ds003787_ReproVBM/sub-wlsubj109/report/cat_sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_shearing>[-0.000760800649784979 0.00576307802459068 -0.0331346768910148]</Affine_shearing>
      <Affine0_translation>[-0.770675671174007 -16.9509510304651 4.66535617836416]</Affine0_translation>
      <Affine0_rotation>[0.384753346462753 -0.0219343887137477 -0.0992766773518602]</Affine0_rotation>
      <Affine0_scaling>[1.08075537071571 1.03535195290328 1.14930583410967]</Affine0_scaling>
      <Affine0_shearing>[-0.000760800649784979 0.00576307802459068 -0.0331346768910148]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109</path>
      <file>sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w</file>
      <fname>/var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/mri/msub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/mri/p0sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.nii</Fp0>
      <fnames>..s/sub-wlsubj109/..s-nyu3t01_acq-highres_run-01_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_1980</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>20</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>
         </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>
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         <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>
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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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      <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
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      <tissue_mn>[5.55249977111816 137.737045288086 344.210784912109 490.661834716797]</tissue_mn>
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      <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
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      <SurfaceIntensityRMSE>1.3411557674408</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.32260179519653</SurfacePositionRMSE>
      <IQR>1.86793408080579</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <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>1980</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>20220712-154238</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>16</SurfaceEulerNumber>
         <SurfaceDefectArea>0.398302737940643</SurfaceDefectArea>
         <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0670577883720398</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0661300867795944</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>16</EC_abs>
      <defect_size>0.398302737940643</defect_size>
      <vol_abs_CGW>[233.518802334417 708.888077192904 494.462638107033 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.14013675226376</vol_abs_WMH>
      <vol_rel_WMH>0.000793486630672542</vol_rel_WMH>
      <surf_TSA>2039.21812733136</surf_TSA>
      <vol_TIV>1436.86951763435</vol_TIV>
      <vol_rel_CGW>[0.16251914280907 0.493355916102953 0.344124941087977 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.45130395696373 0.565379642031025]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.44520258903503 0.682284686705666 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.93214632917568 0.212570461086247 0.313180339939866;2.47998075223606 0.157238905711964 0.420236853408603;3.06065208001432 0.239874433903171 0.266582806651531]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.902308567686209 0.400207268258803 0.516795127985536;3.9693832471644 0.389872397085885 0.483204872014464]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.0323180914082</vol_TIV>
      <vol_rel_CGW>[0.768662765967491 6.71041515989498 4.0302611545973 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.07934866306725</vol_rel_WMH>
      <surf_TSA>8.62259509450053</surf_TSA>
      <SQR>5.49907384187502</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.25009521484375 1 1 7077.00878114196 0.421971091839469]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00786346569657326 0.00502064637839794 0.0961891487240791]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[824.623344057119 455.271248418802 410.207062186772 700.967403573595 2314.23743226092 5375.6868865934]</SPMvols0>
      <SPMvols1>[724.598781754143 429.679344616338 251.59697925728 1476.74385493948 2065.83422132552 4489.63783974306]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[162.104095458984 355.728485107422 482.76611328125]</T3th>
            <Tth>
               <T3th>[0 0 8.63039588928223 162.104095458984 355.728485107422 482.76611328125 643.097106933594 1535.69396972656]</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>[0.0218170937150717 0.0734629184007645 0.0808334052562714 0 0]</dtc>
         <ll>[0.0835530928680066 0 0.0835530928680066 0;0.197113073745123 0.00992775192352332 0.207040825668646 2117.0732421875;0.197113073745123 0.00992775192352332 0.207040825668646 2117.0732421875]</ll>
         <rmsdtc>[0.0480371378362179 0.0971047431230545 0.106512546539307]</rmsdtc>
         <rmsgdt>[0.0342483259737492 0.0422353148460388 0.0511742234230042]</rmsgdt>
         <rmsdt>0.106512546539307</rmsdt>
         <dt>0.0808334052562714</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>[0.010048788972199 0.0363246835768223 0.050200592726469 0.0576610043644905 0.0639314353466034 0.0717656835913658]</dtc>
