CORR_cat12.8.1/XHCUMS/sub-0025995/ses-4/report/cat_sub-0025995_ses-4_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   <filedata>
      <path>/var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4</path>
      <file>sub-0025995_ses-4_run-1_T1w</file>
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      <F>/var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/mri/msub-0025995_ses-4_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/mri/p0sub-0025995_ses-4_run-1_T1w.nii</Fp0>
      <fnames>../XHCUMS/sub-0025995/ses-4/sub-0025995_ses-4_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>
               </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>
                  <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>
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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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                  <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>
                  <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>
            </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>
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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>
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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>
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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>
            </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>
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         </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>
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         <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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         <shootingtpms>
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      <ICR>1.76152634620667</ICR>
      <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
      <SurfaceDefectArea>1.20959607055979</SurfaceDefectArea>
      <SurfaceDefectNumber>1.725</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.3919894695282</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.48493421077728</SurfacePositionRMSE>
      <SIQR>2.30033586138815</SIQR>
      <IQR>2.3787348088308</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>20231031-035851</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>30</SurfaceEulerNumber>
         <SurfaceDefectArea>0.838384282239144</SurfaceDefectArea>
         <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0695994719862938</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0742467120289803</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>30</EC_abs>
      <defect_size>0.838384282239144</defect_size>
      <vol_abs_CGW>[222.205520916644 597.312829367675 482.734329887888 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.686831334169365</vol_abs_WMH>
      <vol_rel_WMH>0.000527417869532462</vol_rel_WMH>
      <surf_TSA>1799.96763960615</surf_TSA>
      <vol_TIV>1302.25268017221</vol_TIV>
      <vol_rel_CGW>[0.17063164798959 0.458676598222618 0.370691753787792 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.38348328629598 0.629936379381665]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.36868166923523 0.75170462557939 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.78978359073814 0.242250549112837 0.333727446357486;2.42405642742279 0.180141225288086 0.413601796595703;3.08353642921058 0.266130160055734 0.252670757046811]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.836467356717746 0.263647294361097 0.493301731244847;4.08950172518966 0.385449600209703 0.506698268755153]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.22427206913684</vol_TIV>
      <vol_rel_CGW>[0.914361494065912 6.08758258302115 4.5073950033727 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.05274178695325</vol_rel_WMH>
      <surf_TSA>8.58520851242078</surf_TSA>
      <SQR>5.0323231179177</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11534.3353473706 0.508386749150519]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00150824431329966 0.00131147797219455 0.0269673559814692]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[715.572885504483 433.248418927636 392.093409462643 534.106899566245 657.731998540513 9272.86629752499]</SPMvols0>
      <SPMvols1>[619.092498738877 402.312044185751 236.500727960975 482.192529918164 598.657884194475 9196.0822429921]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[160.80029296875 329.134490966797 423.413208007812]</T3th>
            <Tth>
               <T3th>[-7.40838003158569 -7.40838432312012 4.28499031066895 160.80029296875 329.134490966797 423.413208007812 554.719665527344 1462.34594726562]</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>[0.0217070244252682 0.0806831568479538 0.0889695957303047 0 0]</dtc>
         <ll>[0.0835813146059205 0 0.0835813146059205 0;0.189500037075377 0.011289658380442 0.200789695455819 2407.4970703125;0.189500037075377 0.011289658380442 0.200789695455819 2407.4970703125]</ll>
         <rmsdtc>[0.0461163073778152 0.103178039193153 0.113704763352871]</rmsdtc>
         <rmsgdt>[0.0328157991170883 0.0461747124791145 0.0562377162277699]</rmsgdt>
         <rmsdt>0.113704763352871</rmsdt>
         <dt>0.0889695957303047</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>[0.00975606124848127 0.0367130972445011 0.0522448495030403 0.0604530982673168 0.066113606095314 0.074144721031189]</dtc>
         <ll>[0.0836020782848589 0 0.0836020782848589 0;0.218223565323565 0.0145765415140415 0.232800106837607 7461.3671875;0.194049928999378 0.0177300235958099 0.211779952595187 12760.5107421875;0.172776195964469 0.0195019424018244 0.192278138366293 21028.3984375;0.156348661476557 0.0220484909277887 0.178397152404346 38570.59375;0.156348661476557 0.0220484909277887 0.178397152404346 38570.59375]</ll>
