CORR_cat12.8.1/MPG_1/sub-0027449/ses-1/report/cat_sub-0027449_ses-1_acq-inv1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <path>/var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1</path>
      <file>sub-0027449_ses-1_acq-inv1_run-1_T1w</file>
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      <Fp0>/var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/mri/p0sub-0027449_ses-1_acq-inv1_run-1_T1w.nii</Fp0>
      <fnames>..s/MPG_1/sub-0027449/ses-1/sub-0027449_ses-1_acq-inv1_run-1_T1w</fnames>
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         <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>
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         </darteltpm>
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         </shootingtpm>
         <shootingT1>
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         </shootingT1>
         <brainmask>
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         </brainmask>
         <T1>
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         </T1>
         <cat12atlas>
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         <pbtres>0.5</pbtres>
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         <add_parahipp>0.1</add_parahipp>
         <colormap>BCGWHw</colormap>
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         <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>
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               <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/lpba40.nii</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</td>
               <td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
               <td>0</td>
               <td>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
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               <td>
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            <tr>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
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            <tr>
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               <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>
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               <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/anatomy3.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/julichbrain.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
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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/Schaefer2018_200Parcels_17Networks_order.nii</td>
               <td>1</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>
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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>
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            <tr>
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                  <item>csf</item>
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               <td>[false]</td>
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            <tr>
               <td>Desikan</td>
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               <td>0</td>
               <td>1</td>
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            <tr>
               <td>Destrieux</td>
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               <td>0</td>
               <td>1</td>
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            <tr>
               <td>HCP</td>
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               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_100P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_200P_17N</td>
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               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_400P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_600P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <VT>15</VT>
            <NV>17</NV>
            <HC>19</HC>
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            <PH>25</PH>
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         <inv_weighting>[true]</inv_weighting>
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      <contrastr>3.1272919178009</contrastr>
      <NCR>7.93789196014404</NCR>
      <ICR>2.73153805732727</ICR>
      <SurfaceEulerNumber>3.24489795918367</SurfaceEulerNumber>
      <SurfaceDefectArea>1.34462581693939</SurfaceDefectArea>
      <SurfaceDefectNumber>2.6</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>2.65834641456604</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>2.66187143325806</SurfacePositionRMSE>
      <SIQR>7.00747624989803</SIQR>
      <IQR>7.27907987383551</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>
      <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>20231031-032159</date>
      <cat_warnings>
         <item>
            <identifier>cat_run_job1639:nonT1contrast</identifier>
            <message>A non-T1 contrast was detected and the NEW EXPERIMENTAL &lt;/br&gt;PIPELINE is used! If it is was a high-resolution T1 image, &lt;/br&gt;the initial segmentation might have failed, probably due &lt;/br&gt;to alignment problems (please check the image orientation).</message>
            <level>1</level>
            <data>[94.74383 33.28801 64.88709 14.9017 39.8669 11.65636]</data>
         </item>
         <item>
            <identifier>cat_main:skipLAS</identifier>
            <message>Skip LAS due to image contrast. Use global normalization.</message>
            <level>0</level>
         </item>
      </cat_warnings>
   </software>
   <subjectmeasures>
      <software/>
      <qualitymeasures>
         <software/>
         <SurfaceEulerNumber>46</SurfaceEulerNumber>
