CORR_cat12.8.1/MPG_1/sub-0027438/ses-1/report/cat_sub-0027438_ses-1_acq-inv1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine0_translation>[1.33678122160016 -56.3928507241559 -28.1857080790387]</Affine0_translation>
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   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1</path>
      <file>sub-0027438_ses-1_acq-inv1_run-1_T1w</file>
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      <Fm>/var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/mri/msub-0027438_ses-1_acq-inv1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/mri/p0sub-0027438_ses-1_acq-inv1_run-1_T1w.nii</Fp0>
      <fnames>..s/MPG_1/sub-0027438/ses-1/sub-0027438_ses-1_acq-inv1_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>
                  <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>
               </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/cobra.nii</td>
               <td>0</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/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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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <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>
            </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>
               <td>/var/lib/condor/execute/dir_1682720/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <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>
            </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>
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         <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>
         <regmethod>
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               <shootingtpm>
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               <regstr>0.5</regstr>
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         <restypes>
            <optimal>[1 0.3]</optimal>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
         <darteltpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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         <shootingtpms>
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         </shootingtpms>
         <inv_weighting>[true]</inv_weighting>
         <histth>[0.96 0.9999]</histth>
         <templates>
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      <ICR>0.94232189655304</ICR>
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      <contrast>0.5</contrast>
      <contrastr>3.04745197296143</contrastr>
      <NCR>9.07718849182129</NCR>
      <ICR>2.79692935943604</ICR>
      <SurfaceEulerNumber>3.14285714285714</SurfaceEulerNumber>
      <SurfaceDefectArea>1.44178213424148</SurfaceDefectArea>
      <SurfaceDefectNumber>3.275</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>2.57044792175293</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>2.71390748023987</SurfacePositionRMSE>
      <SIQR>7.94793535192849</SIQR>
      <IQR>8.32381888108574</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>20231031-073358</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>[95.12668 30.15452 56.62549 16.10738 42.18223 46.76078]</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>44</SurfaceEulerNumber>
         <SurfaceDefectArea>1.76712853696594</SurfaceDefectArea>
         <SurfaceDefectNumber>45.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.128522396087646</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.135695368051529</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>44</EC_abs>
      <defect_size>1.76712853696594</defect_size>
      <vol_abs_CGW>[276.542259634659 790.131530076423 310.479498610162 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0</vol_abs_WMH>
      <vol_rel_WMH>0</vol_rel_WMH>
      <surf_TSA>1337.38279911799</surf_TSA>
      <vol_TIV>1377.15328832124</vol_TIV>
      <vol_rel_CGW>[0.200807173740089 0.573742615856218 0.225450210403693 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[3.05719703448791 1.03017469542254]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[3.15285015106201 1.74632524205252 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.1571728585655 0.589450469934237 0.154599021272346;2.90579633369964 0.37995875186849 0.494733769176993;4.08599946262693 0.454098651084102 0.350667209550661]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[5 0.000362578536322622 1;5 1.64196824077708e-06 0]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.01242585143662</vol_TIV>
      <vol_rel_CGW>[1.4563069996424 8.15414180776254 1.89889027305483 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1</vol_rel_WMH>
      <surf_TSA>6.20487084606873</surf_TSA>
