CORR_cat12.8.1/XHCUMS/sub-0025998/ses-5/report/cat_sub-0025998_ses-5_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   <filedata>
      <path>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5</path>
      <file>sub-0025998_ses-5_run-1_T1w</file>
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      <F>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/sub-0025998_ses-5_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/mri/msub-0025998_ses-5_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/mri/p0sub-0025998_ses-5_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0025998/ses-5/sub-0025998_ses-5_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>
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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>
                  <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/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>
                  <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>
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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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                  <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/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>
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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>
               </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>
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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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               <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>
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               <td>[false]</td>
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            <tr>
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               <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>
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               <regstr>0.5</regstr>
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            <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>
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         <shootingtpms>
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      <ICR>1.93631911277771</ICR>
      <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
      <SurfaceDefectArea>1.12179530249037</SurfaceDefectArea>
      <SurfaceDefectNumber>1.675</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.23064208030701</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.27246844768524</SurfacePositionRMSE>
      <SIQR>2.18166492694858</SIQR>
      <IQR>2.20764972759085</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>20231031-035823</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>22</SurfaceEulerNumber>
         <SurfaceDefectArea>0.48718120996147</SurfaceDefectArea>
         <SurfaceDefectNumber>13.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0615321025252342</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.063623420894146</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>22</EC_abs>
      <defect_size>0.48718120996147</defect_size>
      <vol_abs_CGW>[292.094591784072 589.344375580004 453.241724506288 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.555721552996322</vol_abs_WMH>
      <vol_rel_WMH>0.000416370414572761</vol_rel_WMH>
      <surf_TSA>1765.93395195887</surf_TSA>
      <vol_TIV>1334.68069187036</vol_TIV>
      <vol_rel_CGW>[0.218849791986384 0.441562074861608 0.339588133152008 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.31914340810094 0.631247449975625]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.29836583137512 0.820241031285041 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.69545548564541 0.282466861539605 0.324322591217733;2.34673546514759 0.1845763236617 0.438023241729664;3.03707859288285 0.300050229810228 0.237654167052604]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.750208942157439 0.199256178871816 0.470835639180963;4.16058289847646 0.399025522626184 0.529164360819037]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.10097736154071</vol_TIV>
      <vol_rel_CGW>[1.78034827561753 5.7802096778306 3.94878112701164 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.04163704145728</vol_rel_WMH>
      <surf_TSA>8.56574518960393</surf_TSA>
