ds003799_ReproVBM/sub-season102/report/cat_sub-season102_ses-1_acq-MPrageHiRes_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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      <ll>-6.52135038375854</ll>
      <Affine_translation>[-2.89229012993834 -10.760035723789 -42.1278630686357]</Affine_translation>
      <Affine_rotation>[0.113104808324257 -0.0302373243682009 0.0585427003126773]</Affine_rotation>
      <Affine_scaling>[1.04300541115833 0.971024440745681 1.08940675120755]</Affine_scaling>
      <Affine_shearing>[-0.00654065507090229 0.00474731201293253 0.0565624155234998]</Affine_shearing>
      <Affine0_translation>[-2.89229012993834 -10.760035723789 -42.1278630686357]</Affine0_translation>
      <Affine0_rotation>[0.113104808324257 -0.0302373243682009 0.0585427003126773]</Affine0_rotation>
      <Affine0_scaling>[1.04300541115833 0.971024440745681 1.08940675120755]</Affine0_scaling>
      <Affine0_shearing>[-0.00654065507090229 0.00474731201293253 0.0565624155234998]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_11856/ds/sub-season102</path>
      <file>sub-season102_ses-1_acq-MPrageHiRes_T1w</file>
      <fname>/var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_11856/ds/sub-season102/mri/msub-season102_ses-1_acq-MPrageHiRes_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_11856/ds/sub-season102/mri/p0sub-season102_ses-1_acq-MPrageHiRes_T1w.nii</Fp0>
      <fnames>..s/sub-season102/..son102_ses-1_acq-MPrageHiRes_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>20</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>6</SurfaceEulerNumber>
      <SurfaceDefectArea>0.0897510648877681</SurfaceDefectArea>
      <SurfaceDefectNumber>7</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0618025064468384</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0592489391565323</SurfacePositionRMSE>
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      <res_vx_voli>[0.880001084567847 0.874999984718353 0.875000034588071]</res_vx_voli>
      <res_RMS>0.876670203858164</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[9.64000034332275 326.269470214844 874.493530273438 1241.46374511719]</tissue_mn>
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      <NCR>0.104034133255482</NCR>
      <ICR>0.342988163232803</ICR>
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   <qualityratings>
      <res_vx_vol>[1.76000217027721 1.74999997022818 1.75000006308956]</res_vx_vol>
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      <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>3.61471247673035</contrastr>
      <NCR>1.82449221611023</NCR>
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      <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
      <SurfaceDefectArea>1.02243776622194</SurfaceDefectArea>
      <SurfaceDefectNumber>1.35</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.23605012893677</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.184978723526</SurfacePositionRMSE>
      <IQR>1.7913830467905</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>20220712-181228</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>6</SurfaceEulerNumber>
         <SurfaceDefectArea>0.0897510648877681</SurfaceDefectArea>
         <SurfaceDefectNumber>7</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0618025064468384</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0592489391565323</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>6</EC_abs>
      <defect_size>0.0897510648877681</defect_size>
      <vol_abs_CGW>[253.981359288085 793.407124703125 619.409106197429 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.23115945138478</vol_abs_WMH>
      <vol_rel_WMH>0.00073863764780548</vol_rel_WMH>
      <surf_TSA>2227.49724892944</surf_TSA>
      <vol_TIV>1666.79759018864</vol_TIV>
      <vol_rel_CGW>[0.152376845744864 0.476006882523349 0.371616271731787 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.56530736488118 0.590342953239731]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.5663685798645 0.710094127323198 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.97784313055483 0.238481263332384 0.283440160295794;2.57046571919303 0.168152003110027 0.424839206048731;3.18579730001513 0.249485474608859 0.291720633655475]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.924061056658816 0.395862012821314 0.545714030862546;4.08931978283007 0.365990521139158 0.454285969137454]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.52051032975925</vol_TIV>
