ds003639_ReproVBM/sub-NC244/report/cat_sub-NC244_ses-20190715_acq-highres_run-01_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_11677/ds/sub-NC244</path>
      <file>sub-NC244_ses-20190715_acq-highres_run-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_11677/ds/sub-NC244/sub-NC244_ses-20190715_acq-highres_run-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_11677/ds/sub-NC244/sub-NC244_ses-20190715_acq-highres_run-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_11677/ds/sub-NC244/mri/msub-NC244_ses-20190715_acq-highres_run-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_11677/ds/sub-NC244/mri/p0sub-NC244_ses-20190715_acq-highres_run-01_T1w.nii</Fp0>
      <fnames>..77/ds/sub-NC244/..-20190715_acq-highres_run-01_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
         </tpm>
         <ngaus>[1 1 2 3 4 2]</ngaus>
         <affreg>mni</affreg>
         <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
         <tol>0.0001</tol>
         <accstr>0.5</accstr>
         <biasstr>0.5</biasstr>
         <biasreg>0.001</biasreg>
         <biasfwhm>60</biasfwhm>
         <samp>3</samp>
         <redspmres>0</redspmres>
         <fwhm>1</fwhm>
         <biasacc>0</biasacc>
      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
         <BVCstr>0.5</BVCstr>
         <regstr>0.5</regstr>
         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
         <SLC>0</SLC>
         <mrf>1</mrf>
         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>20</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>
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         </darteltpm>
         <shootingtpm>
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         </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>
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         </brainmask>
         <T1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
         </T1>
         <cat12atlas>
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         <pbtres>0.5</pbtres>
         <SRP>22</SRP>
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         <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>
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               <td>0</td>
               <td>
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                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
               <td>0</td>
               <td>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
               <td>0</td>
               <td>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
               <td>0</td>
               <td>
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               <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>
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                  <item>gm</item>
                  <item>wm</item>
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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>
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               <td>[false]</td>
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            <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>
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               <td>[false]</td>
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            <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>
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               <td>[false]</td>
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            <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>
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               <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_100Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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               <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_200Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
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               <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_400Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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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>
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               <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>
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            <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>
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            <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>
                  <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
               </shootingtpm>
               <regstr>0.5</regstr>
            </shooting>
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         <restypes>
            <optimal>[1 0.3]</optimal>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
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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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
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         <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>
            <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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         <AMAPframing>1</AMAPframing>
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   <qualitymeasures>
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         <version_segment>1639</version_segment>
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      <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
