ds003949_ReproVBM/sub-325/report/cat_sub-325_ses-20100414_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <ll>-6.00204753875732</ll>
      <Affine_translation>[-1.00563233064323 -1.16569216492025 0.115577278584204]</Affine_translation>
      <Affine_rotation>[0.13762454907642 0.00831796645256359 0.105086061414734]</Affine_rotation>
      <Affine_scaling>[1.06936604142086 1.05217870684522 1.16499221222394]</Affine_scaling>
      <Affine_shearing>[0.011009714987608 -0.00590348827283239 0.0421589506180681]</Affine_shearing>
      <Affine0_translation>[-1.00563233064323 -1.16569216492025 0.115577278584204]</Affine0_translation>
      <Affine0_rotation>[0.13762454907642 0.00831796645256359 0.105086061414734]</Affine0_rotation>
      <Affine0_scaling>[1.06936604142086 1.05217870684522 1.16499221222394]</Affine0_scaling>
      <Affine0_shearing>[0.011009714987608 -0.00590348827283239 0.0421589506180681]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_41735/ds/sub-325</path>
      <file>sub-325_ses-20100414_T1w</file>
      <fname>/var/lib/condor/execute/dir_41735/ds/sub-325/sub-325_ses-20100414_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_41735/ds/sub-325/sub-325_ses-20100414_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_41735/ds/sub-325/mri/msub-325_ses-20100414_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_41735/ds/sub-325/mri/p0sub-325_ses-20100414_T1w.nii</Fp0>
      <fnames>..1735/ds/sub-325/sub-325_ses-20100414_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>24</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>164</SurfaceEulerNumber>
      <SurfaceDefectArea>4.72640643469003</SurfaceDefectArea>
      <SurfaceDefectNumber>72.5</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0919217169284821</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.212971240282059</SurfacePositionRMSE>
      <res_vx_vol>[3.89999814764538 0.558035770734873 0.558035709276551]</res_vx_vol>
      <res_vx_voli>[1.00000004023791 1.00000001882646 1.00000002885057]</res_vx_voli>
      <res_RMS>2.29730228208979</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[9.01500034332275 343.318725585938 685.855041503906 804.892700195312]</tissue_mn>
      <tissue_mnr>[0.011200251057744 0.426539748907089 0.852107405662537 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[197.109521044626 88.3335879878738 49.8143824899745 26.5916961007242]</tissue_std>
      <tissue_stdr>[0.24766306579113 0.110988892614841 0.0625904947519302 0.0334117859601974]</tissue_stdr>
      <contrast>120.386016845703</contrast>
      <contrastr>0.149567782878876</contrastr>
      <NCR>0.188767194747925</NCR>
      <ICR>0.22328981757164</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[7.79999629529076 1.11607154146975 1.1160714185531]</res_vx_vol>
      <res_RMS>4.59460456417958</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>5.83981657028198</contrastr>
      <NCR>3.04087281227112</NCR>
      <ICR>1.01361560821533</ICR>
      <SurfaceEulerNumber>9.26530612244898</SurfaceEulerNumber>
      <SurfaceDefectArea>2.18160160867251</SurfaceDefectArea>
      <SurfaceDefectNumber>4.625</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.83843433856964</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>4.25942516326904</SurfacePositionRMSE>
      <IQR>4.2323535872849</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>20220712-174141</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>164</SurfaceEulerNumber>
         <SurfaceDefectArea>4.72640643469003</SurfaceDefectArea>
         <SurfaceDefectNumber>72.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0919217169284821</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.212971240282059</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>164</EC_abs>
      <defect_size>4.72640643469003</defect_size>
      <vol_abs_CGW>[211.967559811586 588.308969368206 557.107880350655 0 0]</vol_abs_CGW>
      <vol_abs_WMH>2.82658064065553</vol_abs_WMH>
      <vol_rel_WMH>0.00208237299677938</vol_rel_WMH>
      <surf_TSA>1822.556638938</surf_TSA>
      <vol_TIV>1357.38440953045</vol_TIV>
      <vol_rel_CGW>[0.156158828938451 0.433413677980667 0.410427493080882 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.23400516161466 0.598145087172198]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.24614095687866 0.671967354654146 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.63029791916978 0.258041920062415 0.265558438012015;2.24609820725314 0.169531461228259 0.455079191698525;2.85518804332848 0.253022316077182 0.279362370289459]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.749791443227118 0.214949435367211 0.581896910650346;3.75621440828001 0.335032809575536 0.418103089349654]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.04314576185434</vol_TIV>
