CORR_cat12.8.1/BNU_2/sub-0025970/ses-1/report/cat_sub-0025970_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_shearing>[0.0265286279657015 -0.00907372644393047 0.0224956112318689]</Affine_shearing>
      <Affine0_translation>[0.944787300204365 -36.1396449715351 -10.5596584612561]</Affine0_translation>
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      <Affine0_shearing>[0.0265286279657015 -0.00907372644393047 0.0224956112318689]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1</path>
      <file>sub-0025970_ses-1_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/sub-0025970_ses-1_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/sub-0025970_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/mri/msub-0025970_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/mri/p0sub-0025970_ses-1_run-1_T1w.nii</Fp0>
      <fnames>..s/BNU_2/sub-0025970/ses-1/sub-0025970_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>
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            <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>
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            <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>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/var/lib/condor/execute/dir_1955758/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>
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         </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>
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            <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>
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               <regstr>0.5</regstr>
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         <restypes>
            <optimal>[1 0.3]</optimal>
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         <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>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
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         </darteltpms>
         <shootingtpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
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         <templates>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
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         <AMAPframing>1</AMAPframing>
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      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>1.12084791031237</res_RMS>
      <res_BB>NaN</res_BB>
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      <ICR>0.343947947025299</ICR>
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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>
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      <contrastr>2.95835018157959</contrastr>
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      <SurfaceDefectArea>1.04890945732548</SurfaceDefectArea>
      <SurfaceDefectNumber>1.4</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.28529047966003</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.26111924648285</SurfacePositionRMSE>
      <SIQR>2.6874524252595</SIQR>
      <IQR>2.2696777450499</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>20231030-234221</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>10</SurfaceEulerNumber>
         <SurfaceDefectArea>0.195637829301928</SurfaceDefectArea>
         <SurfaceDefectNumber>8</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0642645210027695</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0630559623241425</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>10</EC_abs>
      <defect_size>0.195637829301928</defect_size>
      <vol_abs_CGW>[202.803658823529 695.045101960784 540.941862745098 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.170698039215686</vol_abs_WMH>
      <vol_rel_WMH>0.000118639944147646</vol_rel_WMH>
      <surf_TSA>1966.61183362871</surf_TSA>
      <vol_TIV>1438.79062352941</vol_TIV>
      <vol_rel_CGW>[0.140954253876109 0.483075918479237 0.375969827644655 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.5345870401321 0.620818431605199]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.54564356803894 0.716021715201605 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.92564518646119 0.235259429991482 0.301895909362562;2.5581091653308 0.177859802484936 0.403793090294114;3.18335890879982 0.255042259658639 0.294311000343324]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.915767712604831 0.334157562150474 0.5282874617737;4.10488959432035 0.359421476727372 0.4717125382263]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.03576561976521</vol_TIV>