      <SQR>6.668183386334</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 8429.56756933594 0.722149638927502]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.061883457005024 0.0582615584135056 0.0974215492606163]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[847.816287429389 342.477899754923 322.593244818832 554.498120509621 1759.6371060819 4597.88750542271]</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>[0.0148060536012053 0.0656754598021507 0.0781877264380455 0 0]</dtc>
         <ll>[0.0916897398607881 0 0.0916897398607881 0;0.0811424850702 0.00261524726315087 0.0837577323333508 1673.08874511719;0.231077159867853 0.0123331555369951 0.243410315404848 2630.02075195312]</ll>
         <rmsdtc>[0.0335570573806763 0.0981321930885315 0.126551300287247]</rmsdtc>
         <rmsgdt>[0.0242037791758776 0.0601315759122372 0.0878491103649139]</rmsgdt>
         <rmsdt>0.126551300287247</rmsdt>
         <dt>0.0781877264380455</dt>
      </reginitp>
      <SPMvols1>[845.736966209548 374.603874037362 261.445192136142 590.090456945418 1766.05043959445 4591.53203668467]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[95.12668 30.15452 56.62549]</T3th>
            <Tth>
               <T3th>[-0.166040018200874 3.99823999404907 30.9462928771973 55.0130805969238 56.9844017028809 521.09033203125]</T3th>
               <T3thx>[0 0.1 1 2 3 4]</T3thx>
            </Tth>
         </gintnorm>
         <uintnorm1postlas>
            <Tthm>
               <CGW>[0.326058431335268 0.886930864348693 1.03691975287318]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.978175294005805 2.66079259304608 3.11075925861953 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.326632653047555 0.885799884973958 1.03636149312005]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.979897959142665 2.65739965492187 3.10908447936015 4 5 6]</T3thx>
            </Tthmi>
         </uintnorm1postlas>
         <uintnorm2postamap>
            <Tthm>
               <CGW>[0.32369553534486 0.58195350544033 1.01970088911768]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.971086606034579 1.74586051632099 3.05910266735305 4 5 6]</T3thx>
            </Tthm>
            <Tthmi>
               <CGW>[0.324259987571583 0.582349772487327 1.019886893066]</CGW>
               <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
               <T3thx>[0 0.972779962714748 1.74704931746198 3.05966067919799 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>[0.0132839437574148 0.0533554069697857 0.0815969854593277 0.09538234770298 0.104963406920433 0.127321317791939]</dtc>
         <ll>[0.0889666553924951 0 0.0889666553924951 0;0.22002731990232 0.0214186527014652 0.241445972603785 10963.6728515625;0.188035326978013 0.0240986748432012 0.212134001821215 17344.10546875;0.166054648664715 0.0244144374488765 0.190469086113592 26325.404296875;0.150819885266153 0.0274143720921392 0.178234257358292 47957.4140625;0.150819885266153 0.0274143720921392 0.178234257358292 47957.4140625]</ll>
         <rmsdtc>[0.0155728105455637 0.0615369826555252 0.0997478663921356 0.147645056247711 0.192530065774918 0.205384314060211]</rmsdtc>
         <rmsgdt>[0.00457624346017838 0.0198318008333445 0.0451692305505276 0.079405389726162 0.114733889698982 0.125859558582306]</rmsgdt>
         <rmsdt>0.205384314060211</rmsdt>
         <dt>0.127321317791939</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./ses-1/sub-0027438_ses-1_acq-inv1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 351s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 12s</item>
      <item>Estimate background 15s</item>
      <item>Initial correction 14s</item>
      <item>Refine background 7s</item>
      <item>Final correction 10s</item>
      <item>Final scaling 16s</item>
      <item>86s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 47s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 44s</item>
      <item>SPM preprocessing 1 (estimate 2): 49s</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 37s</item>
      <item>Update segmentation 61s</item>
      <item>Update skull-stripping 31s</item>
      <item>Update probability maps 3s</item>
      <item>Update registration 49s</item>
      <item>180s</item>
      <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 94s</item>
      <item>------------------------------------------------------------------------</item>
      <item>NOTE 01: cat_main:skipLAS</item>
      <item>Skip LAS due to image contrast. Use global normalization.</item>
      <item>------------------------------------------------------------------------</item>
      <item>212s</item>
      <item>SANLM denoising after LAS (medium) 160s</item>
      <item>254s</item>
      <item>--- Update Ym and Ymi ---</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 9s</item>
      <item>Major structures 1s</item>
      <item>Ventricle detection 3s</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 9s</item>
      <item>26s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 103s</item>
