CORR_cat12.8.1/Utah_1/sub-0026031/ses-1/report/cat_sub-0026031_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine>[1.01216025640937 -0.114587552277048 0.0282978084156567 -2.1740657735466;0.112364951649052 1.04013287729645 0.0617455078964456 -39.3438577620687;-0.037256337326884 -0.0441601233333222 1.13440024479991 -27.5990512052709;0 0 0 1]</Affine>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
      <mn>[222.605558557409 338.870313469317 53.2871799556251 128.448399838492 495.785700113686 74.907044968631 220.861642666236 369.839197122224 609.588310999116 449.557500579258 227.947232800292 33.9742424594874 30.4649069833378]</mn>
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      <ll>-5.12048435211182</ll>
      <Affine_translation>[-2.1740657735466 -39.3438577620687 -27.5990512052709]</Affine_translation>
      <Affine_rotation>[0.0459170504598251 0.0316636616388678 -0.112059664612527]</Affine_rotation>
      <Affine_scaling>[1.01905951822491 1.04735410421025 1.13636518046481]</Affine_scaling>
      <Affine_shearing>[0.00244468164660212 -0.00643597887222304 0.00993849738502081]</Affine_shearing>
      <Affine0_translation>[-2.1740657735466 -39.3438577620687 -27.5990512052709]</Affine0_translation>
      <Affine0_rotation>[0.0459170504598251 0.0316636616388678 -0.112059664612527]</Affine0_rotation>
      <Affine0_scaling>[1.01905951822491 1.04735410421025 1.13636518046481]</Affine0_scaling>
      <Affine0_shearing>[0.00244468164660212 -0.00643597887222304 0.00993849738502081]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1</path>
      <file>sub-0026031_ses-1_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/sub-0026031_ses-1_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/sub-0026031_ses-1_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/mri/msub-0026031_ses-1_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/mri/p0sub-0026031_ses-1_run-1_T1w.nii</Fp0>
      <fnames>../Utah_1/sub-0026031/ses-1/sub-0026031_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>
            </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_3452592/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>
                  <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
               </shootingtpm>
               <regstr>0.5</regstr>
            </shooting>
         </regmethod>
         <restypes>
            <optimal>[1 0.3]</optimal>
         </restypes>
         <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>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
            <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>
         </shootingtpms>
         <templates>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
            <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>
         </templates>
         <inv_weighting>0</inv_weighting>
         <AMAPframing>1</AMAPframing>
      </extopts>
   </parameter>
   <qualitymeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <SurfaceEulerNumber>32</SurfaceEulerNumber>
      <SurfaceDefectArea>0.764141202680489</SurfaceDefectArea>
      <SurfaceDefectNumber>17</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0809759348630905</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0751022398471832</SurfacePositionRMSE>
      <res_vx_vol>[1.19999998513769 0.499999993807371 0.5]</res_vx_vol>
      <res_vx_voli>[0.799999988895774 0.799999991287814 0.800000011920929]</res_vx_voli>
      <res_RMS>0.804155863444773</res_RMS>
      <res_BB>NaN</res_BB>
      <tissue_mn>[23.4680004119873 62.8339996337891 207.619003295898 348.078002929688]</tissue_mn>
      <tissue_mnr>[0.067421667277813 0.180517002940178 0.59647262096405 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[9.82275616106363 39.3249749018858 35.9536670295143 26.8037003804344]</tissue_std>
      <tissue_stdr>[0.0302601754665375 0.12114529311657 0.110759571194649 0.0825720056891441]</tissue_stdr>
      <contrast>120.711074829102</contrast>
      <contrastr>0.346793174743652</contrastr>
      <res_ECR>0.363154232501984</res_ECR>
      <NCR>0.220926970243454</NCR>
