CORR_cat12.8.1/Utah_2/sub-0026017/ses-4/report/cat_sub-0026017_ses-4_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine0_shearing>[0.00481976824176484 0.00573794699291765 0.00382840327934632]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4</path>
      <file>sub-0026017_ses-4_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/sub-0026017_ses-4_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/sub-0026017_ses-4_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/mri/msub-0026017_ses-4_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/mri/p0sub-0026017_ses-4_run-1_T1w.nii</Fp0>
      <fnames>../Utah_2/sub-0026017/ses-4/sub-0026017_ses-4_run-1_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
         </tpm>
         <ngaus>[1 1 2 3 4 2]</ngaus>
         <affreg>mni</affreg>
         <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
         <tol>0.0001</tol>
         <accstr>0.5</accstr>
         <biasstr>0.5</biasstr>
         <biasreg>0.001</biasreg>
         <biasfwhm>60</biasfwhm>
         <samp>3</samp>
         <redspmres>0</redspmres>
         <fwhm>1</fwhm>
         <biasacc>0</biasacc>
      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
         <BVCstr>0.5</BVCstr>
         <regstr>0.5</regstr>
         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
         <SLC>0</SLC>
         <mrf>1</mrf>
         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</nproc>
         <species>human</species>
         <APP>1070</APP>
         <setCOM>1</setCOM>
         <vox>1.5</vox>
         <bb>12</bb>
         <shootingsurf>Template_T1</shootingsurf>
         <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
         <darteltpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
         </darteltpm>
         <shootingtpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
         </shootingtpm>
         <shootingT1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
         </shootingT1>
         <brainmask>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
         </brainmask>
         <T1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
         </T1>
         <cat12atlas>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
         </cat12atlas>
         <pbtres>0.5</pbtres>
         <SRP>22</SRP>
         <reduce_mesh>1</reduce_mesh>
         <vdist>2</vdist>
         <pbtlas>0</pbtlas>
         <thick_measure>1</thick_measure>
         <thick_limit>5</thick_limit>
         <close_parahipp>0</close_parahipp>
         <scale_cortex>0.7</scale_cortex>
         <add_parahipp>0.1</add_parahipp>
         <colormap>BCGWHw</colormap>
         <report/>
         <verb>2</verb>
         <ignoreErrors>1</ignoreErrors>
         <expertgui>1</expertgui>
         <subfolders>1</subfolders>
         <experimental>0</experimental>
         <print>2</print>
         <fontsize>10</fontsize>
         <send_info>1</send_info>
         <gifti_dat>1</gifti_dat>
         <atlas>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
               <td>0</td>
               <td>
                  <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>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
            </tr>
            <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>
               </td>
               <td>[false]</td>
            </tr>
            <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>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/var/lib/condor/execute/dir_2614000/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>
            </tr>
         </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>
            </tr>
         </satlas>
         <LAB>
            <NB>0</NB>
            <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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               </shootingtpm>
               <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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
         </darteltpms>
         <shootingtpms>
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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>
            <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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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
         </shootingtpms>
         <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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
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         <AMAPframing>1</AMAPframing>
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      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
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      <ICR>1.05435156822205</ICR>
      <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
      <SurfaceDefectArea>1.0471436683117</SurfaceDefectArea>
      <SurfaceDefectNumber>1.625</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.321857213974</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.31410670280457</SurfacePositionRMSE>
      <SIQR>2.2466114606773</SIQR>