      <SQR>4.7543674902067</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3355777114 0.518785746483341]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00183331919834018 0.00157350744120777 0.287312746047974]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[707.781089895719 403.796749426469 525.526922473077 4008.98454606031 882.90824967569 5832.84598103392]</SPMvols0>
      <SPMvols1>[583.551889468423 371.968036596245 343.577915826164 5447.66773696611 781.459852529192 4006.73925592738]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[149.311294555664 294.997985839844 383.919403076172]</T3th>
            <Tth>
               <T3th>[-7.09429979324341 -7.09430313110352 7.04771947860718 149.311294555664 294.997985839844 383.919403076172 501.223449707031 1228.70922851562]</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>[0.0191698037087917 0.0827851891517639 0.0932543203234673 0 0]</dtc>
         <ll>[0.0926114097982943 0 0.0926114097982943 0;0.214475285963995 0.013535264874993 0.228010550838988 2886.3681640625;0.214475285963995 0.013535264874993 0.228010550838988 2886.3681640625]</ll>
         <rmsdtc>[0.0446737818419933 0.114400170743465 0.129296377301216]</rmsdtc>
         <rmsgdt>[0.0324707105755806 0.05484314635396 0.0680215433239937]</rmsgdt>
         <rmsdt>0.129296377301216</rmsdt>
         <dt>0.0932543203234673</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>[0.0085271829739213 0.0407141223549843 0.0478054545819759 0.0573131442070007 0.0649645775556564 0.0731911063194275]</dtc>
         <ll>[0.0909900777102837 0 0.0909900777102837 0;0.224049511599512 0.0188300423534799 0.242879553952991 9638.6279296875;0.211159897986973 0.0202241866798803 0.231384084666853 14555.58984375;0.190231497131522 0.0213700681217262 0.211601565253248 23042.74609375;0.172510493879737 0.024229933599022 0.196740427478759 42386.70703125;0.172510493879737 0.024229933599022 0.196740427478759 42386.70703125]</ll>
         <rmsdtc>[0.0106875896453857 0.0397785492241383 0.0662820339202881 0.0903116017580032 0.116075716912746 0.123195119202137]</rmsdtc>
         <rmsgdt>[0.00340614328160882 0.0134280184283853 0.0306725148111582 0.052011601626873 0.0718075484037399 0.0776960402727127]</rmsgdt>
         <rmsdt>0.123195119202137</rmsdt>
         <dt>0.0731911063194275</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025998/ses-5/sub-0025998_ses-5_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 28s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 4s</item>
      <item>Estimate background 3s</item>
      <item>Initial correction 3s</item>
      <item>Refine background 2s</item>
      <item>Final correction 3s</item>
      <item>Final scaling 3s</item>
      <item>22s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 5s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 6s</item>
      <item>Use initial fine affine registration. 35s</item>
      <item>SPM preprocessing 1 (estimate 2): 33s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 10s</item>
      <item>Update Segmentation 12s</item>
      <item>Update Skull-Stripping 25s</item>
      <item>Update probability maps 6s</item>
      <item>53s</item>
      <item>Global intensity correction: 10s</item>
      <item>SANLM denoising after intensity normalization (medium): 13s</item>
      <item>Fast Optimized Shooting registration 20s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 2s</item>
      <item>Prepare partitions 1s</item>
      <item>Prepare segments (LASmod = 1.13) 8s</item>
      <item>Estimate local tissue thresholds (WM) 10s</item>
      <item>Estimate local tissue thresholds (GM) 13s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 25s</item>
      <item>62s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 4s</item>
      <item>Major structures 2s</item>
      <item>Ventricle detection 5s</item>
      <item>Blood vessel detection 5s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.22) 10s</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>32s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 20s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 2s</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>6s</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 | 0.0910 0.0000 0.0910 | 32.0000</item>
      <item>2 | 2.50 | 0.0877 0.0014 0.0891 | 29.4886</item>
      <item>3 | 2.50 | 0.0868 0.0021 0.0889 | 26.9772</item>
      <item>4 | 2.50 | 0.0863 0.0024 0.0887 | 24.6107</item>
      <item>5 | 2.50 | 0.0859 0.0025 0.0885 | 22.6548</item>
      <item>6 | 2.50 | 0.0856 0.0026 0.0882 | 20.6989</item>
      <item>7 | 2.50 | 0.0853 0.0028 0.0880 | 18.9688</item>
      <item>8 | 2.50 | 0.0849 0.0029 0.0878 | 17.4455</item>
