CORR_cat12.8.1/IACAS/sub-0025472/ses-1/report/cat_sub-0025472_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine0_shearing>[0.00601533488863608 -0.00939180298255496 0.0355030826430431]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1</path>
      <file>sub-0025472_ses-1_run-1_T1w</file>
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      <F>/var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/mri/msub-0025472_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/mri/p0sub-0025472_ses-1_run-1_T1w.nii</Fp0>
      <fnames>..s/IACAS/sub-0025472/ses-1/sub-0025472_ses-1_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>
            </tr>
            <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>
            </tr>
            <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>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.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/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>
               </td>
               <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>
               </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_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_578211/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</item>
               </td>
               <td>[false]</td>
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         </atlas>
         <satlas>
            <tr>
               <td>Desikan</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <tr>
               <td>Destrieux</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <tr>
               <td>HCP</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_100P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_200P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_400P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_600P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
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         </satlas>
         <LAB>
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            <CT>1</CT>
            <CB>3</CB>
            <BG>5</BG>
            <BV>7</BV>
            <TH>9</TH>
            <ON>11</ON>
            <MB>13</MB>
            <BS>13</BS>
            <VT>15</VT>
            <NV>17</NV>
            <HC>19</HC>
            <HD>21</HD>
            <HI>23</HI>
            <PH>25</PH>
            <LE>27</LE>
         </LAB>
         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
         <regmethod>
            <shooting>
               <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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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
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         </darteltpms>
         <shootingtpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
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         <templates>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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      <contrastr>4.99687004089355</contrastr>
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      <SurfaceDefectArea>1.28849353636743</SurfaceDefectArea>
      <SurfaceDefectNumber>2.2</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.44947075843811</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.51752948760986</SurfacePositionRMSE>
      <SIQR>2.58180075194146</SIQR>
      <IQR>2.71561028071994</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>2040</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20231031-000203</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>36</SurfaceEulerNumber>
         <SurfaceDefectArea>1.15397414546973</SurfaceDefectArea>
         <SurfaceDefectNumber>24</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0724735409021378</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0758764743804932</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>36</EC_abs>
      <defect_size>1.15397414546973</defect_size>
      <vol_abs_CGW>[269.140250980392 721.034509803922 622.442164705882 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.16714509803922</vol_abs_WMH>
      <vol_rel_WMH>0.000723758432390527</vol_rel_WMH>
      <surf_TSA>2197.52415716223</surf_TSA>
      <vol_TIV>1612.6169254902</vol_TIV>
      <vol_rel_CGW>[0.166896580785037 0.447120762784221 0.385982656430742 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.35187309779044 0.662321017731071]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.38452100753784 0.749483567528309 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.62894888566025 0.296997928145014 0.268843017652796;2.3822501169767 0.196240435413958 0.458124383248599;3.06667881548825 0.287939284683261 0.273032599098605]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.756405626466738 0.170930404801457 0.551920674578389;4.00824375014663 0.302113512153683 0.448079325421611]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.00441585028935</vol_TIV>