      <ICR>0.319525063037872</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.39999997027538 0.999999987614742 1]</res_vx_vol>
      <res_RMS>1.60831172688955</res_RMS>
      <res_ECR>2.75078678131104</res_ECR>
      <res_BB>NaN</res_BB>
      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
      <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
      <contrast>0.5</contrast>
      <contrastr>2.88143563270569</contrastr>
      <NCR>3.50254058837891</NCR>
      <ICR>1.25229430198669</ICR>
      <SurfaceEulerNumber>2.53061224489796</SurfaceEulerNumber>
      <SurfaceDefectArea>1.19103530067012</SurfaceDefectArea>
      <SurfaceDefectNumber>1.85</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.61951875686646</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.50204479694366</SurfacePositionRMSE>
      <SIQR>3.10581118977069</SIQR>
      <IQR>3.21263672114396</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>20231031-012130</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>32</SurfaceEulerNumber>
         <SurfaceDefectArea>0.764141202680489</SurfaceDefectArea>
         <SurfaceDefectNumber>17</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0809759348630905</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0751022398471832</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>32</EC_abs>
      <defect_size>0.764141202680489</defect_size>
      <vol_abs_CGW>[238.650634695653 892.856847282197 487.360732068496 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.1211434556017</vol_abs_WMH>
      <vol_rel_WMH>0.000692547698369725</vol_rel_WMH>
      <surf_TSA>2200.15076903738</surf_TSA>
      <vol_TIV>1618.86821404635</vol_TIV>
      <vol_rel_CGW>[0.147418197865006 0.551531520314745 0.301050281820249 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.75730591084381 0.648321505249924]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.77075695991516 0.817069657501293 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[2.08036289672787 0.278673522886544 0.280580927725948;2.78785849366591 0.194888277764425 0.456834747119512;3.49604275073725 0.294825610956832 0.26258432515454]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.922336585426209 0.404472022930632 0.53988035892323;4.46367201675961 0.296211346501765 0.46011964107677]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.05997902224582</vol_TIV>
      <vol_rel_CGW>[0.5 7.75523563783666 3.25665017636942 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.06925476983697</vol_rel_WMH>
      <surf_TSA>8.62390414122726</surf_TSA>
      <SQR>6.34272986726483</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11796.4797077951 0.420152863193204]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00130149070173502 0.000912726914975792 0.183193489909172]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[1068.88967980369 433.797651812815 428.284190910366 967.134047866776 110.592581183032 9308.04048764937]</SPMvols0>
      <SPMvols1>[930.407214033168 405.137663013317 238.71883309498 770.490982827124 90.6684668071215 9364.5397774447]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[72.8469009399414 212.717498779297 341.127502441406]</T3th>
            <Tth>
               <T3th>[-183.201461791992 -55.1867370605469 8.83008193969727 72.8469009399414 212.717498779297 341.127502441406 475.267822265625 878.868103027344]</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>[0.0165608897805214 0.0549185648560524 0.0609731450676918 0 0]</dtc>
         <ll>[0.0826006061604329 0 0.0826006061604329 0;0.203072244522809 0.00951091610655493 0.212583160629364 2028.18383789062;0.203072244522809 0.00951091610655493 0.212583160629364 2028.18383789062]</ll>
         <rmsdtc>[0.0384400859475136 0.0842826664447784 0.0973045155405998]</rmsdtc>
         <rmsgdt>[0.0277044232934713 0.0485981851816177 0.0606035925447941]</rmsgdt>
         <rmsdt>0.0973045155405998</rmsdt>
         <dt>0.0609731450676918</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>[0.00701675238087773 0.0297736432403326 0.0383961871266365 0.0513954013586044 0.0617475137114525 0.071114294230938]</dtc>
