CORR_cat12.8.1/MPG_1/sub-0027441/ses-1/report/cat_sub-0027441_ses-1_acq-inv1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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   <filedata>
      <path>/var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1</path>
      <file>sub-0027441_ses-1_acq-inv1_run-1_T1w</file>
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      <Fm>/var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/mri/msub-0027441_ses-1_acq-inv1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/mri/p0sub-0027441_ses-1_acq-inv1_run-1_T1w.nii</Fp0>
      <fnames>..s/MPG_1/sub-0027441/ses-1/sub-0027441_ses-1_acq-inv1_run-1_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
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         </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>
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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>
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         <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>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.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/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>
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                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
               <td>0</td>
               <td>
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                  <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>
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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>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
               <td>0</td>
               <td>
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                  <item>wm</item>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
               <td>1</td>
               <td>
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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>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </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>
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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>1</td>
               <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>
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            <tr>
               <td>Schaefer2018_100P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_200P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
               <td>0</td>
               <td>0</td>
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            <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>
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            <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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            <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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               <shootingtpm>
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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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         <inv_weighting>[true]</inv_weighting>
         <histth>[0.96 0.9999]</histth>
         <templates>
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      <contrast>0.5</contrast>
      <contrastr>3.41183614730835</contrastr>
      <NCR>8.07161140441895</NCR>
      <ICR>2.98165130615234</ICR>
      <SurfaceEulerNumber>3.95918367346939</SurfaceEulerNumber>
      <SurfaceDefectArea>1.53118769076233</SurfaceDefectArea>
      <SurfaceDefectNumber>2.85</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>2.56755471229553</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>2.57195782661438</SurfacePositionRMSE>
      <SIQR>7.11473579210876</SIQR>
      <IQR>7.40170105087974</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>20231031-094653</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>[80.26205 25.96825 56.92492 13.1604 38.56848 35.75709]</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>60</SurfaceEulerNumber>
         <SurfaceDefectArea>2.12475076304934</SurfaceDefectArea>
         <SurfaceDefectNumber>37</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.128377735614777</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.128597885370255</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>60</EC_abs>
      <defect_size>2.12475076304934</defect_size>
      <vol_abs_CGW>[210.165775722909 811.059791467667 329.850188877767 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>1453.42432147115</surf_TSA>
      <vol_TIV>1351.07575606834</vol_TIV>
      <vol_rel_CGW>[0.155554397878099 0.600306672534682 0.244138929587218 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[3.0634339790902 0.965864718636392]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[3.13982319831848 1.60815963310642 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.25052321527883 0.61527789517753 0.148258427794402;2.88338542416606 0.364453731132339 0.486129331819991;4.01484485182175 0.462905615837352 0.365612240385608]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[5 0.0097852782988285 1;5 0.000456744535050289 0]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.05681433380172</vol_TIV>
