ds003639_ReproVBM/sub-NC250/report/cat_sub-NC250_ses-20190814_acq-highres_run-02_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_28111/ds/sub-NC250</path>
      <file>sub-NC250_ses-20190814_acq-highres_run-02_T1w</file>
      <fname>/var/lib/condor/execute/dir_28111/ds/sub-NC250/sub-NC250_ses-20190814_acq-highres_run-02_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_28111/ds/sub-NC250/sub-NC250_ses-20190814_acq-highres_run-02_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_28111/ds/sub-NC250/mri/msub-NC250_ses-20190814_acq-highres_run-02_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_28111/ds/sub-NC250/mri/p0sub-NC250_ses-20190814_acq-highres_run-02_T1w.nii</Fp0>
      <fnames>..11/ds/sub-NC250/..-20190814_acq-highres_run-02_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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
         </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>
            <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>
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         <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>
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                  <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/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>
                  <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/hammers.nii</td>
               <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/thalamus.nii</td>
               <td>0</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/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>
                  <item>csf</item>
                  <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/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>
               </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/anatomy3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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               <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>
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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>
                  <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_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>
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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>
            </tr>
            <tr>
               <td>Schaefer2018_200P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_400P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_600P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
         </satlas>
         <LAB>
            <NB>0</NB>
            <CT>1</CT>
            <CB>3</CB>
            <BG>5</BG>
            <BV>7</BV>
            <TH>9</TH>
            <ON>11</ON>
            <MB>13</MB>
            <BS>13</BS>
            <VT>15</VT>
            <NV>17</NV>
            <HC>19</HC>
            <HD>21</HD>
            <HI>23</HI>
            <PH>25</PH>
            <LE>27</LE>
         </LAB>
         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
         <regmethod>
            <shooting>
               <shootingtpm>
                  <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
               </shootingtpm>
               <regstr>0.5</regstr>
            </shooting>
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         <restypes>
            <optimal>[1 0.3]</optimal>
         </restypes>
         <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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
         </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>
         </shootingtpms>
         <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>
         </templates>
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         <AMAPframing>1</AMAPframing>
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   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>182</SurfaceEulerNumber>
      <SurfaceDefectArea>5.80865297090949</SurfaceDefectArea>
      <SurfaceDefectNumber>61</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0960851758718491</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.14111715555191</SurfacePositionRMSE>
      <res_vx_vol>[1 1 1]</res_vx_vol>
      <res_vx_voli>[1 1 1]</res_vx_voli>
      <res_RMS>1</res_RMS>
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      <tissue_mn>[7.62799978256226 50.559684753418 149.703033447266 245.847732543945]</tissue_mn>
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      <tissue_weighting>T1</tissue_weighting>
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      <contrast>86.6893463134766</contrast>
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      <NCR>0.266371637582779</NCR>
      <ICR>0.347301155328751</ICR>
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   <qualityratings>
      <res_vx_vol>[2 2 2]</res_vx_vol>
      <res_RMS>2</res_RMS>
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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>2.79412364959717</contrastr>
      <NCR>4.1549186706543</NCR>
      <ICR>1.32118344306946</ICR>
      <SurfaceEulerNumber>10.1836734693878</SurfaceEulerNumber>
      <SurfaceDefectArea>2.45216324272737</SurfaceDefectArea>