      <vol_rel_CGW>[0.5 6.52578876579089 4.60218799649164 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.01186399441476</vol_rel_WMH>
      <surf_TSA>8.61981276455946</surf_TSA>
      <SQR>5.37632719166382</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11156.849 0.404533548164579]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0019264854490757 0.00169066654052585 0.0305054374039173]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[865.672215686275 456.228784313725 359.227054901961 435.987690196078 1069.51374901961 8478.34419215686]</SPMvols0>
      <SPMvols1>[758.762901960784 432.93302745098 189.203650980392 324.237094117647 881.039619607843 8555.00186666667]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[41.1604995727539 184.852798461914 306.648498535156]</T3th>
            <Tth>
               <T3th>[-31.4870204925537 -31.4870223999023 2.41820549964905 41.1604995727539 184.852798461914 306.648498535156 439.392517089844 615.475158691406]</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>[0.0209556221961975 0.071026898920536 0.0777601227164268 0 0]</dtc>
         <ll>[0.0796938098970057 0 0.0796938098970057 0;0.188616071428571 0.00887080715770195 0.197486878586273 1891.68188476562;0.188616071428571 0.00887080715770195 0.197486878586273 1891.68188476562]</ll>
         <rmsdtc>[0.0438520610332489 0.0920303240418434 0.101439766585827]</rmsdtc>
         <rmsgdt>[0.0310283880680799 0.042102288454771 0.0523965694010258]</rmsgdt>
         <rmsdt>0.101439766585827</rmsdt>
         <dt>0.0777601227164268</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>[0.00935500115156174 0.0333965942263603 0.0454409420490265 0.0523897223174572 0.0569591894745827 0.0636424273252487]</dtc>
         <ll>[0.0799082448265589 0 0.0799082448265589 0;0.209340308302808 0.011646688034188 0.220986996336996 5961.6484375;0.190478665424503 0.0143046408559083 0.204783306280411 10295.2216796875;0.172242355708949 0.0162875509669638 0.188529906675913 17562.41015625;0.159100643209232 0.0172412404043095 0.176341883613542 30161.015625;0.159100643209232 0.0172412404043095 0.176341883613542 30161.015625]</ll>
         <rmsdtc>[0.0108678704127669 0.0386788472533226 0.0563062429428101 0.0780490264296532 0.100185431540012 0.105151891708374]</rmsdtc>
         <rmsgdt>[0.00321501493453979 0.012357440777123 0.0264059323817492 0.0454942360520363 0.0635381266474724 0.0676048472523689]</rmsgdt>
         <rmsdt>0.105151891708374</rmsdt>
         <dt>0.0636424273252487</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025970/ses-1/sub-0025970_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 22s</item>
      <item>Internal resampling (1.33x1.00x1.00mm &gt; 1.00x1.00x1.00mm): 1s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 4s</item>
      <item>Estimate background 3s</item>
      <item>Initial correction 3s</item>
      <item>Refine background 2s</item>
      <item>Final correction 3s</item>
      <item>Final scaling 3s</item>
      <item>22s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 5s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 42s</item>
      <item>SPM preprocessing 1 (estimate 2): 38s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 11s</item>
      <item>Update Segmentation 13s</item>
      <item>Update Skull-Stripping 28s</item>
      <item>Update probability maps 6s</item>
      <item>58s</item>
      <item>Global intensity correction: 10s</item>
      <item>SANLM denoising after intensity normalization (medium): 17s</item>
      <item>Fast Optimized Shooting registration 22s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 2s</item>
      <item>Prepare partitions 1s</item>
      <item>Prepare segments (LASmod = 1.13) 9s</item>
      <item>Estimate local tissue thresholds (WM) 12s</item>
      <item>Estimate local tissue thresholds (GM) 17s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 25s</item>
      <item>70s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 5s</item>
      <item>Major structures 2s</item>
      <item>Ventricle detection 7s</item>
      <item>Blood vessel detection 6s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 12s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 2s</item>
      <item>Final corrections 3s</item>
