CORR_cat12.8.1/BNU_2/sub-0025934/ses-1/report/cat_sub-0025934_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_shearing>[0.0461291179470805 0.0217598061489791 -0.00630888178139498]</Affine_shearing>
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      <Affine0_shearing>[0.0461291179470805 0.0217598061489791 -0.00630888178139498]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1</path>
      <file>sub-0025934_ses-1_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/sub-0025934_ses-1_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/sub-0025934_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/mri/msub-0025934_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/mri/p0sub-0025934_ses-1_run-1_T1w.nii</Fp0>
      <fnames>..s/BNU_2/sub-0025934/ses-1/sub-0025934_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>
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            <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_2677246/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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               </shootingtpm>
               <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>
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            <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>
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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>
            <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>
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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>
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         <AMAPframing>1</AMAPframing>
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      <res_vx_voli>[1.00000005099085 1 0.999999991497377]</res_vx_voli>
      <res_RMS>1.12084789616714</res_RMS>
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      <ICR>0.392363518476486</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>2.94004464149475</contrastr>
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      <ICR>1.43294525146484</ICR>
      <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
      <SurfaceDefectArea>1.23972519126883</SurfaceDefectArea>
      <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.375155210495</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.43437886238098</SurfacePositionRMSE>
      <SIQR>2.92963377348629</SIQR>
      <IQR>2.73122146193658</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>20231031-003141</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>18</SurfaceEulerNumber>
         <SurfaceDefectArea>0.958900765075315</SurfaceDefectArea>
         <SurfaceDefectNumber>13</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0687577575445175</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0717189460992813</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>18</EC_abs>
      <defect_size>0.958900765075315</defect_size>
      <vol_abs_CGW>[308.252824861821 768.303083624225 573.314898868935 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.432698057600258</vol_abs_WMH>
      <vol_rel_WMH>0.000262261781753655</vol_rel_WMH>
      <surf_TSA>2123.51448451377</surf_TSA>
      <vol_TIV>1649.87080735498</vol_TIV>
      <vol_rel_CGW>[0.186834522732117 0.465674694163444 0.347490783104439 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.52936647899711 0.629809401923486]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.52561545372009 0.68837612813745 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.91611308841103 0.232396626579566 0.314540320123737;2.55609654115043 0.181564198126386 0.40928265098076;3.21228282899517 0.250603649445693 0.276177028895503]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.943206163142472 0.346072469303074 0.499873150105708;4.05648252631024 0.293407194192085 0.500126849894292]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.3514029107165</vol_TIV>
      <vol_rel_CGW>[1.20536139964291 6.2132667773607 4.09071090345616 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.02622617817537</vol_rel_WMH>
      <surf_TSA>8.62363973966719</surf_TSA>
      <SQR>5.10307991778449</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[1.19209289550781e-07 1 1 11156.847329872 0.415929865493334]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00181183323729783 0.00169981620274484 0.0682201161980629]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[977.543433690946 485.708448087869 619.595947894158 1217.19123995159 1054.23394283174 7591.12872645514]</SPMvols0>
      <SPMvols1>[822.979148692412 452.294156472077 328.688719847752 699.133292450029 884.694692491066 7953.50730655784]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[58.7215995788574 211.705001831055 348.175903320312]</T3th>
            <Tth>
               <T3th>[-38.5757293701172 -38.5757255554199 2.89810228347778 58.7215995788574 211.705001831055 348.175903320312 492.903076171875 752.298950195312]</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>[0.0200543850660324 0.0770383179187775 0.085932545363903 0 0]</dtc>
         <ll>[0.0881066049466662 0 0.0881066049466662 0;0.20339467574139 0.0119320914095619 0.215326767150952 2544.49462890625;0.20339467574139 0.0119320914095619 0.215326767150952 2544.49462890625]</ll>
         <rmsdtc>[0.047925528138876 0.105093561112881 0.117528103291988]</rmsdtc>
         <rmsgdt>[0.0349418260157108 0.0482730008661747 0.0598334074020386]</rmsgdt>
         <rmsdt>0.117528103291988</rmsdt>
         <dt>0.085932545363903</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>[0.00903128646314144 0.0379182919859886 0.04910072311759 0.0569887682795525 0.0632735341787338 0.0709894746541977]</dtc>
         <ll>[0.0883889743695972 0 0.0883889743695972 0;0.224518864468864 0.0188707799145299 0.243389644383394 9659.48046875;0.205956188899171 0.0195932241169037 0.225549413016074 14101.478515625;0.184691281513384 0.0207310139510253 0.20542229546441 22353.671875;0.167533636007141 0.0234931857663948 0.191026821773536 41097.875;0.167533636007141 0.0234931857663948 0.191026821773536 41097.875]</ll>
         <rmsdtc>[0.010940725915134 0.0411070249974728 0.0642435029149055 0.0867862701416016 0.108813531696796 0.115474529564381]</rmsdtc>