      <SurfaceDefectNumber>4.05</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.92170357704163</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>2.82234311103821</SurfacePositionRMSE>
      <IQR>3.81144821725625</IQR>
   </qualityratings>
   <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>20220712-141652</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>182</SurfaceEulerNumber>
         <SurfaceDefectArea>5.80865297090949</SurfaceDefectArea>
         <SurfaceDefectNumber>61</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0960851758718491</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.14111715555191</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>182</EC_abs>
      <defect_size>5.80865297090949</defect_size>
      <vol_abs_CGW>[245.214003921569 723.332956862745 559.838219607843 0 0]</vol_abs_CGW>
      <vol_abs_WMH>2.83906666666667</vol_abs_WMH>
      <vol_rel_WMH>0.00185755966695399</vol_rel_WMH>
      <surf_TSA>2136.40570858223</surf_TSA>
      <vol_TIV>1528.38518039216</vol_TIV>
      <vol_rel_CGW>[0.160439925136313 0.473266141377497 0.36629393348619 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.30659382289605 0.697408488729705]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.34824514389038 0.842896031271453 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.55371149933791 0.329992647321181 0.259854434989808;2.3168992805345 0.207369551439441 0.422437790438333;3.04354677896314 0.287651130428968 0.317707774571859]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.545462570578426 0.216504546888728 0.699639724310777;3.95460248969524 0.321543277768952 0.300360275689223]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.3827593052017</vol_TIV>
      <vol_rel_CGW>[0.73132049454586 6.34960742416481 4.4284111617491 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.1857559666954</vol_rel_WMH>
      <surf_TSA>8.62370999475165</surf_TSA>
      <SQR>5.22796204817952</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.267603614113548 1 1 8447.706 0.529158587878315]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0205974839627743 0.00748235918581486 0.311133682727814]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[871.55028627451 536.23457254902 478.655419607843 1072.78565490196 2359.66285098039 7090.67334117647]</SPMvols0>
      <SPMvols1>[714.156909803922 490.697133333333 265.166945098039 822.30977254902 1412.33780784314 7830.86952156863]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[66.923698425293 155.50439453125 237.255706787109]</T3th>
            <Tth>
               <T3th>[0 1.77474975585938 10.2783536911011 66.923698425293 155.50439453125 237.255706787109 322.421691894531 860.04638671875]</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>[0.0214205402880907 0.0734774023294449 0.0806465297937393 0 0]</dtc>
         <ll>[0.0857039715300183 0 0.0857039715300183 0;0.20175573891666 0.00991091894216183 0.211666657858822 2113.48364257812;0.20175573891666 0.00991091894216183 0.211666657858822 2113.48364257812]</ll>
         <rmsdtc>[0.0462703816592693 0.0954690501093864 0.105517856776714]</rmsdtc>
         <rmsgdt>[0.0328494720160961 0.0448358170688152 0.0551156029105186]</rmsgdt>
         <rmsdt>0.105517856776714</rmsdt>
         <dt>0.0806465297937393</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>[0.00931434333324432 0.035722590982914 0.0465615727007389 0.0554253235459328 0.0621544793248177 0.0690545216202736]</dtc>
         <ll>[0.0866801124745765 0 0.0866801124745765 0;0.22308601953602 0.0152973624465812 0.238383381982601 7830.33740234375;0.208780756226102 0.0167667734411473 0.225547529667249 12067.248046875;0.189353761736371 0.0191264700459392 0.20848023178231 20623.537109375;0.173288692305098 0.0224865881664535 0.195775280471551 39336.98046875;0.173288692305098 0.0224865881664535 0.195775280471551 39336.98046875]</ll>
         <rmsdtc>[0.0111543433740735 0.0387797839939594 0.0589596480131149 0.0814817473292351 0.105378895998001 0.110663086175919]</rmsdtc>
         <rmsgdt>[0.00332429748959839 0.0124419210478663 0.0268663242459297 0.0460622012615204 0.0682916566729546 0.0709713771939278]</rmsgdt>
         <rmsdt>0.110663086175919</rmsdt>
         <dt>0.0690545216202736</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-NC250_ses-20190814_acq-highres_run-02_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 53s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 5s</item>
      <item>Final correction 7s</item>
      <item>Final scaling 8s</item>
      <item>53s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 13s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 90s</item>
      <item>SPM preprocessing 1 (estimate 2): 91s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 22s</item>
      <item>Update Segmentation 24s</item>
      <item>Update Skull-Stripping 52s</item>
      <item>Update probability maps 10s</item>
      <item>108s</item>
      <item>Global intensity correction: 20s</item>
      <item>SANLM denoising after intensity normalization (medium): 11s</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 = 1.15) 20s</item>
      <item>Estimate local tissue thresholds (WM) 22s</item>
      <item>Estimate local tissue thresholds (GM) 28s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 27s</item>