      <vol_rel_CGW>[0.847280545708275 5.88004243506144 4.78201609969006 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.07237584323905</vol_rel_WMH>
      <surf_TSA>8.6238995540698</surf_TSA>
      <SQR>4.91489748019768</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 12320.768 0.27552449714789]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00151735148392618 0.00134809361770749 0.0692135691642761]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[887.035858823529 612.833423529412 461.749921568627 707.564431372549 1503.9805254902 8780.55543137255]</SPMvols0>
      <SPMvols1>[728.590988235294 558.028505882353 280.177211764706 433.908882352941 1081.75114901961 9238.4334745098]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[964.441284179688 2169.80297851562 2735.14282226562]</T3th>
            <Tth>
               <T3th>[-36.9756507873535 -36.9756469726562 18.1707916259766 964.441284179688 2169.80297851562 2735.14282226562 3620.49365234375 5613.1005859375]</T3th>
               <T3thx>[0 0.02 0.05 1 2 3 4 5]</T3thx>
            </Tth>
         </gintnorm>
      </tths>
      <reginitp>
         <opt>
            <nits>16</nits>
            <vxreg>1.5</vxreg>
            <rres>3</rres>
            <stepsize>0.5</stepsize>
            <resfac>[1 1 1 1 1]</resfac>
            <ll1th>0.015</ll1th>
            <ll3th>[0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03]</ll3th>
            <regstr>15</regstr>
         </opt>
         <fast>0</fast>
         <clsn>2</clsn>
         <regra>1</regra>
         <testfolder>Shooting_Template_0_GS_tr1.5_rr3.0-3.0_or1.5_regstr15.0</testfolder>
         <dtc>[0.0208031199872494 0.0741585791110992 0.0811366438865662 0 0]</dtc>
         <ll>[0.0840892204049589 0 0.0840892204049589 0;0.19857385092709 0.0100614174502809 0.20863526837737 2145.5771484375;0.19857385092709 0.0100614174502809 0.20863526837737 2145.5771484375]</ll>
         <rmsdtc>[0.0447165928781033 0.0943777561187744 0.104376673698425]</rmsdtc>
         <rmsgdt>[0.032004427164793 0.0436443202197552 0.0537406206130981]</rmsgdt>
         <rmsdt>0.104376673698425</rmsdt>
         <dt>0.0811366438865662</dt>
      </reginitp>
      <reg>
         <opt>
            <nits>64</nits>
            <vxreg>1.5</vxreg>
            <rres>1.5</rres>
            <stepsize>0.25</stepsize>
            <resfac>[1.66666666666667 1.5 1.33333333333333 1.16666666666667 1]</resfac>
            <ll1th>0.051</ll1th>
            <ll3th>[0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501]</ll3th>
            <regstr>0.5</regstr>
         </opt>
         <fast>0</fast>
         <clsn>2</clsn>
         <regra>1</regra>
         <testfolder>Shooting_Template_0_GS_tr1.5_rr2.5-1.5_or1.5_regstr0.5</testfolder>
         <dtc>[0.00970292370766401 0.0382552891969681 0.0510874539613724 0.0592814274132252 0.0657895132899284 0.0738514587283134]</dtc>
         <ll>[0.0853722845206983 0 0.0853722845206983 0;0.221994658119658 0.0155572916666667 0.237551949786325 7963.388671875;0.203932506162187 0.0172804704021365 0.221212976564324 12436.9619140625;0.18296243028197 0.019485982621384 0.202448412903354 21011.189453125;0.166452093288204 0.0226572986019688 0.189109391890173 39635.61328125;0.166452093288204 0.0226572986019688 0.189109391890173 39635.61328125]</ll>
         <rmsdtc>[0.011332361958921 0.0416355468332767 0.0626334697008133 0.0858571827411652 0.108983099460602 0.11695346981287]</rmsdtc>
         <rmsgdt>[0.00337932305410504 0.0130603276193142 0.029162185266614 0.04974415153265 0.0688300877809525 0.0749190598726273]</rmsgdt>
         <rmsdt>0.11695346981287</rmsdt>
         <dt>0.0738514587283134</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 25s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 5s</item>
      <item>Estimate background 4s</item>
      <item>Initial correction 4s</item>
      <item>Refine background 2s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 4s</item>
      <item>28s</item>
      <item>Correct center-of-mass 2s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 26s</item>
      <item>Use previous fine affine registration. 51s</item>
      <item>SPM preprocessing 1 (estimate 2): 65s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 36s</item>
      <item>Update probability maps 8s</item>
      <item>77s</item>
      <item>Global intensity correction: 13s</item>
      <item>SANLM denoising after intensity normalization (medium): 20s</item>
      <item>Fast Optimized Shooting registration 26s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 3s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 11s</item>
      <item>Estimate local tissue thresholds (WM) 15s</item>
      <item>Estimate local tissue thresholds (GM) 21s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 35s</item>