      <item>AMAP peaks: [0.95 0.06,0.34 0.08,0.58 0.06]</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 | 0.0890 0.0000 0.0890 | 32.0000</item>
      <item>2 | 2.50 | 0.0846 0.0017 0.0863 | 29.4886</item>
      <item>3 | 2.50 | 0.0832 0.0027 0.0859 | 26.9772</item>
      <item>4 | 2.50 | 0.0825 0.0031 0.0856 | 24.6107</item>
      <item>5 | 2.50 | 0.0820 0.0033 0.0853 | 22.6548</item>
      <item>6 | 2.50 | 0.0815 0.0035 0.0850 | 20.6989</item>
      <item>7 | 2.50 | 0.0809 0.0037 0.0846 | 18.9688</item>
      <item>8 | 2.50 | 0.0804 0.0039 0.0843 | 17.4455</item>
      <item>9 | 2.50 | 0.0799 0.0040 0.0839 | 15.9223</item>
      <item>10 | 2.50 | 0.0793 0.0043 0.0835 | 14.6627</item>
      <item>11 | 2.50 | 0.0787 0.0044 0.0831 | 13.4764</item>
      <item>12 | 2.50 | 0.0781 0.0046 0.0827 | 12.3015</item>
      <item>13 | 2.50 | 0.0774 0.0048 0.0822 | 11.3776</item>
      <item>14 | 2.50 | 0.0768 0.0050 0.0818 | 10.4537</item>
      <item>15 | 2.25 | 0.0771 0.0052 0.0822 | 9.5920</item>
      <item>16 | 2.25 | 0.0733 0.0071 0.0805 | 8.8725</item>
      <item>29 | 2.00 | 0.0738 0.0032 0.0770 | 3.3283</item>
      <item>30 | 2.00 | 0.0655 0.0068 0.0722 | 3.1221</item>
      <item>31 | 2.00 | 0.0627 0.0080 0.0707 | 2.9160</item>
      <item>43 | 1.75 | 0.0613 0.0048 0.0661 | 1.5785</item>
      <item>44 | 1.75 | 0.0568 0.0073 0.0641 | 1.5194</item>
      <item>45 | 1.75 | 0.0554 0.0081 0.0635 | 1.4626</item>
      <item>57 | 1.50 | 0.0546 0.0062 0.0607 | 1.0900</item>
      <item>58 | 1.50 | 0.0513 0.0084 0.0597 | 1.0730</item>
      <item>59 | 1.50 | 0.0503 0.0091 0.0594 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 159s</item>
      <item>Prepare output 22s</item>
      <item>181s</item>
      <item>Jacobian determinant (RMS): 0.016 0.062 0.100 0.148 0.193 | 0.205384</item>
      <item>Template Matching: 0.089 0.220 0.188 0.166 0.151 | 0.150820</item>
      <item>Write result maps: 68s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 24s</item>
      <item>CSF distance: 16s</item>
      <item>PBT2x thickness: 46s</item>
      <item>92s</item>
      <item>Create initial surface 72s</item>
      <item>Topology correction: 58s</item>
      <item>Surface refinement: 63s</item>
      <item>Reduction of surface collisions with optimization: 87s</item>
      <item>Spherical mapping with areal smoothing 60s</item>
      <item>Spherical registration 295s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 29s</item>
      <item>CSF distance: 19s</item>
      <item>PBT2x thickness: 54s</item>
      <item>109s</item>
      <item>Create initial surface 86s</item>
      <item>Topology correction: 69s</item>
      <item>Surface refinement: 87s</item>
      <item>Reduction of surface collisions with optimization: 97s</item>
      <item>Spherical mapping with areal smoothing 78s</item>
      <item>Spherical registration 286s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 3.0572 1.0302 mm</item>
      <item>Surface intensity / position RMSE: 0.1285 / 0.1357</item>
      <item>Euler number / defect number / defect size: 44.0 / 45.5 / 1.77%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/surf/lh.thickness.sub-0027438_ses-1_acq-inv1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/surf/rh.thickness.sub-0027438_ses-1_acq-inv1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/sub-0027438_ses-1_acq-inv1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 2524s</item>
      <item>Surface and thickness estimation takes: 2130s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 18s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 61s</item>
      <item>ROI estimation of 'lpba40' atlas 17s</item>
      <item>ROI estimation of 'hammers' atlas 43s</item>
      <item>ROI estimation of 'thalamus' atlas 3s</item>
      <item>ROI estimation of 'ibsr' atlas 15s</item>
      <item>ROI estimation of 'aal3' atlas 26s</item>
      <item>ROI estimation of 'mori' atlas 38s</item>
      <item>ROI estimation of 'anatomy3' atlas 55s</item>
      <item>ROI estimation of 'julichbrain' atlas 72s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 51s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 178s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s</item>
      <item>Write results 16s</item>
      <item>739s</item>
      <item>Quality check: 26s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/report/catreport_sub-0027438_ses-1_acq-inv1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 70 minute(s) and 19 second(s).</item>
      <item>Image Quality Rating (IQR): 21.76% (F)</item>
      <item>GM volume (GMV): 57.37% (790.13 / 1377.15 ml)</item>
      <item>GM thickness (GMT): 3.06 1.03 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_1682720/ds/MPG_1/sub-0027438/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>