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      <SurfacePositionRMSE>0.0641345754265785</SurfacePositionRMSE>
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      <tissue_mn>[6.96099996566772 40.9547119140625 149.979049682617 254.10270690918]</tissue_mn>
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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>2.84726786613464</contrastr>
      <NCR>2.71229720115662</NCR>
      <ICR>1.16716516017914</ICR>
      <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
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      <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.29400753974915</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.28269147872925</SurfacePositionRMSE>
      <IQR>2.51337619331913</IQR>
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   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>1980</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20220712-135226</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>16</SurfaceEulerNumber>
         <SurfaceDefectArea>0.573537605415768</SurfaceDefectArea>
         <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0647003799676895</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0641345754265785</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>16</EC_abs>
      <defect_size>0.573537605415768</defect_size>
      <vol_abs_CGW>[235.024917647059 540.389466666667 438.896819607843 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.21621568627451</vol_abs_WMH>
      <vol_rel_WMH>0.000178056239270666</vol_rel_WMH>
      <surf_TSA>1570.78029799253</surf_TSA>
      <vol_TIV>1214.31120392157</vol_TIV>
      <vol_rel_CGW>[0.193545869368623 0.445017278043306 0.361436852588071 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.39695457262268 0.662169670309343]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.38499307632446 0.801861733472964 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.74782491809482 0.277741478753641 0.312954437212256;2.43417340975671 0.193760455639123 0.451309731703445;3.16720502901342 0.298816388543988 0.235735831084299]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.769361878396398 0.210152473936065 0.512341485507246;4.17629190982564 0.316760072968278 0.487658514492754]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.77878315024608</vol_TIV>
      <vol_rel_CGW>[1.32589564239624 5.84226433267432 4.34117910538921 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.01780562392707</vol_rel_WMH>
      <surf_TSA>8.18610115606297</surf_TSA>
      <SQR>4.83097668367921</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.212956862016158 1 1 9078.02 0.459885324394127]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.017170362174511 0.0133113218471408 0.176086694002151]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[694.950152941176 395.47377254902 370.417831372549 1928.35619215686 1916.3179372549 7110.1426]</SPMvols0>
      <SPMvols1>[599.062109803922 369.472545098039 210.749321568627 1249.55146666667 1319.63452941176 7786.78983137255]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[44.5242004394531 158.401702880859 251.811996459961]</T3th>
            <Tth>
               <T3th>[0 0 22.2621002197266 44.5242004394531 158.401702880859 251.811996459961 355.455902099609 827.393615722656]</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>[0.0227955561131239 0.0872135534882545 0.0977890640497208 0 0]</dtc>
         <ll>[0.0839872325883478 0 0.0839872325883478 0;0.191080906239449 0.0120625833646447 0.203143489604094 2572.32177734375;0.191080906239449 0.0120625833646447 0.203143489604094 2572.32177734375]</ll>
         <rmsdtc>[0.0464065372943878 0.115597359836102 0.129185780882835]</rmsdtc>
         <rmsgdt>[0.0323861800134182 0.0512855723500252 0.0630864277482033]</rmsgdt>
         <rmsdt>0.129185780882835</rmsdt>
         <dt>0.0977890640497208</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>[0.0112851765006781 0.045796450227499 0.0645069256424904 0.0737545415759087 0.0795103535056114 0.0913585871458054]</dtc>
         <ll>[0.0860052327550453 0 0.0860052327550453 0;0.220752625152625 0.0173959478021978 0.238148572954823 8904.55078125;0.197682328139589 0.0197431321704029 0.217425460309992 14209.369140625;0.175000892631915 0.0210168572232934 0.196017749855208 22661.888671875;0.157909917266555 0.023396944827602 0.181306862094157 40929.515625;0.157909917266555 0.023396944827602 0.181306862094157 40929.515625]</ll>
         <rmsdtc>[0.0130643676966429 0.049192301928997 0.0779221951961517 0.108041264116764 0.133386522531509 0.141925975680351]</rmsdtc>
         <rmsgdt>[0.00373771996237338 0.0152852395549417 0.0330440104007721 0.0557468384504318 0.0752500146627426 0.0804847478866577]</rmsgdt>
         <rmsdt>0.141925975680351</rmsdt>
         <dt>0.0913585871458054</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-NC244_ses-20190715_acq-highres_run-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 85s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 9s</item>
      <item>Refine background 5s</item>
      <item>Final correction 7s</item>
      <item>Final scaling 9s</item>
      <item>56s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 14s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 94s</item>
      <item>SPM preprocessing 1 (estimate 2): 86s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 21s</item>
      <item>Update Segmentation 23s</item>
      <item>Update Skull-Stripping 51s</item>
      <item>Update probability maps 11s</item>
      <item>106s</item>
      <item>Global intensity correction: 21s</item>
      <item>SANLM denoising after intensity normalization (medium): 13s</item>
