CORR_cat12.8.1/Utah_1/sub-0026043/ses-2/report/cat_sub-0026043_ses-2_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_rotation>[0.107277214483709 0.0533424333809597 -0.0225957398048394]</Affine_rotation>
      <Affine_scaling>[1.03165093110903 0.948783488661654 1.04548040344574]</Affine_scaling>
      <Affine_shearing>[0.00276948675606707 -0.00663352187646533 0.0321487518554741]</Affine_shearing>
      <Affine0_translation>[3.97740691068966 -51.589014828542 -5.44642928164551]</Affine0_translation>
      <Affine0_rotation>[0.107277214483709 0.0533424333809597 -0.0225957398048394]</Affine0_rotation>
      <Affine0_scaling>[1.03165093110903 0.948783488661654 1.04548040344574]</Affine0_scaling>
      <Affine0_shearing>[0.00276948675606707 -0.00663352187646533 0.0321487518554741]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2</path>
      <file>sub-0026043_ses-2_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/mri/msub-0026043_ses-2_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/mri/p0sub-0026043_ses-2_run-1_T1w.nii</Fp0>
      <fnames>../Utah_1/sub-0026043/ses-2/sub-0026043_ses-2_run-1_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_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</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>
            <tr>
               <td>/var/lib/condor/execute/dir_2624533/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</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>
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         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>14</SurfaceEulerNumber>
      <SurfaceDefectArea>0.597511053149701</SurfaceDefectArea>
      <SurfaceDefectNumber>9</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0661619380116463</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0705456808209419</SurfacePositionRMSE>
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      <res_vx_voli>[0.79999995841116 0.500000002027555 0.799999985521795]</res_vx_voli>
      <res_RMS>0.804155868021604</res_RMS>
      <res_BB>NaN</res_BB>
      <tissue_mn>[23.4209995269775 53.7519989013672 225.520004272461 369.720001220703]</tissue_mn>
      <tissue_mnr>[0.0633479356765747 0.145385697484016 0.609975099563599 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
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      <tissue_stdr>[0.0332135632634163 0.114564277231693 0.116096392273903 0.0702471807599068]</tissue_stdr>
      <contrast>129.421493530273</contrast>
      <contrastr>0.350052714347839</contrastr>
      <res_ECR>0.342326521873474</res_ECR>
      <NCR>0.145379602909088</NCR>
      <ICR>0</ICR>
   </qualitymeasures>
   <qualityratings>
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      <res_RMS>1.60831173604321</res_RMS>
      <res_ECR>2.64452314376831</res_ECR>
      <res_BB>NaN</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>2.83254241943359</contrastr>
      <NCR>2.41802477836609</NCR>
      <ICR>0.5</ICR>
      <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
      <SurfaceDefectArea>1.14937776328743</SurfaceDefectArea>
      <SurfaceDefectNumber>1.45</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.3232387304306</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.41091358661652</SurfacePositionRMSE>
      <SIQR>2.42650295478917</SIQR>
      <IQR>2.22778209808669</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
         <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>2040</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>20231031-001416</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>14</SurfaceEulerNumber>
         <SurfaceDefectArea>0.597511053149701</SurfaceDefectArea>
         <SurfaceDefectNumber>9</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0661619380116463</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0705456808209419</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>14</EC_abs>
      <defect_size>0.597511053149701</defect_size>
      <vol_abs_CGW>[396.605654753821 798.122379301017 625.753366682319 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.21383395906781</vol_abs_WMH>
      <vol_rel_WMH>0.000666765372376943</vol_rel_WMH>
      <surf_TSA>2288.80301958416</surf_TSA>
      <vol_TIV>1820.48140073716</vol_TIV>
      <vol_rel_CGW>[0.217857570307077 0.438412817059179 0.343729612633744 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.48245012721041 0.597255170651757]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.49862766265869 0.714282216393919 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.8932765840551 0.244636350625704 0.28563401284829;2.50580120530916 0.171774136724094 0.427224542502553;3.12324069515071 0.249441618024966 0.287141444649157]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.835698634257609 0.377783908488569 0.592146552455262;3.9855093044262 0.341068415842581 0.407853447544738]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>4.23638076185221</vol_TIV>