      <vol_rel_CGW>[0.64357754809805 8.63122615902806 2.23453537333366 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>7.48587091880874</surf_TSA>
      <SQR>7.05833621091085</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 8429.56756933594 0.618708300048426]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0616436004638672 0.058249220252037 0.0766554772853851]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[899.965764397746 350.165306138323 257.40484300245 854.366280217186 2386.19178935163 3676.80797715681]</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>[0.0187420230358839 0.0569361746311188 0.0684636458754539 0 0]</dtc>
         <ll>[0.10570369505224 0 0.10570369505224 0;0.0801980460152811 0.00303156827153469 0.0832296142868158 1939.42761230469;0.227703996637718 0.0135546657933193 0.241258662431037 2890.50537109375]</ll>
         <rmsdtc>[0.0561137199401855 0.0885038301348686 0.116867944598198]</rmsdtc>
         <rmsgdt>[0.043345719575882 0.0599721781909466 0.0880098566412926]</rmsgdt>
         <rmsdt>0.116867944598198</rmsdt>
         <dt>0.0684636458754539</dt>
      </reginitp>
      <SPMvols1>[877.618359962089 385.342853332541 198.923038363513 898.284640634605 2388.72411673984 3680.10134759055]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[80.26205 25.96825 56.92492]</T3th>
            <Tth>
               <T3th>[-0.0936041697859764 3.97833919525146 28.6802139282227 58.0013885498047 66.0413818359375 401.297943115234]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>
               <CGW>[0.27306265161513 0.717831562155342 1.01626627008717]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.819187954845392 2.15349468646603 3.0487988102615 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.273944619076442 0.716204608993197 1.01585407317433]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.821833857229327 2.14861382697959 3.04756221952298 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.374099697069734 0.687286312405412 0.999382169556741]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.1222990912092 2.06185893721624 2.99814650867022 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.374172244358313 0.685230303741446 0.999445190774324]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 1.12251673307494 2.05569091122434 2.99833557232297 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>[0.0120167713612318 0.0534628629684448 0.0756742060184479 0.0880249738693237 0.0974187329411507 0.117370001971722]</dtc>
         <ll>[0.0984497151007793 0 0.0984497151007793 0;0.212495115995116 0.0307370573870574 0.243232173382173 15733.53125;0.184857232823685 0.0276199916815685 0.212477224505253 19878.439453125;0.16392990938279 0.0261162923611807 0.190046201743971 28160.466796875;0.148929400612684 0.0287325156786538 0.177661916291337 50263.3125;0.148929400612684 0.0287325156786538 0.177661916291337 50263.3125]</ll>
         <rmsdtc>[0.0142139513045549 0.0583508312702179 0.0960170477628708 0.14009889960289 0.184417232871056 0.197642490267754]</rmsdtc>
         <rmsgdt>[0.00454422878101468 0.0194169357419014 0.0443401075899601 0.0774681270122528 0.111740201711655 0.122597269713879]</rmsgdt>
         <rmsdt>0.197642490267754</rmsdt>
         <dt>0.117370001971722</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./ses-1/sub-0027441_ses-1_acq-inv1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 377s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 14s</item>
      <item>Estimate background 16s</item>
      <item>Initial correction 14s</item>
      <item>Refine background 7s</item>
      <item>Final correction 10s</item>
      <item>Final scaling 17s</item>
      <item>93s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 18s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 58s</item>
      <item>SPM preprocessing 1 (estimate 2): 94s</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 40s</item>
      <item>Update segmentation 65s</item>
      <item>Update skull-stripping 33s</item>
      <item>Update probability maps 3s</item>
      <item>Update registration 53s</item>
      <item>194s</item>
      <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 101s</item>
      <item>------------------------------------------------------------------------</item>
      <item>NOTE 01: cat_main:skipLAS</item>
      <item>Skip LAS due to image contrast. Use global normalization.</item>
      <item>------------------------------------------------------------------------</item>
      <item>224s</item>
      <item>SANLM denoising after LAS (medium) 169s</item>
      <item>270s</item>
      <item>--- Update Ym and Ymi ---</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 10s</item>
      <item>Major structures 1s</item>