      <item>Fast Optimized Shooting registration 45s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 16s</item>
      <item>Estimate local tissue thresholds (WM) 19s</item>
      <item>Estimate local tissue thresholds (GM) 24s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 25s</item>
      <item>96s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 10s</item>
      <item>Major structures 4s</item>
      <item>Ventricle detection 13s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.06) 25s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 4s</item>
      <item>Final corrections 6s</item>
      <item>72s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 43s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 5s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>12s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0860 0.0000 0.0860 | 32.0000</item>
      <item>2 | 2.50 | 0.0831 0.0013 0.0844 | 29.4886</item>
      <item>3 | 2.50 | 0.0822 0.0019 0.0842 | 26.9772</item>
      <item>4 | 2.50 | 0.0818 0.0022 0.0840 | 24.6107</item>
      <item>5 | 2.50 | 0.0815 0.0024 0.0838 | 22.6548</item>
      <item>6 | 2.50 | 0.0811 0.0025 0.0836 | 20.6989</item>
      <item>7 | 2.50 | 0.0808 0.0026 0.0834 | 18.9688</item>
      <item>8 | 2.50 | 0.0804 0.0027 0.0832 | 17.4455</item>
      <item>9 | 2.50 | 0.0801 0.0028 0.0829 | 15.9223</item>
      <item>10 | 2.50 | 0.0797 0.0030 0.0827 | 14.6627</item>
      <item>11 | 2.50 | 0.0793 0.0031 0.0824 | 13.4764</item>
      <item>12 | 2.50 | 0.0790 0.0032 0.0821 | 12.3015</item>
      <item>13 | 2.50 | 0.0785 0.0033 0.0819 | 11.3776</item>
      <item>14 | 2.50 | 0.0781 0.0034 0.0816 | 10.4537</item>
      <item>15 | 2.25 | 0.0783 0.0035 0.0818 | 9.5920</item>
      <item>16 | 2.25 | 0.0750 0.0051 0.0802 | 8.8725</item>
      <item>17 | 2.25 | 0.0736 0.0058 0.0794 | 8.1530</item>
      <item>29 | 2.00 | 0.0748 0.0027 0.0774 | 3.3283</item>
      <item>30 | 2.00 | 0.0682 0.0054 0.0737 | 3.1221</item>
      <item>31 | 2.00 | 0.0659 0.0066 0.0725 | 2.9160</item>
      <item>43 | 1.75 | 0.0643 0.0038 0.0681 | 1.5785</item>
      <item>44 | 1.75 | 0.0599 0.0062 0.0660 | 1.5194</item>
      <item>45 | 1.75 | 0.0583 0.0070 0.0653 | 1.4626</item>
      <item>57 | 1.50 | 0.0567 0.0052 0.0619 | 1.0900</item>
      <item>58 | 1.50 | 0.0537 0.0072 0.0608 | 1.0730</item>
      <item>59 | 1.50 | 0.0526 0.0078 0.0604 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 236s</item>
      <item>Prepare output 11s</item>
      <item>246s</item>
      <item>Jacobian determinant (RMS): 0.013 0.049 0.078 0.108 0.133 | 0.141926</item>
      <item>Template Matching: 0.086 0.221 0.198 0.175 0.158 | 0.157910</item>
      <item>Write result maps: 52s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 39s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 47s</item>
      <item>110s</item>
      <item>Create initial surface 87s</item>
      <item>Topology correction: 81s</item>
      <item>Surface refinement: 99s</item>
      <item>Reduction of surface collisions with optimization: 63s</item>
      <item>Spherical mapping with areal smoothing 80s</item>
      <item>Spherical registration 276s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 33s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 47s</item>
      <item>102s</item>
      <item>Create initial surface 86s</item>
      <item>Topology correction: 80s</item>
      <item>Surface refinement: 73s</item>
      <item>Reduction of surface collisions with optimization: 60s</item>
      <item>Spherical mapping with areal smoothing 77s</item>
      <item>Spherical registration 279s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3969 0.6619 mm</item>
      <item>Surface intensity / position RMSE: 0.0647 / 0.0641</item>
      <item>Euler number / defect number / defect size: 16.0 / 10.5 / 0.57%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_11677/ds/sub-NC244/surf/lh.thickness.sub-NC244_ses-20190715_acq-highres_run-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_11677/ds/sub-NC244/surf/rh.thickness.sub-NC244_ses-20190715_acq-highres_run-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_11677/ds/sub-NC244/sub-NC244_ses-20190715_acq-highres_run-01_T1w.nii</item>
      <item>Surface ROI estimation: 8s</item>
      <item>Surface and thickness estimation takes: 1652s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 18s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 62s</item>
      <item>ROI estimation of 'lpba40' atlas 18s</item>
      <item>ROI estimation of 'hammers' atlas 42s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 15s</item>
      <item>ROI estimation of 'aal3' atlas 25s</item>
      <item>ROI estimation of 'mori' atlas 38s</item>
      <item>ROI estimation of 'anatomy3' atlas 55s</item>
      <item>ROI estimation of 'julichbrain' atlas 72s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 117s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 175s</item>
      <item>Write results 176s</item>
      <item>706s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_11677/ds/sub-NC244/report/catreport_sub-NC244_ses-20190715_acq-highres_run-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 58 minute(s) and 27 second(s).</item>
      <item>Image Quality Rating (IQR): 79.87% (C+)</item>
      <item>GM volume (GMV): 44.50% (540.39 / 1214.31 ml)</item>
      <item>GM thickness (GMT): 2.40 0.66 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_11677/ds/sub-NC244/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_11677/ds/sub-NC244/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_11677/ds/sub-NC244/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>