      <item>90s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 6s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 10s</item>
      <item>Blood vessel detection 7s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.04) 19s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>52s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 3s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
      <item>9s</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 | 0.0854 0.0000 0.0854 | 32.0000</item>
      <item>2 | 2.50 | 0.0826 0.0012 0.0838 | 29.4886</item>
      <item>3 | 2.50 | 0.0817 0.0019 0.0836 | 26.9772</item>
      <item>4 | 2.50 | 0.0813 0.0021 0.0834 | 24.6107</item>
      <item>5 | 2.50 | 0.0809 0.0023 0.0832 | 22.6548</item>
      <item>6 | 2.50 | 0.0807 0.0024 0.0830 | 20.6989</item>
      <item>7 | 2.50 | 0.0804 0.0025 0.0828 | 18.9688</item>
      <item>8 | 2.50 | 0.0800 0.0026 0.0826 | 17.4455</item>
      <item>9 | 2.50 | 0.0797 0.0027 0.0824 | 15.9223</item>
      <item>10 | 2.50 | 0.0794 0.0028 0.0822 | 14.6627</item>
      <item>11 | 2.50 | 0.0791 0.0029 0.0819 | 13.4764</item>
      <item>12 | 2.50 | 0.0787 0.0029 0.0816 | 12.3015</item>
      <item>13 | 2.50 | 0.0784 0.0030 0.0814 | 11.3776</item>
      <item>14 | 2.50 | 0.0780 0.0031 0.0811 | 10.4537</item>
      <item>15 | 2.25 | 0.0781 0.0032 0.0813 | 9.5920</item>
      <item>16 | 2.25 | 0.0752 0.0046 0.0799 | 8.8725</item>
      <item>17 | 2.25 | 0.0740 0.0052 0.0792 | 8.1530</item>
      <item>29 | 2.00 | 0.0758 0.0024 0.0782 | 3.3283</item>
      <item>30 | 2.00 | 0.0700 0.0048 0.0748 | 3.1221</item>
      <item>31 | 2.00 | 0.0680 0.0058 0.0737 | 2.9160</item>
      <item>43 | 1.75 | 0.0670 0.0033 0.0703 | 1.5785</item>
      <item>44 | 1.75 | 0.0625 0.0056 0.0682 | 1.5194</item>
      <item>45 | 1.75 | 0.0610 0.0065 0.0675 | 1.4626</item>
      <item>57 | 1.50 | 0.0598 0.0047 0.0645 | 1.0900</item>
      <item>58 | 1.50 | 0.0566 0.0068 0.0634 | 1.0730</item>
      <item>59 | 1.50 | 0.0555 0.0076 0.0630 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 137s</item>
      <item>Prepare output 8s</item>
      <item>146s</item>
      <item>Jacobian determinant (RMS): 0.011 0.042 0.063 0.086 0.109 | 0.116953</item>
      <item>Template Matching: 0.085 0.222 0.204 0.183 0.166 | 0.166452</item>
      <item>Write result maps: 31s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 34s</item>
      <item>CSF distance: 11s</item>
      <item>PBT2x thickness: 34s</item>
      <item>84s</item>
      <item>Create initial surface 65s</item>
      <item>Topology correction: 79s</item>
      <item>Surface refinement: 83s</item>
      <item>Reduction of surface collisions with optimization: 60s</item>
      <item>Spherical mapping with areal smoothing 68s</item>
      <item>Spherical registration 200s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 30s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 34s</item>
      <item>81s</item>
      <item>Create initial surface 67s</item>
      <item>Topology correction: 79s</item>
      <item>Surface refinement: 75s</item>
      <item>Reduction of surface collisions with optimization: 55s</item>
      <item>Spherical mapping with areal smoothing 74s</item>
      <item>Spherical registration 237s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.3520 0.6623 mm</item>
      <item>Surface intensity / position RMSE: 0.0725 / 0.0759</item>
      <item>Euler number / defect number / defect size: 36.0 / 24.0 / 1.15%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/surf/lh.thickness.sub-0025472_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/surf/rh.thickness.sub-0025472_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1391s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 21s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 86s</item>
      <item>ROI estimation of 'lpba40' atlas 26s</item>
      <item>ROI estimation of 'hammers' atlas 60s</item>
      <item>ROI estimation of 'thalamus' atlas 5s</item>
      <item>ROI estimation of 'ibsr' atlas 23s</item>
      <item>ROI estimation of 'aal3' atlas 38s</item>
      <item>ROI estimation of 'mori' atlas 52s</item>
      <item>ROI estimation of 'anatomy3' atlas 70s</item>
      <item>ROI estimation of 'julichbrain' atlas 90s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 36s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 61s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 133s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s</item>
      <item>Write results 12s</item>
      <item>830s</item>
      <item>Quality check: 10s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/report/catreport_sub-0025472_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 50 minute(s) and 43 second(s).</item>
      <item>Image Quality Rating (IQR): 77.84% (C+)</item>
      <item>GM volume (GMV): 44.71% (721.03 / 1612.62 ml)</item>
      <item>GM thickness (GMT): 2.35 0.66 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>