CORR_cat12.8.1/JHNU/sub-0025624/ses-1/report/cat_sub-0025624_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_translation>[-1.45964053366796 -21.6449390704569 -0.614740840853979]</Affine_translation>
      <Affine_rotation>[0.2114245164663 -0.0536776394106458 0.0194739619076702]</Affine_rotation>
      <Affine_scaling>[1.01185620258842 1.01168111992026 1.07498675630858]</Affine_scaling>
      <Affine_shearing>[0.00155631467353408 0.0105339887697708 0.0152019304441567]</Affine_shearing>
      <Affine0_translation>[-1.45964053366796 -21.6449390704569 -0.614740840853979]</Affine0_translation>
      <Affine0_rotation>[0.2114245164663 -0.0536776394106458 0.0194739619076702]</Affine0_rotation>
      <Affine0_scaling>[1.01185620258842 1.01168111992026 1.07498675630858]</Affine0_scaling>
      <Affine0_shearing>[0.00155631467353408 0.0105339887697708 0.0152019304441567]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1</path>
      <file>sub-0025624_ses-1_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/sub-0025624_ses-1_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/sub-0025624_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/mri/msub-0025624_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/mri/p0sub-0025624_ses-1_run-1_T1w.nii</Fp0>
      <fnames>..ds/JHNU/sub-0025624/ses-1/sub-0025624_ses-1_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_2351002/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>
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         <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>
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   </parameter>
   <qualitymeasures>
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      </software>
      <SurfaceEulerNumber>22</SurfaceEulerNumber>
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      <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
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      <SurfacePositionRMSE>0.07308329641819</SurfacePositionRMSE>
      <res_vx_vol>[1 1 1]</res_vx_vol>
      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>1</res_RMS>
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      <contrast>133.307769775391</contrast>
      <contrastr>0.357484519481659</contrastr>
      <res_ECR>0.404356837272644</res_ECR>
      <NCR>0.128516301512718</NCR>
      <ICR>0.310169875621796</ICR>
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   <qualityratings>
      <res_vx_vol>[2 2 2]</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>2.72106552124023</contrastr>
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      <ICR>1.22909200191498</ICR>
      <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
      <SurfaceDefectArea>1.25591829033864</SurfaceDefectArea>
      <SurfaceDefectNumber>1.475</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.21656668186188</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.46166586875916</SurfacePositionRMSE>
      <SIQR>2.62032687471614</SIQR>
      <IQR>2.10072684527845</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>20231031-000206</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>22</SurfaceEulerNumber>
         <SurfaceDefectArea>1.02367316135456</SurfaceDefectArea>
         <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0608283318579197</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.07308329641819</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>22</EC_abs>
      <defect_size>1.02367316135456</defect_size>
      <vol_abs_CGW>[377.596788235294 764.275498039216 605.738247058824 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.677219607843137</vol_abs_WMH>
      <vol_rel_WMH>0.000387511745280816</vol_rel_WMH>
      <surf_TSA>2131.02914738327</surf_TSA>
      <vol_TIV>1747.61053333333</vol_TIV>
      <vol_rel_CGW>[0.2160646099535 0.437325985087457 0.346609404959044 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.5927947202538 0.640391525484592]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.60797238349915 0.814828315875905 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.9336035155315 0.279297078307216 0.257835939993616;2.60263339987807 0.185905268258391 0.449415314975481;3.27720466604651 0.299160289711186 0.292748745030903]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.813242596797027 0.300868593787079 0.584324086305592;4.26022319030964 0.319548667974088 0.415675913694408]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>3.39773025179379</vol_TIV>