      <vol_rel_CGW>[1.76252820235411 5.72364973166629 4.02316114643937 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06667653723769</vol_rel_WMH>
      <surf_TSA>8.62398130399869</surf_TSA>
      <SQR>4.71463464304106</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11796.4797613106 0.395480862891463]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00126425817143172 0.00103956880047917 0.0294565875083208]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[996.696569169814 532.581124991224 804.073363692395 430.869947393355 1038.61997346049 8670.23030563361]</SPMvols0>
      <SPMvols1>[831.597088933863 505.893150596533 449.826586769124 422.267154549621 921.932399047571 8665.0350080943]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[80.7192001342773 230.497497558594 373.517303466797]</T3th>
            <Tth>
               <T3th>[-117.081878662109 -52.2063903808594 9.50435161590576 80.7192001342773 230.497497558594 373.517303466797 519.916381835938 962.813049316406]</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>[0.0247680637985468 0.0877955034375191 0.0981742963194847 0 0]</dtc>
         <ll>[0.0919332576780712 0 0.0919332576780712 0;0.209301072724011 0.0124238942708431 0.221724966994855 2649.37060546875;0.209301072724011 0.0124238942708431 0.221724966994855 2649.37060546875]</ll>
         <rmsdtc>[0.0558146350085735 0.115472368896008 0.127834111452103]</rmsdtc>
         <rmsgdt>[0.0400100536644459 0.052115723490715 0.064171127974987]</rmsgdt>
         <rmsdt>0.127834111452103</rmsdt>
         <dt>0.0981742963194847</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>[0.0113629661500454 0.0486531369388103 0.057738084346056 0.066001832485199 0.07288508862257 0.0817316994071007]</dtc>
         <ll>[0.0903414732625551 0 0.0903414732625551 0;0.223942521367521 0.0187095314407814 0.242652052808303 9576.94140625;0.21107394780829 0.0193332202129984 0.230407168021288 13914.3505859375;0.191121274363055 0.0209010849651108 0.212022359328166 22537.0546875;0.172219332661847 0.0244852110144436 0.196704543676291 42833.27734375;0.172219332661847 0.0244852110144436 0.196704543676291 42833.27734375]</ll>
         <rmsdtc>[0.0131491394713521 0.0470572896301746 0.0710624828934669 0.0922369733452797 0.11596766859293 0.122991427779198]</rmsdtc>
         <rmsgdt>[0.00341040664352477 0.0131064923480153 0.0290080811828375 0.0495313890278339 0.0708552896976471 0.0766235068440437]</rmsgdt>
         <rmsdt>0.122991427779198</rmsdt>
         <dt>0.0817316994071007</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 218s</item>
      <item>Internal resampling (1.20x0.50x0.50mm &gt; 0.80x0.50x0.80mm): 3s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 3s</item>
      <item>Final correction 7s</item>
      <item>Final scaling 11s</item>
      <item>57s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 26s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 63s</item>
      <item>SPM preprocessing 1 (estimate 2): 35s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 37s</item>
      <item>Update Segmentation 44s</item>
      <item>Update Skull-Stripping 104s</item>
      <item>Update probability maps 19s</item>
      <item>205s</item>
      <item>Global intensity correction: 33s</item>
      <item>SANLM denoising after intensity normalization (medium): 154s</item>
      <item>Fast Optimized Shooting registration 39s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 8s</item>
      <item>Prepare partitions 6s</item>
      <item>Prepare segments (LASmod = 1.07) 39s</item>
      <item>Estimate local tissue thresholds (WM) 29s</item>
      <item>Estimate local tissue thresholds (GM) 39s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 137s</item>
      <item>266s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 13s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 12s</item>
      <item>Blood vessel detection 12s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.19) 24s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 10s</item>
      <item>82s</item>
      <item>Blood vessel correction (BVCstr=0.50): 4s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 73s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.37 0.05,0.68 0.08,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 10s</item>
      <item>Level 1 cleanup (brain masking) 6s</item>
      <item>Level 2 cleanup (CSF correction) 3s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