         <ll>[0.0867376860238306 0 0.0867376860238306 0;0.223878235653236 0.0156370096916972 0.239515245344933 8004.1943359375;0.213430663063837 0.0183177125559425 0.231748375619779 13183.4775390625;0.193049286845063 0.0213765201405582 0.214425806985621 23049.703125;0.174529454604074 0.0253828643182651 0.199912318922339 44403.58984375;0.174529454604074 0.0253828643182651 0.199912318922339 44403.58984375]</ll>
         <rmsdtc>[0.00906551163643599 0.0336046405136585 0.0627083778381348 0.0998653396964073 0.139543741941452 0.146757692098618]</rmsdtc>
         <rmsgdt>[0.00330098136328161 0.0139069389551878 0.033942449837923 0.0614969804883003 0.0894045829772949 0.0958311930298805]</rmsgdt>
         <rmsdt>0.146757692098618</rmsdt>
         <dt>0.071114294230938</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0026031/ses-1/sub-0026031_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 354s</item>
      <item>Internal resampling (1.20x0.50x0.50mm &gt; 0.80x0.80x0.80mm): 3s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 16s</item>
      <item>Estimate background 12s</item>
      <item>Initial correction 14s</item>
      <item>Refine background 7s</item>
      <item>Final correction 12s</item>
      <item>Final scaling 10s</item>
      <item>86s</item>
      <item>Correct center-of-mass 9s</item>
      <item>Affine registration 59s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 7s</item>
      <item>Use initial fine affine registration. 146s</item>
      <item>SPM preprocessing 1 (estimate 2): 68s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 41s</item>
      <item>Update Segmentation 43s</item>
      <item>Update Skull-Stripping 107s</item>
      <item>Update probability maps 23s</item>
      <item>214s</item>
      <item>Global intensity correction: 43s</item>
      <item>SANLM denoising after intensity normalization (medium): 82s</item>
      <item>Fast Optimized Shooting registration 59s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 10s</item>
      <item>Prepare partitions 7s</item>
      <item>Prepare segments (LASmod = 1.00) 39s</item>
      <item>Estimate local tissue thresholds (WM) 55s</item>
      <item>Estimate local tissue thresholds (GM) 86s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 106s</item>
      <item>314s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 20s</item>
      <item>Major structures 9s</item>
      <item>Ventricle detection 41s</item>
      <item>Blood vessel detection 31s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 73s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 4s</item>
      <item>Side alignment 10s</item>
      <item>Final corrections 12s</item>
      <item>201s</item>
      <item>Blood vessel correction (BVCstr=0.50): 4s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 75s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 11s</item>
      <item>Level 1 cleanup (brain masking) 7s</item>
      <item>Level 2 cleanup (CSF correction) 4s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
      <item>28s</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 | 0.0867 0.0000 0.0867 | 32.0000</item>
      <item>2 | 2.50 | 0.0844 0.0011 0.0855 | 29.4886</item>
      <item>3 | 2.50 | 0.0837 0.0017 0.0854 | 26.9772</item>
      <item>4 | 2.50 | 0.0834 0.0018 0.0853 | 24.6107</item>
      <item>5 | 2.50 | 0.0832 0.0020 0.0851 | 22.6548</item>
      <item>6 | 2.50 | 0.0829 0.0020 0.0849 | 20.6989</item>
      <item>7 | 2.50 | 0.0827 0.0021 0.0848 | 18.9688</item>
      <item>8 | 2.50 | 0.0824 0.0022 0.0846 | 17.4455</item>
      <item>9 | 2.50 | 0.0822 0.0022 0.0844 | 15.9223</item>
      <item>10 | 2.50 | 0.0819 0.0023 0.0842 | 14.6627</item>
      <item>11 | 2.50 | 0.0817 0.0024 0.0840 | 13.4764</item>
      <item>12 | 2.50 | 0.0814 0.0024 0.0838 | 12.3015</item>
      <item>13 | 2.50 | 0.0811 0.0025 0.0836 | 11.3776</item>
      <item>14 | 2.50 | 0.0808 0.0025 0.0834 | 10.4537</item>
      <item>15 | 2.25 | 0.0816 0.0026 0.0841 | 9.5920</item>
      <item>16 | 2.25 | 0.0782 0.0042 0.0824 | 8.8725</item>