      <vol_rel_CGW>[0.586509442256893 6.39883050508889 4.52399913311399 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.07386376478055</vol_rel_WMH>
      <surf_TSA>8.62394141664225</surf_TSA>
      <SQR>5.27250213487135</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.254767486027309 1 1 7370.87532818575 0.307907428196062]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00731452461332083 0 0.338345289230347]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[948.744968862865 547.195195946309 413.744959137307 513.151162864622 1917.26843543053 6125.72857048625]</SPMvols0>
      <SPMvols1>[838.228957178395 519.561643225367 256.453353781424 530.577728476709 1415.50074754776 6330.42361018354]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[410.561401367188 906.107604980469 1230.60595703125]</T3th>
            <Tth>
               <T3th>[0 0 23.1649742126465 410.561401367188 906.107604980469 1230.60595703125 1640.62817382812 2694.13354492188]</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>[0.0204503294080496 0.0674047768115997 0.0731644853949547 0 0]</dtc>
         <ll>[0.0813701457145358 0 0.0813701457145358 0;0.194975707568184 0.00893423394137929 0.203909941509563 1905.20751953125;0.194975707568184 0.00893423394137929 0.203909941509563 1905.20751953125]</ll>
         <rmsdtc>[0.0431797280907631 0.0852848887443542 0.0939331203699112]</rmsdtc>
         <rmsgdt>[0.0306115243583918 0.0394845344126225 0.0484254583716393]</rmsgdt>
         <rmsdt>0.0939331203699112</rmsdt>
         <dt>0.0731644853949547</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>[0.00929920095950365 0.0328448861837387 0.0448141135275364 0.0525176003575325 0.0585501790046692 0.0651033222675323]</dtc>
         <ll>[0.0816123525528528 0 0.0816123525528528 0;0.215070283882784 0.0117880713904151 0.226858355273199 6034.01904296875;0.196326295275054 0.0149142881979181 0.211240583472973 10733.9921875;0.176263285724752 0.0177948490733321 0.194058134798084 19187.6875;0.158677254533533 0.0209594231052852 0.179636677638818 36665.4296875;0.158677254533533 0.0209594231052852 0.179636677638818 36665.4296875]</ll>
         <rmsdtc>[0.0106100142002106 0.0368716269731522 0.0535049811005592 0.0764260515570641 0.0994382575154305 0.106667101383209]</rmsdtc>
         <rmsgdt>[0.00309705315157771 0.0116917649284005 0.0260947942733765 0.0464084297418594 0.0647245943546295 0.0704523846507072]</rmsgdt>
         <rmsdt>0.106667101383209</rmsdt>
         <dt>0.0651033222675323</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-season102_ses-1_acq-MPrageHiRes_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 28s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 10s</item>
      <item>Estimate background 12s</item>
      <item>Initial correction 24s</item>
      <item>Refine background 5s</item>
      <item>Final correction 18s</item>
      <item>Final scaling 11s</item>
      <item>90s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 15s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 139s</item>
      <item>SPM preprocessing 1 (estimate 2): 122s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 27s</item>
      <item>Update Segmentation 34s</item>
      <item>Update Skull-Stripping 69s</item>
      <item>Update probability maps 13s</item>
      <item>144s</item>
      <item>Global intensity correction: 26s</item>
      <item>SANLM denoising after intensity normalization (medium): 14s</item>
      <item>Fast Optimized Shooting registration 47s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 9s</item>
      <item>Prepare partitions 4s</item>
      <item>Prepare segments (LASmod = 1.00) 29s</item>
      <item>Estimate local tissue thresholds (WM) 29s</item>
      <item>Estimate local tissue thresholds (GM) 40s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 34s</item>
      <item>151s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 15s</item>
      <item>Major structures 7s</item>
      <item>Ventricle detection 28s</item>
      <item>Blood vessel detection 18s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.03) 54s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 3s</item>
      <item>Side alignment 8s</item>
      <item>Final corrections 8s</item>
      <item>142s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 68s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 8s</item>
      <item>Level 1 cleanup (brain masking) 5s</item>
      <item>Level 2 cleanup (CSF correction) 3s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
      <item>21s</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 | 0.0816 0.0000 0.0816 | 32.0000</item>