      <item>27s</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 | 0.0903 0.0000 0.0903 | 32.0000</item>
      <item>2 | 2.50 | 0.0869 0.0014 0.0883 | 29.4886</item>
      <item>3 | 2.50 | 0.0859 0.0022 0.0880 | 26.9772</item>
      <item>4 | 2.50 | 0.0853 0.0025 0.0878 | 24.6107</item>
      <item>5 | 2.50 | 0.0849 0.0027 0.0876 | 22.6548</item>
      <item>6 | 2.50 | 0.0846 0.0028 0.0874 | 20.6989</item>
      <item>7 | 2.50 | 0.0842 0.0029 0.0871 | 18.9688</item>
      <item>8 | 2.50 | 0.0838 0.0030 0.0869 | 17.4455</item>
      <item>9 | 2.50 | 0.0835 0.0031 0.0866 | 15.9223</item>
      <item>10 | 2.50 | 0.0830 0.0033 0.0863 | 14.6627</item>
      <item>11 | 2.50 | 0.0827 0.0034 0.0860 | 13.4764</item>
      <item>12 | 2.50 | 0.0822 0.0034 0.0857 | 12.3015</item>
      <item>13 | 2.50 | 0.0818 0.0036 0.0854 | 11.3776</item>
      <item>14 | 2.50 | 0.0814 0.0036 0.0850 | 10.4537</item>
      <item>15 | 2.25 | 0.0814 0.0037 0.0852 | 9.5920</item>
      <item>16 | 2.25 | 0.0780 0.0054 0.0834 | 8.8725</item>
      <item>17 | 2.25 | 0.0767 0.0060 0.0826 | 8.1530</item>
      <item>18 | 2.25 | 0.0758 0.0062 0.0820 | 7.5234</item>
      <item>19 | 2.25 | 0.0752 0.0063 0.0815 | 6.9630</item>
      <item>20 | 2.25 | 0.0746 0.0062 0.0809 | 6.4027</item>
      <item>29 | 2.00 | 0.0769 0.0035 0.0803 | 3.3283</item>
      <item>30 | 2.00 | 0.0720 0.0057 0.0777 | 3.1221</item>
      <item>31 | 2.00 | 0.0704 0.0064 0.0768 | 2.9160</item>
      <item>43 | 1.75 | 0.0699 0.0036 0.0735 | 1.5785</item>
      <item>44 | 1.75 | 0.0652 0.0061 0.0714 | 1.5194</item>
      <item>45 | 1.75 | 0.0637 0.0070 0.0707 | 1.4626</item>
      <item>57 | 1.50 | 0.0622 0.0050 0.0672 | 1.0900</item>
      <item>58 | 1.50 | 0.0586 0.0074 0.0660 | 1.0730</item>
      <item>59 | 1.50 | 0.0574 0.0082 0.0656 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 115s</item>
      <item>Prepare output 16s</item>
      <item>131s</item>
      <item>Jacobian determinant (RMS): 0.013 0.047 0.071 0.092 0.116 | 0.122991</item>
      <item>Template Matching: 0.090 0.224 0.211 0.191 0.172 | 0.172219</item>
      <item>Write result maps: 143s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 37s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 36s</item>
      <item>91s</item>
      <item>Create initial surface 68s</item>
      <item>Topology correction: 75s</item>
      <item>Surface refinement: 72s</item>
      <item>Reduction of surface collisions with optimization: 59s</item>
      <item>Spherical mapping with areal smoothing 69s</item>
      <item>Spherical registration 196s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 36s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 36s</item>
      <item>91s</item>
      <item>Create initial surface 66s</item>
      <item>Topology correction: 76s</item>
      <item>Surface refinement: 70s</item>
      <item>Reduction of surface collisions with optimization: 58s</item>
      <item>Spherical mapping with areal smoothing 81s</item>
      <item>Spherical registration 196s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4824 0.5970 mm</item>
      <item>Surface intensity / position RMSE: 0.0662 / 0.0705</item>
      <item>Euler number / defect number / defect size: 14.0 / 9.0 / 0.60%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/surf/lh.thickness.sub-0026043_ses-2_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/surf/rh.thickness.sub-0026043_ses-2_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/sub-0026043_ses-2_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1395s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 20s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 72s</item>
      <item>ROI estimation of 'lpba40' atlas 21s</item>
      <item>ROI estimation of 'hammers' atlas 50s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 17s</item>
      <item>ROI estimation of 'aal3' atlas 29s</item>
      <item>ROI estimation of 'mori' atlas 42s</item>
      <item>ROI estimation of 'anatomy3' atlas 61s</item>
      <item>ROI estimation of 'julichbrain' atlas 79s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 57s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s</item>
      <item>Write results 17s</item>
      <item>807s</item>
      <item>Quality check: 31s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/report/catreport_sub-0026043_ses-2_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 64 minute(s) and 57 second(s).</item>
      <item>Image Quality Rating (IQR): 82.72% (B-)</item>
      <item>GM volume (GMV): 43.84% (798.12 / 1820.48 ml)</item>
      <item>GM thickness (GMT): 2.48 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-2/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>