         <rmsgdt>[0.00337337865494192 0.0131924133747816 0.0301155280321836 0.0481914989650249 0.065982311964035 0.0713611096143723]</rmsgdt>
         <rmsdt>0.115474529564381</rmsdt>
         <dt>0.0709894746541977</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025934/ses-1/sub-0025934_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 24s</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 4s</item>
      <item>Initial correction 4s</item>
      <item>Refine background 2s</item>
      <item>Final correction 3s</item>
      <item>Final scaling 3s</item>
      <item>24s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 6s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 49s</item>
      <item>SPM preprocessing 1 (estimate 2): 48s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 11s</item>
      <item>Update Segmentation 14s</item>
      <item>Update Skull-Stripping 28s</item>
      <item>Update probability maps 6s</item>
      <item>60s</item>
      <item>Global intensity correction: 10s</item>
      <item>SANLM denoising after intensity normalization (medium): 19s</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 = 1.00) 10s</item>
      <item>Estimate local tissue thresholds (WM) 12s</item>
      <item>Estimate local tissue thresholds (GM) 18s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 26s</item>
      <item>73s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 5s</item>
      <item>Major structures 2s</item>
      <item>Ventricle detection 10s</item>
      <item>Blood vessel detection 7s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.07) 15s</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>45s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.37 0.05,0.67 0.08,0.98 0.05]</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 | 0.0884 0.0000 0.0884 | 32.0000</item>
      <item>2 | 2.50 | 0.0852 0.0014 0.0865 | 29.4886</item>
      <item>3 | 2.50 | 0.0842 0.0021 0.0863 | 26.9772</item>
      <item>4 | 2.50 | 0.0837 0.0024 0.0861 | 24.6107</item>
      <item>5 | 2.50 | 0.0833 0.0026 0.0859 | 22.6548</item>
      <item>6 | 2.50 | 0.0830 0.0027 0.0856 | 20.6989</item>
      <item>7 | 2.50 | 0.0826 0.0028 0.0854 | 18.9688</item>
      <item>8 | 2.50 | 0.0822 0.0029 0.0852 | 17.4455</item>
      <item>9 | 2.50 | 0.0819 0.0030 0.0849 | 15.9223</item>
      <item>10 | 2.50 | 0.0815 0.0031 0.0846 | 14.6627</item>
      <item>11 | 2.50 | 0.0811 0.0032 0.0843 | 13.4764</item>
      <item>12 | 2.50 | 0.0807 0.0033 0.0840 | 12.3015</item>
      <item>13 | 2.50 | 0.0803 0.0034 0.0837 | 11.3776</item>
      <item>14 | 2.50 | 0.0799 0.0035 0.0834 | 10.4537</item>
      <item>15 | 2.25 | 0.0808 0.0036 0.0844 | 9.5920</item>
      <item>16 | 2.25 | 0.0773 0.0053 0.0826 | 8.8725</item>
      <item>17 | 2.25 | 0.0758 0.0060 0.0818 | 8.1530</item>
      <item>18 | 2.25 | 0.0748 0.0063 0.0811 | 7.5234</item>
      <item>29 | 2.00 | 0.0767 0.0030 0.0797 | 3.3283</item>
      <item>30 | 2.00 | 0.0708 0.0056 0.0763 | 3.1221</item>
      <item>31 | 2.00 | 0.0687 0.0065 0.0752 | 2.9160</item>
      <item>43 | 1.75 | 0.0676 0.0037 0.0713 | 1.5785</item>
      <item>44 | 1.75 | 0.0630 0.0061 0.0692 | 1.5194</item>
      <item>45 | 1.75 | 0.0616 0.0069 0.0685 | 1.4626</item>
      <item>57 | 1.50 | 0.0602 0.0051 0.0652 | 1.0900</item>
      <item>58 | 1.50 | 0.0569 0.0072 0.0641 | 1.0730</item>
      <item>59 | 1.50 | 0.0558 0.0078 0.0637 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 115s</item>
      <item>Prepare output 7s</item>
      <item>122s</item>
      <item>Jacobian determinant (RMS): 0.011 0.041 0.064 0.087 0.109 | 0.115475</item>
      <item>Template Matching: 0.088 0.225 0.206 0.185 0.168 | 0.167534</item>
      <item>Write result maps: 35s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 11s</item>
      <item>PBT2x thickness: 32s</item>
      <item>75s</item>
      <item>Create initial surface 58s</item>
      <item>Topology correction: 70s</item>
      <item>Surface refinement: 60s</item>
      <item>Reduction of surface collisions with optimization: 51s</item>
      <item>Spherical mapping with areal smoothing 59s</item>
      <item>Spherical registration 198s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 27s</item>
      <item>CSF distance: 11s</item>
      <item>PBT2x thickness: 31s</item>
      <item>74s</item>
      <item>Create initial surface 58s</item>
      <item>Topology correction: 71s</item>
      <item>Surface refinement: 53s</item>
      <item>Reduction of surface collisions with optimization: 54s</item>
      <item>Spherical mapping with areal smoothing 70s</item>
      <item>Spherical registration 208s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5293 0.6295 mm</item>
      <item>Surface intensity / position RMSE: 0.0688 / 0.0717</item>
      <item>Euler number / defect number / defect size: 18.0 / 13.0 / 0.96%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/surf/lh.thickness.sub-0025934_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/surf/rh.thickness.sub-0025934_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/sub-0025934_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1229s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 6s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 23s</item>
      <item>ROI estimation of 'lpba40' atlas 7s</item>
      <item>ROI estimation of 'hammers' atlas 16s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 6s</item>
      <item>ROI estimation of 'aal3' atlas 9s</item>
      <item>ROI estimation of 'mori' atlas 14s</item>
      <item>ROI estimation of 'anatomy3' atlas 19s</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 19s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
      <item>Write results 6s</item>
      <item>262s</item>
      <item>Quality check: 7s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/report/catreport_sub-0025934_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 35 minute(s) and 22 second(s).</item>
      <item>Image Quality Rating (IQR): 77.69% (C+)</item>
      <item>GM volume (GMV): 46.57% (768.30 / 1649.87 ml)</item>
      <item>GM thickness (GMT): 2.53 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2677246/ds/BNU_2/sub-0025934/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>