      <item>2 | 2.50 | 0.0793 0.0011 0.0803 | 29.4886</item>
      <item>3 | 2.50 | 0.0786 0.0016 0.0802 | 26.9772</item>
      <item>4 | 2.50 | 0.0783 0.0018 0.0801 | 24.6107</item>
      <item>5 | 2.50 | 0.0780 0.0019 0.0799 | 22.6548</item>
      <item>6 | 2.50 | 0.0778 0.0020 0.0798 | 20.6989</item>
      <item>7 | 2.50 | 0.0775 0.0021 0.0796 | 18.9688</item>
      <item>8 | 2.50 | 0.0773 0.0022 0.0795 | 17.4455</item>
      <item>9 | 2.50 | 0.0770 0.0022 0.0793 | 15.9223</item>
      <item>10 | 2.50 | 0.0767 0.0023 0.0791 | 14.6627</item>
      <item>11 | 2.50 | 0.0765 0.0024 0.0789 | 13.4764</item>
      <item>12 | 2.50 | 0.0762 0.0025 0.0787 | 12.3015</item>
      <item>13 | 2.50 | 0.0759 0.0025 0.0785 | 11.3776</item>
      <item>14 | 2.50 | 0.0757 0.0026 0.0783 | 10.4537</item>
      <item>15 | 2.25 | 0.0743 0.0027 0.0769 | 9.5920</item>
      <item>16 | 2.25 | 0.0717 0.0039 0.0756 | 8.8725</item>
      <item>29 | 2.00 | 0.0730 0.0018 0.0748 | 3.3283</item>
      <item>30 | 2.00 | 0.0674 0.0040 0.0714 | 3.1221</item>
      <item>31 | 2.00 | 0.0654 0.0050 0.0704 | 2.9160</item>
      <item>43 | 1.75 | 0.0646 0.0029 0.0674 | 1.5785</item>
      <item>44 | 1.75 | 0.0602 0.0051 0.0653 | 1.5194</item>
      <item>45 | 1.75 | 0.0588 0.0059 0.0647 | 1.4626</item>
      <item>57 | 1.50 | 0.0571 0.0043 0.0613 | 1.0900</item>
      <item>58 | 1.50 | 0.0539 0.0063 0.0603 | 1.0730</item>
      <item>59 | 1.50 | 0.0529 0.0070 0.0599 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 225s</item>
      <item>Prepare output 14s</item>
      <item>239s</item>
      <item>Jacobian determinant (RMS): 0.011 0.037 0.054 0.076 0.099 | 0.106667</item>
      <item>Template Matching: 0.082 0.215 0.196 0.176 0.159 | 0.158677</item>
      <item>Write result maps: 43s</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: 25s</item>
      <item>PBT2x thickness: 65s</item>
      <item>150s</item>
      <item>Create initial surface 111s</item>
      <item>Topology correction: 126s</item>
      <item>Surface refinement: 113s</item>
      <item>Reduction of surface collisions with optimization: 112s</item>
      <item>Spherical mapping with areal smoothing 112s</item>
      <item>Spherical registration 264s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 43s</item>
      <item>CSF distance: 21s</item>
      <item>PBT2x thickness: 63s</item>
      <item>137s</item>
      <item>Create initial surface 111s</item>
      <item>Topology correction: 126s</item>
      <item>Surface refinement: 122s</item>
      <item>Reduction of surface collisions with optimization: 110s</item>
      <item>Spherical mapping with areal smoothing 109s</item>
      <item>Spherical registration 258s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5653 0.5902 mm</item>
      <item>Surface intensity / position RMSE: 0.0618 / 0.0592</item>
      <item>Euler number / defect number / defect size: 6.0 / 7.0 / 0.09%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_11856/ds/sub-season102/surf/lh.thickness.sub-season102_ses-1_acq-MPrageHiRes_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_11856/ds/sub-season102/surf/rh.thickness.sub-season102_ses-1_acq-MPrageHiRes_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_11856/ds/sub-season102/sub-season102_ses-1_acq-MPrageHiRes_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 2086s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 17s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 65s</item>
      <item>ROI estimation of 'lpba40' atlas 19s</item>
      <item>ROI estimation of 'hammers' atlas 46s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 16s</item>
      <item>ROI estimation of 'aal3' atlas 26s</item>
      <item>ROI estimation of 'mori' atlas 39s</item>
      <item>ROI estimation of 'anatomy3' atlas 56s</item>
      <item>ROI estimation of 'julichbrain' atlas 76s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 34s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 148s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 220s</item>
      <item>Write results 222s</item>
      <item>812s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_11856/ds/sub-season102/report/catreport_sub-season102_ses-1_acq-MPrageHiRes_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 72 minute(s) and 38 second(s).</item>
      <item>Image Quality Rating (IQR): 87.09% (B+)</item>
      <item>GM volume (GMV): 47.60% (793.41 / 1666.80 ml)</item>
      <item>GM thickness (GMT): 2.57 0.59 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_11856/ds/sub-season102/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>