      <item>38s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 23s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 3s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>7s</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 | 0.0799 0.0000 0.0799 | 32.0000</item>
      <item>2 | 2.50 | 0.0777 0.0010 0.0787 | 29.4886</item>
      <item>3 | 2.50 | 0.0770 0.0015 0.0786 | 26.9772</item>
      <item>4 | 2.50 | 0.0767 0.0017 0.0785 | 24.6107</item>
      <item>5 | 2.50 | 0.0765 0.0019 0.0783 | 22.6548</item>
      <item>6 | 2.50 | 0.0762 0.0020 0.0782 | 20.6989</item>
      <item>7 | 2.50 | 0.0760 0.0020 0.0780 | 18.9688</item>
      <item>8 | 2.50 | 0.0758 0.0021 0.0779 | 17.4455</item>
      <item>9 | 2.50 | 0.0755 0.0022 0.0777 | 15.9223</item>
      <item>10 | 2.50 | 0.0753 0.0023 0.0776 | 14.6627</item>
      <item>11 | 2.50 | 0.0750 0.0024 0.0774 | 13.4764</item>
      <item>12 | 2.50 | 0.0747 0.0024 0.0772 | 12.3015</item>
      <item>13 | 2.50 | 0.0745 0.0025 0.0770 | 11.3776</item>
      <item>14 | 2.50 | 0.0742 0.0026 0.0768 | 10.4537</item>
      <item>15 | 2.25 | 0.0723 0.0026 0.0749 | 9.5920</item>
      <item>16 | 2.25 | 0.0698 0.0039 0.0737 | 8.8725</item>
      <item>29 | 2.00 | 0.0707 0.0018 0.0724 | 3.3283</item>
      <item>30 | 2.00 | 0.0653 0.0039 0.0692 | 3.1221</item>
      <item>31 | 2.00 | 0.0635 0.0048 0.0683 | 2.9160</item>
      <item>43 | 1.75 | 0.0625 0.0027 0.0652 | 1.5785</item>
      <item>44 | 1.75 | 0.0587 0.0047 0.0634 | 1.5194</item>
      <item>45 | 1.75 | 0.0574 0.0054 0.0628 | 1.4626</item>
      <item>57 | 1.50 | 0.0558 0.0039 0.0598 | 1.0900</item>
      <item>58 | 1.50 | 0.0530 0.0057 0.0588 | 1.0730</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 95s</item>
      <item>Prepare output 7s</item>
      <item>102s</item>
      <item>Jacobian determinant (RMS): 0.011 0.039 0.056 0.078 0.100 | 0.105152</item>
      <item>Template Matching: 0.080 0.209 0.190 0.172 0.159 | 0.159101</item>
      <item>Write result maps: 36s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 21s</item>
      <item>CSF distance: 9s</item>
      <item>PBT2x thickness: 29s</item>
      <item>64s</item>
      <item>Create initial surface 54s</item>
      <item>Topology correction: 64s</item>
      <item>Surface refinement: 52s</item>
      <item>Reduction of surface collisions with optimization: 46s</item>
      <item>Spherical mapping with areal smoothing 56s</item>
      <item>Spherical registration 181s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 16s</item>
      <item>CSF distance: 9s</item>
      <item>PBT2x thickness: 27s</item>
      <item>56s</item>
      <item>Create initial surface 51s</item>
      <item>Topology correction: 62s</item>
      <item>Surface refinement: 52s</item>
      <item>Reduction of surface collisions with optimization: 43s</item>
      <item>Spherical mapping with areal smoothing 55s</item>
      <item>Spherical registration 187s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5347 0.6208 mm</item>
      <item>Surface intensity / position RMSE: 0.0643 / 0.0631</item>
      <item>Euler number / defect number / defect size: 10.0 / 8.0 / 0.20%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/surf/lh.thickness.sub-0025970_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/surf/rh.thickness.sub-0025970_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/sub-0025970_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 6s</item>
      <item>Surface and thickness estimation takes: 1089s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 6s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 20s</item>
      <item>ROI estimation of 'lpba40' atlas 6s</item>
      <item>ROI estimation of 'hammers' atlas 14s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 5s</item>
      <item>ROI estimation of 'aal3' atlas 8s</item>
      <item>ROI estimation of 'mori' atlas 13s</item>
      <item>ROI estimation of 'anatomy3' atlas 20s</item>
      <item>ROI estimation of 'julichbrain' atlas 26s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
      <item>Write results 7s</item>
      <item>277s</item>
      <item>Quality check: 8s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/report/catreport_sub-0025970_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 32 minute(s) and 40 second(s).</item>
      <item>Image Quality Rating (IQR): 82.30% (B-)</item>
      <item>GM volume (GMV): 48.31% (695.05 / 1438.79 ml)</item>
      <item>GM thickness (GMT): 2.53 0.62 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_1955758/ds/BNU_2/sub-0025970/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>