      <IQR>2.30752719738926</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>20231031-093516</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>12</SurfaceEulerNumber>
         <SurfaceDefectArea>0.1885746732468</SurfaceDefectArea>
         <SurfaceDefectNumber>12.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0660928636789322</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0657053366303444</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>12</EC_abs>
      <defect_size>0.1885746732468</defect_size>
      <vol_abs_CGW>[295.094803213129 706.643384270108 577.599140459084 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.37412149228477</vol_abs_WMH>
      <vol_rel_WMH>0.000870062062089721</vol_rel_WMH>
      <surf_TSA>1972.87928446874</surf_TSA>
      <vol_TIV>1579.33732794232</vol_TIV>
      <vol_rel_CGW>[0.186847228892893 0.447430306222658 0.365722464884449 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.51596141854717 0.655323777031556]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.51098871231079 0.7965725808929 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.83834174117384 0.265876215480645 0.289240398508433;2.52940745135408 0.190569784650144 0.439842009956401;3.22702895849612 0.291115354972589 0.270917591535166]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.846762059011427 0.276100539534675 0.487588138703757;4.26494128980466 0.351486804699247 0.512411861296243]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.7290083506882</vol_TIV>
      <vol_rel_CGW>[1.20558959936948 5.88560176405637 4.41814771703392 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.08700620620897</vol_rel_WMH>
      <surf_TSA>8.62017829957728</surf_TSA>
      <SQR>4.87118772058907</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 14680.0632000532 0.336003249526091]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00133722950704396 0.00111148389987648 0.0444892570376396]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[843.227604132817 511.756838234762 431.860125026561 452.234351345601 1502.37636751219 11471.8916175529]</SPMvols0>
      <SPMvols1>[744.016041017307 481.949467341764 295.464399271026 358.386611461503 966.028389467181 11834.2304523243]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[164.114807128906 364.788909912109 468.880187988281]</T3th>
            <Tth>
               <T3th>[-5.88184976577759 -5.8818507194519 3.80928730964661 164.114807128906 364.788909912109 468.880187988281 621.262878417969 683.721496582031]</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>[0.0225363187491894 0.08183803409338 0.0903827473521233 0 0]</dtc>
         <ll>[0.0820356340778499 0 0.0820356340778499 0;0.186404059914982 0.0107193565597626 0.197123416474744 2285.88134765625;0.186404059914982 0.0107193565597626 0.197123416474744 2285.88134765625]</ll>
         <rmsdtc>[0.0479379743337631 0.105353206396103 0.11574349552393]</rmsdtc>
         <rmsgdt>[0.0339405536651611 0.0448987670242786 0.0549742206931114]</rmsgdt>
         <rmsdt>0.11574349552393</rmsdt>
         <dt>0.0903827473521233</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>[0.0105956755578518 0.0391573272645473 0.0546384230256081 0.061653058975935 0.0665406584739685 0.0746466293931007]</dtc>
         <ll>[0.0811978979895752 0 0.0811978979895752 0;0.208641575091575 0.0140025373931624 0.222644112484737 7167.548828125;0.185265121673669 0.0165889000999705 0.20185402177364 11939.23046875;0.16577523748646 0.0178893887192888 0.183664626205749 19289.626953125;0.149702248845716 0.0201737219060418 0.169875970751758 35290.9609375;0.149702248845716 0.0201737219060418 0.169875970751758 35290.9609375]</ll>
         <rmsdtc>[0.0122733060270548 0.0446376986801624 0.0655029639601707 0.0884446874260902 0.108677051961422 0.115933768451214]</rmsdtc>
         <rmsgdt>[0.00341920834034681 0.0131181329488754 0.0279985778033733 0.0477931760251522 0.0649295821785927 0.0702940821647644]</rmsgdt>
         <rmsdt>0.115933768451214</rmsdt>
         <dt>0.0746466293931007</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0026017/ses-4/sub-0026017_ses-4_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 64s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 6s</item>
      <item>Initial correction 7s</item>
      <item>Refine background 4s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 6s</item>
      <item>45s</item>
      <item>Correct center-of-mass 4s</item>
      <item>Affine registration 10s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 81s</item>
      <item>SPM preprocessing 1 (estimate 2): 78s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 18s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 42s</item>
      <item>Update probability maps 9s</item>
      <item>87s</item>
      <item>Global intensity correction: 17s</item>
      <item>SANLM denoising after intensity normalization (medium): 24s</item>
      <item>Fast Optimized Shooting registration 30s</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) 13s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 25s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 47s</item>