         <SurfaceDefectArea>1.37850326775757</SurfaceDefectArea>
         <SurfaceDefectNumber>32</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.132917314767838</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.133093565702438</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>46</EC_abs>
      <defect_size>1.37850326775757</defect_size>
      <vol_abs_CGW>[180.256899712062 752.493786378803 278.739952176178 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>1206.93676390916</surf_TSA>
      <vol_TIV>1211.49063826704</vol_TIV>
      <vol_rel_CGW>[0.148789345966311 0.621130500401716 0.230080153631973 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[3.18507791575397 1.02500556511015]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[3.24338006973267 1.68748467533885 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.30101040711338 0.629707041336518 0.148440235423579;2.97471644562144 0.3893271915438 0.498907914700635;4.23052372846984 0.45838411954175 0.352651849875786]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[NaN NaN NaN;NaN NaN NaN]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.80132341820635</vol_TIV>
      <vol_rel_CGW>[0.522078770946676 9.00521732043312 1.98204298907997 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>4.12007171981312</surf_TSA>
      <SQR>7.36416051992067</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 8429.56756933594 0.657423735570972]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0621318072080612 0.0599515065550804 0.0941659584641457]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[878.352592512587 301.898270513965 229.182012468637 723.214055785463 2096.41611444664 4196.04485712427]</SPMvols0>
      <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>[0.0180902499705553 0.0676496848464012 0.075947031378746 0 0]</dtc>
         <ll>[0.0911938322692358 0 0.0911938322692358 0;0.221442507667129 0.0115109543267991 0.232953461993928 2454.68798828125;0.221442507667129 0.0115109543267991 0.232953461993928 2454.68798828125]</ll>
         <rmsdtc>[0.0497575923800468 0.101227417588234 0.118432931602001]</rmsdtc>
         <rmsgdt>[0.0369273796677589 0.0624098032712936 0.0798940062522888]</rmsgdt>
         <rmsdt>0.118432931602001</rmsdt>
         <dt>0.075947031378746</dt>
      </reginitp>
      <SPMvols1>[830.600994439118 323.781255624001 167.217344013035 809.985947207562 2115.99056420746 4181.92374302762]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[94.74383 33.28801 64.88709]</T3th>
            <Tth>
               <T3th>[-0.127660170197487 4.91036224365234 34.6372947692871 65.2189483642578 78.9006576538086 523.622619628906]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>
               <CGW>[0.31894044897248 0.671240948527448 1.02768523254572]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.956821346917441 2.01372284558234 3.08305569763715 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.319234971989729 0.670231880116328 1.02735403487076]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.957704915969188 2.01069564034898 3.08206210461228 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.32916268959301 0.666295964152386 0.999953720789361]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.98748806877903 1.99888789245716 2.99986116236808 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.329325781602537 0.666185632007913 0.999957178218079]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.987977344807611 1.99855689602374 2.99987153465424 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm2postamap>
      </tths>
      <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>[0.0140672195702791 0.0615053661167622 0.0878453403711319 0.100819818675518 0.109916098415852 0.134528338909149]</dtc>
         <ll>[0.0897145172617075 0 0.0897145172617075 0;0.208448244810745 0.0273504502442002 0.235798695054945 14000.01171875;0.178515590263883 0.0263978366954421 0.204913426959325 18998.83984375;0.158248234791407 0.0248100882128999 0.183058323004307 26752.0234375;0.14482067620143 0.0269393482547548 0.171760024456185 47126.4296875;0.14482067620143 0.0269393482547548 0.171760024456185 47126.4296875]</ll>
         <rmsdtc>[0.0165568273514509 0.0668538138270378 0.110047586262226 0.159203201532364 0.204876691102982 0.215512335300446]</rmsdtc>
         <rmsgdt>[0.00475508067756891 0.0210950989276171 0.0480326190590858 0.0840151906013489 0.120366543531418 0.128809154033661]</rmsgdt>
         <rmsdt>0.215512335300446</rmsdt>
         <dt>0.134528338909149</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./ses-1/sub-0027449_ses-1_acq-inv1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 242s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 9s</item>
      <item>Estimate background 9s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 5s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 11s</item>
      <item>57s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 26s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 30s</item>
      <item>SPM preprocessing 1 (estimate 2): 47s</item>
      <item>----------------------------------------------------------------------------</item>
      <item>WARNING 01: cat_run_job1639:nonT1contrast</item>
      <item>A non-T1 contrast was detected and the NEW EXPERIMENTAL</item>
      <item>PIPELINE is used! If it is was a high-resolution T1 image,</item>
      <item>the initial segmentation might have failed, probably due</item>
      <item>to alignment problems (please check the image orientation).</item>
      <item>----------------------------------------------------------------------------</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 26s</item>
      <item>Update segmentation 44s</item>
      <item>Update skull-stripping 21s</item>
      <item>Update probability maps 2s</item>