      <item>Ventricle detection 4s</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 10s</item>
      <item>28s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 94s</item>
      <item>AMAP peaks: [0.98 0.05,0.37 0.08,0.62 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 | 0.0984 0.0000 0.0984 | 32.0000</item>
      <item>2 | 2.50 | 0.0889 0.0026 0.0915 | 29.4886</item>
      <item>3 | 2.50 | 0.0855 0.0044 0.0899 | 26.9772</item>
      <item>4 | 2.50 | 0.0840 0.0052 0.0891 | 24.6107</item>
      <item>5 | 2.50 | 0.0829 0.0056 0.0885 | 22.6548</item>
      <item>6 | 2.50 | 0.0821 0.0058 0.0879 | 20.6989</item>
      <item>7 | 2.50 | 0.0813 0.0060 0.0873 | 18.9688</item>
      <item>8 | 2.50 | 0.0806 0.0062 0.0868 | 17.4455</item>
      <item>9 | 2.50 | 0.0798 0.0063 0.0861 | 15.9223</item>
      <item>10 | 2.50 | 0.0790 0.0065 0.0855 | 14.6627</item>
      <item>11 | 2.50 | 0.0783 0.0066 0.0849 | 13.4764</item>
      <item>12 | 2.50 | 0.0775 0.0067 0.0842 | 12.3015</item>
      <item>13 | 2.50 | 0.0767 0.0069 0.0836 | 11.3776</item>
      <item>14 | 2.50 | 0.0760 0.0069 0.0829 | 10.4537</item>
      <item>15 | 2.25 | 0.0770 0.0074 0.0844 | 9.5920</item>
      <item>16 | 2.25 | 0.0728 0.0095 0.0823 | 8.8725</item>
      <item>17 | 2.25 | 0.0708 0.0102 0.0811 | 8.1530</item>
      <item>29 | 2.00 | 0.0717 0.0048 0.0766 | 3.3283</item>
      <item>30 | 2.00 | 0.0642 0.0081 0.0723 | 3.1221</item>
      <item>31 | 2.00 | 0.0616 0.0092 0.0708 | 2.9160</item>
      <item>43 | 1.75 | 0.0605 0.0055 0.0660 | 1.5785</item>
      <item>44 | 1.75 | 0.0561 0.0080 0.0641 | 1.5194</item>
      <item>45 | 1.75 | 0.0546 0.0087 0.0633 | 1.4626</item>
      <item>57 | 1.50 | 0.0539 0.0067 0.0606 | 1.0900</item>
      <item>58 | 1.50 | 0.0507 0.0089 0.0596 | 1.0730</item>
      <item>59 | 1.50 | 0.0496 0.0096 0.0592 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 180s</item>
      <item>Prepare output 21s</item>
      <item>202s</item>
      <item>Jacobian determinant (RMS): 0.014 0.058 0.096 0.140 0.184 | 0.197642</item>
      <item>Template Matching: 0.098 0.212 0.185 0.164 0.149 | 0.148929</item>
      <item>Write result maps: 74s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 25s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 49s</item>
      <item>97s</item>
      <item>Create initial surface 76s</item>
      <item>Topology correction: 63s</item>
      <item>Surface refinement: 76s</item>
      <item>Reduction of surface collisions with optimization: 53s</item>
      <item>Spherical mapping with areal smoothing 68s</item>
      <item>Spherical registration 297s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 49s</item>
      <item>100s</item>
      <item>Create initial surface 75s</item>
      <item>Topology correction: 70s</item>
      <item>Surface refinement: 64s</item>
      <item>Reduction of surface collisions with optimization: 101s</item>
      <item>Spherical mapping with areal smoothing 68s</item>
      <item>Spherical registration 295s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 3.0636 0.9654 mm</item>
      <item>Surface intensity / position RMSE: 0.1284 / 0.1286</item>
      <item>Euler number / defect number / defect size: 60.0 / 37.0 / 2.12%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/surf/lh.thickness.sub-0027441_ses-1_acq-inv1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/surf/rh.thickness.sub-0027441_ses-1_acq-inv1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/sub-0027441_ses-1_acq-inv1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 2569s</item>
      <item>Surface and thickness estimation takes: 2120s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 18s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 65s</item>
      <item>ROI estimation of 'lpba40' atlas 19s</item>
      <item>ROI estimation of 'hammers' atlas 46s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 16s</item>
      <item>ROI estimation of 'aal3' atlas 27s</item>
      <item>ROI estimation of 'mori' atlas 39s</item>
      <item>ROI estimation of 'anatomy3' atlas 56s</item>
      <item>ROI estimation of 'julichbrain' atlas 75s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 30s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 52s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 119s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 179s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s</item>
      <item>Write results 16s</item>
      <item>762s</item>
      <item>Quality check: 26s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/report/catreport_sub-0027441_ses-1_acq-inv1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 72 minute(s) and 52 second(s).</item>
      <item>Image Quality Rating (IQR): 30.98% (F)</item>
      <item>GM volume (GMV): 60.03% (811.06 / 1351.08 ml)</item>
      <item>GM thickness (GMT): 3.06 0.97 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3452511/ds/MPG_1/sub-0027441/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>