      <item>9 | 2.50 | 0.0846 0.0030 0.0875 | 15.9223</item>
      <item>10 | 2.50 | 0.0842 0.0031 0.0873 | 14.6627</item>
      <item>11 | 2.50 | 0.0838 0.0032 0.0870 | 13.4764</item>
      <item>12 | 2.50 | 0.0834 0.0033 0.0867 | 12.3015</item>
      <item>13 | 2.50 | 0.0830 0.0034 0.0864 | 11.3776</item>
      <item>14 | 2.50 | 0.0827 0.0035 0.0861 | 10.4537</item>
      <item>15 | 2.25 | 0.0826 0.0036 0.0862 | 9.5920</item>
      <item>16 | 2.25 | 0.0791 0.0053 0.0844 | 8.8725</item>
      <item>17 | 2.25 | 0.0778 0.0059 0.0837 | 8.1530</item>
      <item>18 | 2.25 | 0.0770 0.0061 0.0831 | 7.5234</item>
      <item>19 | 2.25 | 0.0763 0.0062 0.0826 | 6.9630</item>
      <item>20 | 2.25 | 0.0758 0.0062 0.0820 | 6.4027</item>
      <item>21 | 2.25 | 0.0752 0.0063 0.0815 | 5.9447</item>
      <item>22 | 2.25 | 0.0747 0.0063 0.0810 | 5.5083</item>
      <item>29 | 2.00 | 0.0762 0.0040 0.0802 | 3.3283</item>
      <item>30 | 2.00 | 0.0719 0.0060 0.0779 | 3.1221</item>
      <item>31 | 2.00 | 0.0704 0.0067 0.0771 | 2.9160</item>
      <item>43 | 1.75 | 0.0695 0.0038 0.0733 | 1.5785</item>
      <item>44 | 1.75 | 0.0649 0.0063 0.0712 | 1.5194</item>
      <item>45 | 1.75 | 0.0634 0.0071 0.0705 | 1.4626</item>
      <item>57 | 1.50 | 0.0619 0.0052 0.0671 | 1.0900</item>
      <item>58 | 1.50 | 0.0586 0.0074 0.0660 | 1.0730</item>
      <item>59 | 1.50 | 0.0575 0.0081 0.0656 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 107s</item>
      <item>Prepare output 6s</item>
      <item>113s</item>
      <item>Jacobian determinant (RMS): 0.011 0.040 0.066 0.090 0.116 | 0.123195</item>
      <item>Template Matching: 0.091 0.224 0.211 0.190 0.173 | 0.172510</item>
      <item>Write result maps: 20s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 23s</item>
      <item>CSF distance: 9s</item>
      <item>PBT2x thickness: 24s</item>
      <item>59s</item>
      <item>Create initial surface 43s</item>
      <item>Topology correction: 45s</item>
      <item>Surface refinement: 40s</item>
      <item>Reduction of surface collisions with optimization: 32s</item>
      <item>Spherical mapping with areal smoothing 44s</item>
      <item>Spherical registration 168s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 15s</item>
      <item>CSF distance: 8s</item>
      <item>PBT2x thickness: 23s</item>
      <item>49s</item>
      <item>Create initial surface 41s</item>
      <item>Topology correction: 44s</item>
      <item>Surface refinement: 51s</item>
      <item>Reduction of surface collisions with optimization: 32s</item>
      <item>Spherical mapping with areal smoothing 44s</item>
      <item>Spherical registration 160s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3192 0.6311 mm</item>
      <item>Surface intensity / position RMSE: 0.0615 / 0.0636</item>
      <item>Euler number / defect number / defect size: 22.0 / 13.5 / 0.49%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/surf/lh.thickness.sub-0025998_ses-5_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/surf/rh.thickness.sub-0025998_ses-5_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/sub-0025998_ses-5_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 5s</item>
      <item>Surface and thickness estimation takes: 905s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 6s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 20s</item>
      <item>ROI estimation of 'lpba40' atlas 6s</item>
      <item>ROI estimation of 'hammers' atlas 14s</item>
      <item>ROI estimation of 'thalamus' atlas 1s</item>
      <item>ROI estimation of 'ibsr' atlas 5s</item>
      <item>ROI estimation of 'aal3' atlas 8s</item>
      <item>ROI estimation of 'mori' atlas 11s</item>
      <item>ROI estimation of 'anatomy3' atlas 16s</item>
      <item>ROI estimation of 'julichbrain' atlas 21s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 15s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 34s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 51s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s</item>
      <item>Write results 5s</item>
      <item>221s</item>
      <item>Quality check: 7s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/report/catreport_sub-0025998_ses-5_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 27 minute(s) and 39 second(s).</item>
      <item>Image Quality Rating (IQR): 82.92% (B-)</item>
      <item>GM volume (GMV): 44.16% (589.34 / 1334.68 ml)</item>
      <item>GM thickness (GMT): 2.32 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-5/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>