      <item>17 | 2.25 | 0.0770 0.0048 0.0817 | 8.1530</item>
      <item>18 | 2.25 | 0.0762 0.0050 0.0812 | 7.5234</item>
      <item>19 | 2.25 | 0.0756 0.0051 0.0808 | 6.9630</item>
      <item>20 | 2.25 | 0.0751 0.0051 0.0803 | 6.4027</item>
      <item>21 | 2.25 | 0.0746 0.0052 0.0798 | 5.9447</item>
      <item>29 | 2.00 | 0.0776 0.0031 0.0807 | 3.3283</item>
      <item>30 | 2.00 | 0.0727 0.0053 0.0781 | 3.1221</item>
      <item>31 | 2.00 | 0.0711 0.0061 0.0772 | 2.9160</item>
      <item>43 | 1.75 | 0.0711 0.0034 0.0745 | 1.5785</item>
      <item>44 | 1.75 | 0.0659 0.0063 0.0722 | 1.5194</item>
      <item>45 | 1.75 | 0.0643 0.0071 0.0715 | 1.4626</item>
      <item>57 | 1.50 | 0.0632 0.0052 0.0683 | 1.0900</item>
      <item>58 | 1.50 | 0.0593 0.0078 0.0671 | 1.0730</item>
      <item>59 | 1.50 | 0.0582 0.0085 0.0666 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 215s</item>
      <item>Prepare output 24s</item>
      <item>239s</item>
      <item>Jacobian determinant (RMS): 0.009 0.034 0.063 0.100 0.140 | 0.146758</item>
      <item>Template Matching: 0.087 0.224 0.213 0.193 0.175 | 0.174529</item>
      <item>Write result maps: 369s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 59s</item>
      <item>CSF distance: 25s</item>
      <item>PBT2x thickness: 72s</item>
      <item>163s</item>
      <item>Create initial surface 116s</item>
      <item>Topology correction: 137s</item>
      <item>Surface refinement: 118s</item>
      <item>Reduction of surface collisions with optimization: 109s</item>
      <item>Spherical mapping with areal smoothing 141s</item>
      <item>Spherical registration 367s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 50s</item>
      <item>CSF distance: 25s</item>
      <item>PBT2x thickness: 71s</item>
      <item>155s</item>
      <item>Create initial surface 114s</item>
      <item>Topology correction: 130s</item>
      <item>Surface refinement: 140s</item>
      <item>Reduction of surface collisions with optimization: 103s</item>
      <item>Spherical mapping with areal smoothing 123s</item>
      <item>Spherical registration 343s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.7573 0.6483 mm</item>
      <item>Surface intensity / position RMSE: 0.0810 / 0.0751</item>
      <item>Euler number / defect number / defect size: 32.0 / 17.0 / 0.76%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/surf/lh.thickness.sub-0026031_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/surf/rh.thickness.sub-0026031_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/sub-0026031_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 11s</item>
      <item>Surface and thickness estimation takes: 2474s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 19s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 70s</item>
      <item>ROI estimation of 'lpba40' atlas 20s</item>
      <item>ROI estimation of 'hammers' atlas 51s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 18s</item>
      <item>ROI estimation of 'aal3' atlas 30s</item>
      <item>ROI estimation of 'mori' atlas 45s</item>
      <item>ROI estimation of 'anatomy3' atlas 69s</item>
      <item>ROI estimation of 'julichbrain' atlas 85s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 39s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 75s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 164s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 249s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 22s</item>
      <item>Write results 24s</item>
      <item>961s</item>
      <item>Quality check: 71s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/report/catreport_sub-0026031_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 100 minute(s) and 17 second(s).</item>
      <item>Image Quality Rating (IQR): 72.87% (C-)</item>
      <item>GM volume (GMV): 55.15% (892.86 / 1618.87 ml)</item>
      <item>GM thickness (GMT): 2.76 0.65 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_3452592/ds/Utah_1/sub-0026031/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>