      <item>112s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 9s</item>
      <item>Blood vessel detection 8s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.07) 22s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 1s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 5s</item>
      <item>58s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s</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) 4s</item>
      <item>Level 1 cleanup (brain masking) 2s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>10s</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 | 0.0812 0.0000 0.0812 | 32.0000</item>
      <item>2 | 2.50 | 0.0785 0.0012 0.0798 | 29.4886</item>
      <item>3 | 2.50 | 0.0778 0.0018 0.0796 | 26.9772</item>
      <item>4 | 2.50 | 0.0774 0.0021 0.0794 | 24.6107</item>
      <item>5 | 2.50 | 0.0770 0.0022 0.0793 | 22.6548</item>
      <item>6 | 2.50 | 0.0768 0.0023 0.0791 | 20.6989</item>
      <item>7 | 2.50 | 0.0765 0.0024 0.0789 | 18.9688</item>
      <item>8 | 2.50 | 0.0762 0.0025 0.0787 | 17.4455</item>
      <item>9 | 2.50 | 0.0758 0.0026 0.0785 | 15.9223</item>
      <item>10 | 2.50 | 0.0755 0.0027 0.0783 | 14.6627</item>
      <item>11 | 2.50 | 0.0752 0.0028 0.0780 | 13.4764</item>
      <item>12 | 2.50 | 0.0748 0.0029 0.0778 | 12.3015</item>
      <item>13 | 2.50 | 0.0745 0.0030 0.0775 | 11.3776</item>
      <item>14 | 2.50 | 0.0741 0.0031 0.0772 | 10.4537</item>
      <item>15 | 2.25 | 0.0727 0.0032 0.0758 | 9.5920</item>
      <item>16 | 2.25 | 0.0695 0.0047 0.0742 | 8.8725</item>
      <item>29 | 2.00 | 0.0699 0.0021 0.0720 | 3.3283</item>
      <item>30 | 2.00 | 0.0638 0.0045 0.0684 | 3.1221</item>
      <item>31 | 2.00 | 0.0618 0.0055 0.0673 | 2.9160</item>
      <item>43 | 1.75 | 0.0604 0.0032 0.0636 | 1.5785</item>
      <item>44 | 1.75 | 0.0566 0.0052 0.0618 | 1.5194</item>
      <item>45 | 1.75 | 0.0553 0.0060 0.0612 | 1.4626</item>
      <item>57 | 1.50 | 0.0536 0.0044 0.0579 | 1.0900</item>
      <item>58 | 1.50 | 0.0508 0.0061 0.0570 | 1.0730</item>
      <item>59 | 1.50 | 0.0499 0.0067 0.0566 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 133s</item>
      <item>Prepare output 9s</item>
      <item>143s</item>
      <item>Jacobian determinant (RMS): 0.012 0.045 0.066 0.088 0.109 | 0.115934</item>
      <item>Template Matching: 0.081 0.209 0.185 0.166 0.150 | 0.149702</item>
      <item>Write result maps: 33s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 47s</item>
      <item>CSF distance: 13s</item>
      <item>PBT2x thickness: 38s</item>
      <item>104s</item>
      <item>Create initial surface 74s</item>
      <item>Topology correction: 79s</item>
      <item>Surface refinement: 71s</item>
      <item>Reduction of surface collisions with optimization: 60s</item>
      <item>Spherical mapping with areal smoothing 66s</item>
      <item>Spherical registration 267s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 63s</item>
      <item>CSF distance: 12s</item>
      <item>PBT2x thickness: 38s</item>
      <item>119s</item>
      <item>Create initial surface 74s</item>
      <item>Topology correction: 79s</item>
      <item>Surface refinement: 69s</item>
      <item>Reduction of surface collisions with optimization: 59s</item>
      <item>Spherical mapping with areal smoothing 66s</item>
      <item>Spherical registration 250s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5160 0.6553 mm</item>
      <item>Surface intensity / position RMSE: 0.0661 / 0.0657</item>
      <item>Euler number / defect number / defect size: 12.0 / 12.5 / 0.19%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/surf/lh.thickness.sub-0026017_ses-4_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/surf/rh.thickness.sub-0026017_ses-4_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/sub-0026017_ses-4_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1522s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 9s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 32s</item>
      <item>ROI estimation of 'lpba40' atlas 9s</item>
      <item>ROI estimation of 'hammers' atlas 22s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 8s</item>
      <item>ROI estimation of 'aal3' atlas 13s</item>
      <item>ROI estimation of 'mori' atlas 19s</item>
      <item>ROI estimation of 'anatomy3' atlas 27s</item>
      <item>ROI estimation of 'julichbrain' atlas 36s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
      <item>Write results 8s</item>
      <item>367s</item>
      <item>Quality check: 11s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/report/catreport_sub-0026017_ses-4_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 47 minute(s) and 18 second(s).</item>
      <item>Image Quality Rating (IQR): 81.92% (B-)</item>
      <item>GM volume (GMV): 44.74% (706.64 / 1579.34 ml)</item>
      <item>GM thickness (GMT): 2.52 0.66 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2614000/ds/Utah_2/sub-0026017/ses-4/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>