      <vol_rel_CGW>[1.73032704657866 5.70413047930059 4.07488155458052 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.03875117452808</vol_rel_WMH>
      <surf_TSA>8.62368244293597</surf_TSA>
      <SQR>4.70310280067371</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11141.12 0.356630519929993]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00135378050617874 0.00109931523911655 0.0669044479727745]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[959.186549019608 523.082478431373 676.437337254902 560.583192156863 993.743411764706 8025.68032941176]</SPMvols0>
      <SPMvols1>[818.318874509804 491.51791372549 388.6208 508.924701960784 920.766345098039 8013.12956470588]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[88.7912979125977 252.865707397461 372.699310302734]</T3th>
            <Tth>
               <T3th>[-5.32263994216919 -5.32264232635498 3.59385704994202 88.7912979125977 252.865707397461 372.699310302734 514.6533203125 842.0283203125]</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>[0.019944803789258 0.0727643668651581 0.0806591883301735 0 0]</dtc>
         <ll>[0.0855825667669411 0 0.0855825667669411 0;0.204407251181723 0.0109354376363583 0.215342688818081 2331.96020507812;0.204407251181723 0.0109354376363583 0.215342688818081 2331.96020507812]</ll>
         <rmsdtc>[0.0448144488036633 0.0980443209409714 0.110788941383362]</rmsdtc>
         <rmsgdt>[0.0322951637208462 0.0489644631743431 0.0609139464795589]</rmsgdt>
         <rmsdt>0.110788941383362</rmsdt>
         <dt>0.0806591883301735</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>[0.00873334985226393 0.0344349630177021 0.0448677949607372 0.0526100285351276 0.058850821107626 0.0659836903214455]</dtc>
         <ll>[0.0860453885016128 0 0.0860453885016128 0;0.224803235653236 0.0146546750992063 0.239457910752442 7501.36181640625;0.207236931230826 0.0169970766084211 0.224234007839247 12233;0.186290222921489 0.0192498916234726 0.205540114544962 20756.619140625;0.168643921495547 0.0222444093437688 0.190888330839316 38913.32421875;0.168643921495547 0.0222444093437688 0.190888330839316 38913.32421875]</ll>
         <rmsdtc>[0.0102529460564256 0.037018496543169 0.0580408237874508 0.081476092338562 0.10494564473629 0.112443692982197]</rmsdtc>
         <rmsgdt>[0.00314740324392915 0.0124798230826855 0.0281387772411108 0.0489791482686996 0.0682443678379059 0.0744730308651924]</rmsgdt>
         <rmsdt>0.112443692982197</rmsdt>
         <dt>0.0659836903214455</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025624/ses-1/sub-0025624_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 40s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 4s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 2s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 5s</item>
      <item>30s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 6s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 64s</item>
      <item>SPM preprocessing 1 (estimate 2): 58s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 16s</item>
      <item>Update Segmentation 17s</item>
      <item>Update Skull-Stripping 34s</item>
      <item>Update probability maps 7s</item>
      <item>75s</item>
      <item>Global intensity correction: 13s</item>
      <item>SANLM denoising after intensity normalization (medium): 23s</item>
      <item>Fast Optimized Shooting registration 26s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.06) 12s</item>
      <item>Estimate local tissue thresholds (WM) 15s</item>
      <item>Estimate local tissue thresholds (GM) 23s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 30s</item>
      <item>89s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 11s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.15) 21s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>58s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>10s</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 | 0.0860 0.0000 0.0860 | 32.0000</item>
      <item>2 | 2.50 | 0.0839 0.0011 0.0850 | 29.4886</item>
      <item>3 | 2.50 | 0.0833 0.0016 0.0848 | 26.9772</item>
      <item>4 | 2.50 | 0.0829 0.0018 0.0847 | 24.6107</item>