      <item>109s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 11s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 20s</item>
      <item>Blood vessel detection 11s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.05) 28s</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>88s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s</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) 6s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>16s</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 | 0.0867 0.0000 0.0867 | 32.0000</item>
      <item>2 | 2.50 | 0.0838 0.0013 0.0850 | 29.4886</item>
      <item>3 | 2.50 | 0.0829 0.0019 0.0848 | 26.9772</item>
      <item>4 | 2.50 | 0.0825 0.0021 0.0847 | 24.6107</item>
      <item>5 | 2.50 | 0.0822 0.0023 0.0845 | 22.6548</item>
      <item>6 | 2.50 | 0.0819 0.0023 0.0843 | 20.6989</item>
      <item>7 | 2.50 | 0.0816 0.0024 0.0841 | 18.9688</item>
      <item>8 | 2.50 | 0.0813 0.0025 0.0839 | 17.4455</item>
      <item>9 | 2.50 | 0.0810 0.0026 0.0836 | 15.9223</item>
      <item>10 | 2.50 | 0.0807 0.0027 0.0834 | 14.6627</item>
      <item>11 | 2.50 | 0.0804 0.0028 0.0832 | 13.4764</item>
      <item>12 | 2.50 | 0.0801 0.0028 0.0829 | 12.3015</item>
      <item>13 | 2.50 | 0.0798 0.0029 0.0826 | 11.3776</item>
      <item>14 | 2.50 | 0.0794 0.0029 0.0824 | 10.4537</item>
      <item>15 | 2.25 | 0.0791 0.0030 0.0821 | 9.5920</item>
      <item>16 | 2.25 | 0.0762 0.0044 0.0806 | 8.8725</item>
      <item>17 | 2.25 | 0.0751 0.0049 0.0800 | 8.1530</item>
      <item>18 | 2.25 | 0.0744 0.0051 0.0795 | 7.5234</item>
      <item>29 | 2.00 | 0.0766 0.0024 0.0790 | 3.3283</item>
      <item>30 | 2.00 | 0.0713 0.0047 0.0761 | 3.1221</item>
      <item>31 | 2.00 | 0.0696 0.0056 0.0752 | 2.9160</item>
      <item>43 | 1.75 | 0.0690 0.0032 0.0722 | 1.5785</item>
      <item>44 | 1.75 | 0.0645 0.0055 0.0701 | 1.5194</item>
      <item>45 | 1.75 | 0.0631 0.0064 0.0695 | 1.4626</item>
      <item>57 | 1.50 | 0.0622 0.0046 0.0668 | 1.0900</item>
      <item>58 | 1.50 | 0.0588 0.0068 0.0657 | 1.0730</item>
      <item>59 | 1.50 | 0.0578 0.0075 0.0653 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 237s</item>
      <item>Prepare output 12s</item>
      <item>249s</item>
      <item>Jacobian determinant (RMS): 0.011 0.039 0.059 0.081 0.105 | 0.110663</item>
      <item>Template Matching: 0.087 0.223 0.209 0.189 0.173 | 0.173289</item>
      <item>Write result maps: 37s</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: 20s</item>
      <item>PBT2x thickness: 64s</item>
      <item>135s</item>
      <item>Create initial surface 120s</item>
      <item>Topology correction: 150s</item>
      <item>Surface refinement: 170s</item>
      <item>Reduction of surface collisions with optimization: 205s</item>
      <item>Spherical mapping with areal smoothing 119s</item>
      <item>Spherical registration 280s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 39s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 65s</item>
      <item>135s</item>
      <item>Create initial surface 121s</item>
      <item>Topology correction: 146s</item>
      <item>Surface refinement: 141s</item>
      <item>Reduction of surface collisions with optimization: 112s</item>
      <item>Spherical mapping with areal smoothing 116s</item>
      <item>Spherical registration 289s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3066 0.6969 mm</item>
      <item>Surface intensity / position RMSE: 0.0961 / 0.1411</item>
      <item>Euler number / defect number / defect size: 182.0 / 61.0 / 5.81%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28111/ds/sub-NC250/surf/lh.thickness.sub-NC250_ses-20190814_acq-highres_run-02_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28111/ds/sub-NC250/surf/rh.thickness.sub-NC250_ses-20190814_acq-highres_run-02_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_28111/ds/sub-NC250/sub-NC250_ses-20190814_acq-highres_run-02_T1w.nii</item>
      <item>Surface ROI estimation: 10s</item>
      <item>Surface and thickness estimation takes: 2365s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 17s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 57s</item>
      <item>ROI estimation of 'lpba40' atlas 17s</item>
      <item>ROI estimation of 'hammers' atlas 43s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 16s</item>
      <item>ROI estimation of 'aal3' atlas 26s</item>
      <item>ROI estimation of 'mori' atlas 39s</item>
      <item>ROI estimation of 'anatomy3' atlas 54s</item>
      <item>ROI estimation of 'julichbrain' atlas 74s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 153s</item>
      <item>Write results 154s</item>
      <item>688s</item>
      <item>Quality check: 7s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_28111/ds/sub-NC250/report/catreport_sub-NC250_ses-20190814_acq-highres_run-02_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 70 minute(s) and 7 second(s).</item>
      <item>Image Quality Rating (IQR): 66.89% (D+)</item>
      <item>GM volume (GMV): 47.33% (723.33 / 1528.39 ml)</item>
      <item>GM thickness (GMT): 2.31 0.70 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_28111/ds/sub-NC250/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>