      <vol_rel_CGW>[0.654432990992301 5.63386634304358 5.22103974642389 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.20823729967794</vol_rel_WMH>
      <surf_TSA>8.59464919731875</surf_TSA>
      <SQR>4.86425588476173</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.277390518707483 1 1 5779.4622914203 0.261621676259769]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00926817953586578 0.0058502652682364 0.454344540834427]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[728.294977753499 543.905538013501 329.160934820517 729.376119025018 1770.61408115363 4401.67068501183]</SPMvols0>
      <SPMvols1>[598.662974200047 492.710639395057 222.908976459774 630.632361324359 1228.60187271834 4782.6735145861]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[455.707611083984 664.621215820312 758.424194335938]</T3th>
            <Tth>
               <T3th>[-341.680511474609 261.243408203125 15.3306646347046 455.707611083984 664.621215820312 758.424194335938 909.782470703125 1713.63146972656]</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>[0.0223069544881582 0.0848353281617165 0.093655601143837 0 0]</dtc>
         <ll>[0.0840857216910202 0 0.0840857216910202 0;0.19121900469172 0.0116601682940022 0.202879172985723 2486.50756835938;0.19121900469172 0.0116601682940022 0.202879172985723 2486.50756835938]</ll>
         <rmsdtc>[0.0471348501741886 0.10600008815527 0.118243470788002]</rmsdtc>
         <rmsgdt>[0.0334949381649494 0.0518461912870407 0.0632508248090744]</rmsgdt>
         <rmsdt>0.118243470788002</rmsdt>
         <dt>0.093655601143837</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>[0.0106127634644508 0.0419899635016918 0.0573883317410946 0.0670498609542847 0.074464850127697 0.0847839638590813]</dtc>
         <ll>[0.0859193181344823 0 0.0859193181344823 0;0.22130927960928 0.0166761675824176 0.237985447191697 8536.11328125;0.201208413052721 0.0180890634248491 0.21929747647757 13018.916015625;0.180804767952799 0.0196447091677703 0.200449477120569 21182.33984375;0.165475714449857 0.0224134048595395 0.187889119309396 39208.95703125;0.165475714449857 0.0224134048595395 0.187889119309396 39208.95703125]</ll>
         <rmsdtc>[0.0121909771114588 0.0450098104774952 0.0693347603082657 0.0961037203669548 0.123171612620354 0.13205286860466]</rmsdtc>
         <rmsgdt>[0.00379641936160624 0.0150128891691566 0.0319063998758793 0.054930504411459 0.0762315168976784 0.0825425684452057]</rmsgdt>
         <rmsdt>0.13205286860466</rmsdt>
         <dt>0.0847839638590813</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./dir_41735/ds/sub-325/sub-325_ses-20100414_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 38s</item>
      <item>Internal resampling (3.90x0.56x0.56mm &gt; 1.00x1.00x1.00mm): 2s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 8s</item>
      <item>Initial correction 7s</item>
      <item>Refine background 3s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 6s</item>
      <item>43s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 11s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 78s</item>
      <item>SPM preprocessing 1 (estimate 2): 83s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 17s</item>
      <item>Update Segmentation 22s</item>
      <item>Update Skull-Stripping 42s</item>
      <item>Update probability maps 12s</item>
      <item>93s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 12s</item>
      <item>Fast Optimized Shooting registration 44s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.27) 17s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 23s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 23s</item>
      <item>92s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 9s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 12s</item>
      <item>Blood vessel detection 10s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.03) 26s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 4s</item>
      <item>72s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 45s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</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>12s</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 | 0.0859 0.0000 0.0859 | 32.0000</item>
      <item>2 | 2.50 | 0.0830 0.0013 0.0842 | 29.4886</item>
      <item>3 | 2.50 | 0.0821 0.0019 0.0840 | 26.9772</item>