      <item>5 | 2.50 | 0.0827 0.0019 0.0846 | 22.6548</item>
      <item>6 | 2.50 | 0.0824 0.0020 0.0844 | 20.6989</item>
      <item>7 | 2.50 | 0.0822 0.0021 0.0843 | 18.9688</item>
      <item>8 | 2.50 | 0.0819 0.0022 0.0841 | 17.4455</item>
      <item>9 | 2.50 | 0.0817 0.0022 0.0839 | 15.9223</item>
      <item>10 | 2.50 | 0.0814 0.0023 0.0837 | 14.6627</item>
      <item>11 | 2.50 | 0.0811 0.0024 0.0835 | 13.4764</item>
      <item>12 | 2.50 | 0.0809 0.0025 0.0833 | 12.3015</item>
      <item>13 | 2.50 | 0.0806 0.0026 0.0831 | 11.3776</item>
      <item>14 | 2.50 | 0.0803 0.0026 0.0829 | 10.4537</item>
      <item>15 | 2.25 | 0.0798 0.0027 0.0825 | 9.5920</item>
      <item>16 | 2.25 | 0.0768 0.0041 0.0810 | 8.8725</item>
      <item>17 | 2.25 | 0.0757 0.0046 0.0803 | 8.1530</item>
      <item>18 | 2.25 | 0.0749 0.0049 0.0798 | 7.5234</item>
      <item>29 | 2.00 | 0.0766 0.0023 0.0789 | 3.3283</item>
      <item>30 | 2.00 | 0.0710 0.0047 0.0757 | 3.1221</item>
      <item>31 | 2.00 | 0.0691 0.0057 0.0747 | 2.9160</item>
      <item>43 | 1.75 | 0.0680 0.0032 0.0712 | 1.5785</item>
      <item>44 | 1.75 | 0.0635 0.0056 0.0691 | 1.5194</item>
      <item>45 | 1.75 | 0.0621 0.0064 0.0685 | 1.4626</item>
      <item>57 | 1.50 | 0.0605 0.0046 0.0651 | 1.0900</item>
      <item>58 | 1.50 | 0.0572 0.0068 0.0640 | 1.0730</item>
      <item>59 | 1.50 | 0.0562 0.0074 0.0636 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 154s</item>
      <item>Prepare output 8s</item>
      <item>162s</item>
      <item>Jacobian determinant (RMS): 0.010 0.037 0.058 0.081 0.105 | 0.112444</item>
      <item>Template Matching: 0.086 0.225 0.207 0.186 0.169 | 0.168644</item>
      <item>Write result maps: 29s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 35s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 37s</item>
      <item>91s</item>
      <item>Create initial surface 67s</item>
      <item>Topology correction: 80s</item>
      <item>Surface refinement: 63s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 75s</item>
      <item>Spherical registration 211s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 35s</item>
      <item>CSF distance: 14s</item>
      <item>PBT2x thickness: 37s</item>
      <item>91s</item>
      <item>Create initial surface 66s</item>
      <item>Topology correction: 80s</item>
      <item>Surface refinement: 66s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 109s</item>
      <item>Spherical registration 245s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5928 0.6404 mm</item>
      <item>Surface intensity / position RMSE: 0.0608 / 0.0731</item>
      <item>Euler number / defect number / defect size: 22.0 / 9.5 / 1.02%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/surf/lh.thickness.sub-0025624_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/surf/rh.thickness.sub-0025624_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/sub-0025624_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1444s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 18s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 61s</item>
      <item>ROI estimation of 'lpba40' atlas 18s</item>
      <item>ROI estimation of 'hammers' atlas 48s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 17s</item>
      <item>ROI estimation of 'aal3' atlas 28s</item>
      <item>ROI estimation of 'mori' atlas 40s</item>
      <item>ROI estimation of 'anatomy3' atlas 58s</item>
      <item>ROI estimation of 'julichbrain' atlas 76s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 32s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 61s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 185s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s</item>
      <item>Write results 16s</item>
      <item>787s</item>
      <item>Quality check: 12s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/report/catreport_sub-0025624_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 50 minute(s) and 59 second(s).</item>
      <item>Image Quality Rating (IQR): 83.99% (B)</item>
      <item>GM volume (GMV): 43.73% (764.28 / 1747.61 ml)</item>
      <item>GM thickness (GMT): 2.59 0.64 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2351002/ds/JHNU/sub-0025624/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>