835/ds/sub-45/sub-45_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 205s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 11s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 10s</item>
      <item>Refine background 5s</item>
      <item>Final correction 9s</item>
      <item>Final scaling 13s</item>
      <item>68s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 12s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 128s</item>
      <item>SPM preprocessing 1 (estimate 2): 68s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 29s</item>
      <item>Update Segmentation 32s</item>
      <item>Update Skull-Stripping 70s</item>
      <item>Update probability maps 14s</item>
      <item>145s</item>
      <item>Global intensity correction: 28s</item>
      <item>SANLM denoising after intensity normalization (medium): 44s</item>
      <item>Fast Optimized Shooting registration 41s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 8s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 26s</item>
      <item>Estimate local tissue thresholds (WM) 31s</item>
      <item>Estimate local tissue thresholds (GM) 45s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 63s</item>
      <item>182s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 12s</item>
      <item>Major structures 6s</item>
      <item>Ventricle detection 24s</item>
      <item>Blood vessel detection 17s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.06) 49s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 3s</item>
      <item>Side alignment 6s</item>
      <item>Final corrections 7s</item>
      <item>125s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 51s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 7s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>18s</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 | 0.0853 0.0000 0.0853 | 32.0000</item>
      <item>2 | 2.50 | 0.0818 0.0014 0.0832 | 29.4886</item>
      <item>3 | 2.50 | 0.0807 0.0022 0.0829 | 26.9772</item>
      <item>4 | 2.50 | 0.0802 0.0025 0.0827 | 24.6107</item>
      <item>5 | 2.50 | 0.0797 0.0027 0.0825 | 22.6548</item>
      <item>6 | 2.50 | 0.0794 0.0028 0.0822 | 20.6989</item>
      <item>7 | 2.50 | 0.0790 0.0030 0.0820 | 18.9688</item>
      <item>8 | 2.50 | 0.0786 0.0031 0.0817 | 17.4455</item>
      <item>9 | 2.50 | 0.0782 0.0032 0.0814 | 15.9223</item>
      <item>10 | 2.50 | 0.0778 0.0034 0.0811 | 14.6627</item>
      <item>11 | 2.50 | 0.0774 0.0035 0.0808 | 13.4764</item>
      <item>12 | 2.50 | 0.0769 0.0036 0.0805 | 12.3015</item>
      <item>13 | 2.50 | 0.0765 0.0037 0.0802 | 11.3776</item>
      <item>14 | 2.50 | 0.0760 0.0038 0.0798 | 10.4537</item>
      <item>15 | 2.25 | 0.0760 0.0039 0.0799 | 9.5920</item>
      <item>16 | 2.25 | 0.0726 0.0056 0.0782 | 8.8725</item>
      <item>29 | 2.00 | 0.0735 0.0025 0.0761 | 3.3283</item>
      <item>30 | 2.00 | 0.0670 0.0052 0.0721 | 3.1221</item>
      <item>31 | 2.00 | 0.0647 0.0062 0.0709 | 2.9160</item>
      <item>43 | 1.75 | 0.0637 0.0036 0.0673 | 1.5785</item>
      <item>44 | 1.75 | 0.0595 0.0059 0.0653 | 1.5194</item>
      <item>45 | 1.75 | 0.0580 0.0066 0.0646 | 1.4626</item>
      <item>57 | 1.50 | 0.0567 0.0049 0.0615 | 1.0900</item>
      <item>58 | 1.50 | 0.0535 0.0069 0.0604 | 1.0730</item>
      <item>59 | 1.50 | 0.0524 0.0076 0.0600 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 155s</item>
      <item>Prepare output 15s</item>
      <item>170s</item>
      <item>Jacobian determinant (RMS): 0.014 0.050 0.074 0.099 0.122 | 0.128531</item>
      <item>Template Matching: 0.085 0.218 0.194 0.174 0.157 | 0.157104</item>
      <item>Write result maps: 38s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 29s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 41s</item>
      <item>90s</item>
      <item>Create initial surface 67s</item>
      <item>Topology correction: 88s</item>
      <item>Surface refinement: 69s</item>
      <item>Reduction of surface collisions with optimization: 68s</item>
      <item>Spherical mapping with areal smoothing 76s</item>
      <item>Spherical registration 287s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 32s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 42s</item>
      <item>93s</item>
      <item>Create initial surface 70s</item>
      <item>Topology correction: 91s</item>
      <item>Surface refinement: 100s</item>
      <item>Reduction of surface collisions with optimization: 64s</item>
      <item>Spherical mapping with areal smoothing 76s</item>
      <item>Spherical registration 303s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4978 0.5778 mm</item>
      <item>Surface intensity / position RMSE: 0.0716 / 0.0712</item>
      <item>Euler number / defect number / defect size: 28.0 / 15.0 / 0.81%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28835/ds/sub-45/surf/lh.thickness.sub-45_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28835/ds/sub-45/surf/rh.thickness.sub-45_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_28835/ds/sub-45/sub-45_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1651s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 15s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 53s</item>
      <item>ROI estimation of 'lpba40' atlas 15s</item>
      <item>ROI estimation of 'hammers' atlas 37s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 13s</item>
      <item>ROI estimation of 'aal3' atlas 21s</item>
      <item>ROI estimation of 'mori' atlas 30s</item>
      <item>ROI estimation of 'anatomy3' atlas 44s</item>
      <item>ROI estimation of 'julichbrain' atlas 60s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 93s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 139s</item>
      <item>Write results 140s</item>
      <item>589s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_28835/ds/sub-45/report/catreport_sub-45_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 62 minute(s) and 17 second(s).</item>
      <item>Image Quality Rating (IQR): 86.78% (B+)</item>
      <item>GM volume (GMV): 49.22% (684.70 / 1391.12 ml)</item>
      <item>GM thickness (GMT): 2.50 0.58 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_28835/ds/sub-45/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_28835/ds/sub-45/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_28835/ds/sub-45/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>