      <item>4 | 2.50 | 0.0817 0.0022 0.0838 | 24.6107</item>
      <item>5 | 2.50 | 0.0813 0.0024 0.0837 | 22.6548</item>
      <item>6 | 2.50 | 0.0810 0.0025 0.0835 | 20.6989</item>
      <item>7 | 2.50 | 0.0807 0.0026 0.0833 | 18.9688</item>
      <item>8 | 2.50 | 0.0804 0.0027 0.0831 | 17.4455</item>
      <item>9 | 2.50 | 0.0801 0.0028 0.0828 | 15.9223</item>
      <item>10 | 2.50 | 0.0797 0.0029 0.0826 | 14.6627</item>
      <item>11 | 2.50 | 0.0794 0.0030 0.0824 | 13.4764</item>
      <item>12 | 2.50 | 0.0790 0.0031 0.0821 | 12.3015</item>
      <item>13 | 2.50 | 0.0786 0.0032 0.0818 | 11.3776</item>
      <item>14 | 2.50 | 0.0783 0.0033 0.0816 | 10.4537</item>
      <item>15 | 2.25 | 0.0783 0.0034 0.0816 | 9.5920</item>
      <item>16 | 2.25 | 0.0751 0.0050 0.0801 | 8.8725</item>
      <item>17 | 2.25 | 0.0738 0.0056 0.0793 | 8.1530</item>
      <item>29 | 2.00 | 0.0749 0.0025 0.0775 | 3.3283</item>
      <item>30 | 2.00 | 0.0691 0.0050 0.0741 | 3.1221</item>
      <item>31 | 2.00 | 0.0671 0.0060 0.0731 | 2.9160</item>
      <item>43 | 1.75 | 0.0660 0.0035 0.0695 | 1.5785</item>
      <item>44 | 1.75 | 0.0617 0.0057 0.0674 | 1.5194</item>
      <item>45 | 1.75 | 0.0603 0.0065 0.0668 | 1.4626</item>
      <item>57 | 1.50 | 0.0593 0.0048 0.0641 | 1.0900</item>
      <item>58 | 1.50 | 0.0562 0.0068 0.0630 | 1.0730</item>
      <item>59 | 1.50 | 0.0552 0.0075 0.0626 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 266s</item>
      <item>Prepare output 12s</item>
      <item>278s</item>
      <item>Jacobian determinant (RMS): 0.012 0.045 0.069 0.096 0.123 | 0.132053</item>
      <item>Template Matching: 0.086 0.221 0.201 0.181 0.165 | 0.165476</item>
      <item>Write result maps: 113s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 45s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 55s</item>
      <item>127s</item>
      <item>Create initial surface 104s</item>
      <item>Topology correction: 124s</item>
      <item>Surface refinement: 102s</item>
      <item>Reduction of surface collisions with optimization: 87s</item>
      <item>Spherical mapping with areal smoothing 102s</item>
      <item>Spherical registration 293s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 41s</item>
      <item>CSF distance: 18s</item>
      <item>PBT2x thickness: 55s</item>
      <item>122s</item>
      <item>Create initial surface 100s</item>
      <item>Topology correction: 118s</item>
      <item>Surface refinement: 139s</item>
      <item>Reduction of surface collisions with optimization: 85s</item>
      <item>Spherical mapping with areal smoothing 102s</item>
      <item>Spherical registration 301s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.2344 0.5965 mm</item>
      <item>Surface intensity / position RMSE: 0.0919 / 0.2130</item>
      <item>Euler number / defect number / defect size: 164.0 / 72.5 / 4.73%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_41735/ds/sub-325/surf/lh.thickness.sub-325_ses-20100414_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_41735/ds/sub-325/surf/rh.thickness.sub-325_ses-20100414_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_41735/ds/sub-325/sub-325_ses-20100414_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 2025s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 11s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 40s</item>
      <item>ROI estimation of 'lpba40' atlas 11s</item>
      <item>ROI estimation of 'hammers' atlas 28s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 10s</item>
      <item>ROI estimation of 'aal3' atlas 16s</item>
      <item>ROI estimation of 'mori' atlas 24s</item>
      <item>ROI estimation of 'anatomy3' atlas 35s</item>
      <item>ROI estimation of 'julichbrain' atlas 46s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 74s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 112s</item>
      <item>Write results 114s</item>
      <item>451s</item>
      <item>Quality check: 13s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_41735/ds/sub-325/report/catreport_sub-325_ses-20100414_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 60 minute(s) and 19 second(s).</item>
      <item>Image Quality Rating (IQR): 62.68% (D-)</item>
      <item>GM volume (GMV): 43.34% (588.31 / 1357.38 ml)</item>
      <item>GM thickness (GMT): 2.23 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_41735/ds/sub-325/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_41735/ds/sub-325/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_41735/ds/sub-325/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>