      <item>Update registration 32s</item>
      <item>125s</item>
      <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 61s</item>
      <item>------------------------------------------------------------------------</item>
      <item>NOTE 01: cat_main:skipLAS</item>
      <item>Skip LAS due to image contrast. Use global normalization.</item>
      <item>------------------------------------------------------------------------</item>
      <item>134s</item>
      <item>SANLM denoising after LAS (medium) 107s</item>
      <item>168s</item>
      <item>--- Update Ym and Ymi ---</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 1s</item>
      <item>Ventricle detection 2s</item>
      <item>Blood vessel detection 1s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 0s</item>
      <item>Side alignment 1s</item>
      <item>Final corrections 7s</item>
      <item>18s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 66s</item>
      <item>AMAP peaks: [0.94 0.05,0.35 0.09,0.64 0.05]</item>
      <item>--- Update Ym and Ymi ---</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 | 0.0897 0.0000 0.0897 | 32.0000</item>
      <item>2 | 2.50 | 0.0842 0.0020 0.0862 | 29.4886</item>
      <item>3 | 2.50 | 0.0825 0.0031 0.0856 | 26.9772</item>
      <item>4 | 2.50 | 0.0816 0.0036 0.0852 | 24.6107</item>
      <item>5 | 2.50 | 0.0809 0.0040 0.0849 | 22.6548</item>
      <item>6 | 2.50 | 0.0803 0.0042 0.0845 | 20.6989</item>
      <item>7 | 2.50 | 0.0796 0.0044 0.0840 | 18.9688</item>
      <item>8 | 2.50 | 0.0790 0.0046 0.0836 | 17.4455</item>
      <item>9 | 2.50 | 0.0783 0.0048 0.0831 | 15.9223</item>
      <item>10 | 2.50 | 0.0776 0.0050 0.0826 | 14.6627</item>
      <item>11 | 2.50 | 0.0769 0.0052 0.0822 | 13.4764</item>
      <item>12 | 2.50 | 0.0762 0.0054 0.0816 | 12.3015</item>
      <item>13 | 2.50 | 0.0755 0.0056 0.0811 | 11.3776</item>
      <item>14 | 2.50 | 0.0748 0.0058 0.0806 | 10.4537</item>
      <item>15 | 2.25 | 0.0756 0.0061 0.0817 | 9.5920</item>
      <item>16 | 2.25 | 0.0714 0.0083 0.0797 | 8.8725</item>
      <item>17 | 2.25 | 0.0695 0.0091 0.0786 | 8.1530</item>
      <item>29 | 2.00 | 0.0696 0.0042 0.0738 | 3.3283</item>
      <item>30 | 2.00 | 0.0620 0.0077 0.0697 | 3.1221</item>
      <item>31 | 2.00 | 0.0595 0.0088 0.0683 | 2.9160</item>
      <item>43 | 1.75 | 0.0582 0.0052 0.0634 | 1.5785</item>
      <item>44 | 1.75 | 0.0541 0.0076 0.0616 | 1.5194</item>
      <item>45 | 1.75 | 0.0527 0.0083 0.0610 | 1.4626</item>
      <item>57 | 1.50 | 0.0521 0.0063 0.0584 | 1.0900</item>
      <item>58 | 1.50 | 0.0492 0.0084 0.0575 | 1.0730</item>
      <item>59 | 1.50 | 0.0483 0.0090 0.0573 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 110s</item>
      <item>Prepare output 12s</item>
      <item>122s</item>
      <item>Jacobian determinant (RMS): 0.017 0.067 0.110 0.159 0.205 | 0.215512</item>
      <item>Template Matching: 0.090 0.208 0.179 0.158 0.145 | 0.144821</item>
      <item>Write result maps: 45s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 15s</item>
      <item>CSF distance: 9s</item>
      <item>PBT2x thickness: 27s</item>
      <item>55s</item>
      <item>Create initial surface 43s</item>
      <item>Topology correction: 36s</item>
      <item>Surface refinement: 41s</item>
      <item>Reduction of surface collisions with optimization: 35s</item>
      <item>Spherical mapping with areal smoothing 33s</item>
      <item>Spherical registration 194s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 15s</item>
      <item>CSF distance: 10s</item>
      <item>PBT2x thickness: 27s</item>
      <item>56s</item>
      <item>Create initial surface 41s</item>
      <item>Topology correction: 36s</item>
      <item>Surface refinement: 32s</item>
      <item>Reduction of surface collisions with optimization: 57s</item>
      <item>Spherical mapping with areal smoothing 33s</item>
      <item>Spherical registration 187s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 3.1854 1.0247 mm</item>
      <item>Surface intensity / position RMSE: 0.1329 / 0.1331</item>
      <item>Euler number / defect number / defect size: 46.0 / 32.0 / 1.38%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/surf/lh.thickness.sub-0027449_ses-1_acq-inv1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/surf/rh.thickness.sub-0027449_ses-1_acq-inv1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/sub-0027449_ses-1_acq-inv1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 1585s</item>
      <item>Surface and thickness estimation takes: 1310s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 13s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 46s</item>
      <item>ROI estimation of 'lpba40' atlas 13s</item>
      <item>ROI estimation of 'hammers' atlas 32s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 11s</item>
      <item>ROI estimation of 'aal3' atlas 18s</item>
      <item>ROI estimation of 'mori' atlas 28s</item>
      <item>ROI estimation of 'anatomy3' atlas 40s</item>
      <item>ROI estimation of 'julichbrain' atlas 53s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 39s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 85s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 128s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s</item>
      <item>Write results 12s</item>
      <item>543s</item>
      <item>Quality check: 15s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/report/catreport_sub-0027449_ses-1_acq-inv1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 46 minute(s) and 22 second(s).</item>
      <item>Image Quality Rating (IQR): 32.21% (F)</item>
      <item>GM volume (GMV): 62.11% (752.49 / 1211.49 ml)</item>
      <item>GM thickness (GMT): 3.19 1.03 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>