         <rmsdtc>[0.0114227766171098 0.0420386157929897 0.0627186670899391 0.0871192812919617 0.111121773719788 0.116150379180908]</rmsdtc>
         <rmsgdt>[0.00349599006585777 0.0136962747201324 0.0291765779256821 0.049230769276619 0.0721405223011971 0.0720494315028191]</rmsgdt>
         <rmsdt>0.116150379180908</rmsdt>
         <dt>0.074144721031189</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 30s</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 3s</item>
      <item>Affine registration 5s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 5s</item>
      <item>Use initial fine affine registration. 34s</item>
      <item>SPM preprocessing 1 (estimate 2): 35s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 10s</item>
      <item>Update Segmentation 11s</item>
      <item>Update Skull-Stripping 24s</item>
      <item>Update probability maps 5s</item>
      <item>51s</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 = 1.00) 7s</item>
      <item>Estimate local tissue thresholds (WM) 11s</item>
      <item>Estimate local tissue thresholds (GM) 15s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 27s</item>
      <item>65s</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'=0.05) 11s</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): 19s</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) 1s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 1s</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 | 0.0836 0.0000 0.0836 | 32.0000</item>
      <item>2 | 2.50 | 0.0808 0.0012 0.0821 | 29.4886</item>
      <item>3 | 2.50 | 0.0800 0.0019 0.0819 | 26.9772</item>
      <item>4 | 2.50 | 0.0796 0.0021 0.0817 | 24.6107</item>
      <item>5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548</item>
      <item>6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989</item>
      <item>7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688</item>
      <item>8 | 2.50 | 0.0783 0.0026 0.0809 | 17.4455</item>
      <item>9 | 2.50 | 0.0780 0.0027 0.0807 | 15.9223</item>
      <item>10 | 2.50 | 0.0776 0.0028 0.0804 | 14.6627</item>
      <item>11 | 2.50 | 0.0772 0.0029 0.0802 | 13.4764</item>
      <item>12 | 2.50 | 0.0769 0.0030 0.0799 | 12.3015</item>
      <item>13 | 2.50 | 0.0765 0.0031 0.0796 | 11.3776</item>
      <item>14 | 2.50 | 0.0761 0.0032 0.0793 | 10.4537</item>
      <item>15 | 2.25 | 0.0759 0.0033 0.0792 | 9.5920</item>
      <item>16 | 2.25 | 0.0727 0.0049 0.0776 | 8.8725</item>
      <item>29 | 2.00 | 0.0736 0.0022 0.0758 | 3.3283</item>
      <item>30 | 2.00 | 0.0670 0.0048 0.0718 | 3.1221</item>
      <item>31 | 2.00 | 0.0647 0.0059 0.0706 | 2.9160</item>
      <item>43 | 1.75 | 0.0634 0.0034 0.0668 | 1.5785</item>
      <item>44 | 1.75 | 0.0590 0.0057 0.0647 | 1.5194</item>
      <item>45 | 1.75 | 0.0576 0.0065 0.0641 | 1.4626</item>
      <item>57 | 1.50 | 0.0562 0.0047 0.0609 | 1.0900</item>
      <item>58 | 1.50 | 0.0531 0.0067 0.0599 | 1.0730</item>
      <item>59 | 1.50 | 0.0521 0.0073 0.0595 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 97s</item>
      <item>Prepare output 6s</item>
      <item>103s</item>
      <item>Jacobian determinant (RMS): 0.011 0.042 0.063 0.087 0.111 | 0.116150</item>
      <item>Template Matching: 0.084 0.218 0.194 0.173 0.156 | 0.156349</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: 21s</item>
      <item>CSF distance: 8s</item>
      <item>PBT2x thickness: 23s</item>
      <item>55s</item>
      <item>Create initial surface 41s</item>
      <item>Topology correction: 54s</item>
      <item>Surface refinement: 50s</item>
      <item>Reduction of surface collisions with optimization: 34s</item>
      <item>Spherical mapping with areal smoothing 45s</item>
      <item>Spherical registration 164s</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>48s</item>
      <item>Create initial surface 41s</item>
      <item>Topology correction: 54s</item>
      <item>Surface refinement: 53s</item>
      <item>Reduction of surface collisions with optimization: 34s</item>
      <item>Spherical mapping with areal smoothing 45s</item>
      <item>Spherical registration 176s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3834 0.6297 mm</item>
      <item>Surface intensity / position RMSE: 0.0696 / 0.0742</item>
      <item>Euler number / defect number / defect size: 30.0 / 14.5 / 0.84%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/surf/lh.thickness.sub-0025995_ses-4_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/surf/rh.thickness.sub-0025995_ses-4_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/sub-0025995_ses-4_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 5s</item>
      <item>Surface and thickness estimation takes: 948s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 6s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 21s</item>
      <item>ROI estimation of 'lpba40' atlas 6s</item>
      <item>ROI estimation of 'hammers' atlas 15s</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 9s</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>224s</item>
      <item>Quality check: 6s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/report/catreport_sub-0025995_ses-4_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 28 minute(s) and 33 second(s).</item>
      <item>Image Quality Rating (IQR): 81.21% (B-)</item>
      <item>GM volume (GMV): 45.87% (597.31 / 1302.25 ml)</item>
      <item>GM thickness (GMT): 2.38 0.63 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3396820/ds/XHCUMS/sub-0025995/ses-4/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>