         <ll>[0.0835435708810335 0 0.0835435708810335 0;0.219949160561661 0.0134543984661172 0.233403559027778 6886.97021484375;0.199410732174814 0.01622195509063 0.215632687265444 11675.1357421875;0.180240917296378 0.0182596262816803 0.198500543578058 19688.84375;0.163249891531326 0.0214657308301984 0.184715622361525 37551.140625;0.163249891531326 0.0214657308301984 0.184715622361525 37551.140625]</ll>
         <rmsdtc>[0.0118028447031975 0.0428890287876129 0.0633228421211243 0.0869581401348114 0.108746394515038 0.11529403179884]</rmsdtc>
         <rmsgdt>[0.00328966090455651 0.0128076747059822 0.0278359986841679 0.0482792071998119 0.0665538534522057 0.0720730945467949]</rmsgdt>
         <rmsdt>0.11529403179884</rmsdt>
         <dt>0.0717656835913658</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 63s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 14s</item>
      <item>Estimate background 11s</item>
      <item>Initial correction 13s</item>
      <item>Refine background 7s</item>
      <item>Final correction 12s</item>
      <item>Final scaling 15s</item>
      <item>86s</item>
      <item>Correct center-of-mass 6s</item>
      <item>Affine registration 18s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 144s</item>
      <item>SPM preprocessing 1 (estimate 2): 52s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 34s</item>
      <item>Update Segmentation 45s</item>
      <item>Update Skull-Stripping 108s</item>
      <item>Update probability maps 19s</item>
      <item>206s</item>
      <item>Global intensity correction: 37s</item>
      <item>SANLM denoising after intensity normalization (medium): 23s</item>
      <item>Fast Optimized Shooting registration 60s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 10s</item>
      <item>Prepare partitions 5s</item>
      <item>Prepare segments (LASmod = 1.05) 34s</item>
      <item>Estimate local tissue thresholds (WM) 38s</item>
      <item>Estimate local tissue thresholds (GM) 54s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 47s</item>
      <item>196s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 20s</item>
      <item>Major structures 9s</item>
      <item>Ventricle detection 39s</item>
      <item>Blood vessel detection 26s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.04) 66s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 4s</item>
      <item>Side alignment 9s</item>
      <item>Final corrections 10s</item>
      <item>184s</item>
      <item>Blood vessel correction (BVCstr=0.50): 3s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 61s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.04]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 10s</item>
      <item>Level 1 cleanup (brain masking) 6s</item>
      <item>Level 2 cleanup (CSF correction) 3s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
      <item>26s</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 | 0.0835 0.0000 0.0835 | 32.0000</item>
      <item>2 | 2.50 | 0.0810 0.0012 0.0822 | 29.4886</item>
      <item>3 | 2.50 | 0.0802 0.0018 0.0820 | 26.9772</item>
      <item>4 | 2.50 | 0.0799 0.0020 0.0819 | 24.6107</item>
      <item>5 | 2.50 | 0.0796 0.0021 0.0817 | 22.6548</item>
      <item>6 | 2.50 | 0.0793 0.0022 0.0815 | 20.6989</item>
      <item>7 | 2.50 | 0.0790 0.0023 0.0814 | 18.9688</item>
      <item>8 | 2.50 | 0.0788 0.0024 0.0812 | 17.4455</item>
      <item>9 | 2.50 | 0.0785 0.0025 0.0810 | 15.9223</item>
      <item>10 | 2.50 | 0.0782 0.0026 0.0808 | 14.6627</item>
      <item>11 | 2.50 | 0.0779 0.0027 0.0805 | 13.4764</item>
      <item>12 | 2.50 | 0.0775 0.0028 0.0803 | 12.3015</item>
      <item>13 | 2.50 | 0.0772 0.0029 0.0801 | 11.3776</item>
      <item>14 | 2.50 | 0.0769 0.0029 0.0798 | 10.4537</item>
      <item>15 | 2.25 | 0.0764 0.0030 0.0794 | 9.5920</item>
      <item>16 | 2.25 | 0.0733 0.0045 0.0778 | 8.8725</item>
      <item>29 | 2.00 | 0.0745 0.0020 0.0765 | 3.3283</item>
      <item>30 | 2.00 | 0.0685 0.0044 0.0729 | 3.1221</item>
      <item>31 | 2.00 | 0.0665 0.0054 0.0719 | 2.9160</item>
      <item>43 | 1.75 | 0.0657 0.0031 0.0688 | 1.5785</item>
      <item>44 | 1.75 | 0.0615 0.0053 0.0668 | 1.5194</item>
      <item>45 | 1.75 | 0.0601 0.0061 0.0662 | 1.4626</item>
      <item>57 | 1.50 | 0.0587 0.0044 0.0631 | 1.0900</item>
      <item>58 | 1.50 | 0.0555 0.0065 0.0620 | 1.0730</item>
      <item>59 | 1.50 | 0.0544 0.0072 0.0616 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 244s</item>
      <item>Prepare output 17s</item>
      <item>262s</item>
      <item>Jacobian determinant (RMS): 0.012 0.043 0.063 0.087 0.109 | 0.115294</item>
      <item>Template Matching: 0.084 0.220 0.199 0.180 0.163 | 0.163250</item>
      <item>Write result maps: 55s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 49s</item>
      <item>CSF distance: 23s</item>
      <item>PBT2x thickness: 61s</item>
      <item>142s</item>
      <item>Create initial surface 100s</item>
      <item>Topology correction: 110s</item>
      <item>Surface refinement: 87s</item>
      <item>Reduction of surface collisions with optimization: 71s</item>
      <item>Spherical mapping with areal smoothing 105s</item>
      <item>Spherical registration 300s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 49s</item>
      <item>CSF distance: 20s</item>
      <item>PBT2x thickness: 58s</item>
      <item>134s</item>
      <item>Create initial surface 96s</item>
      <item>Topology correction: 111s</item>
      <item>Surface refinement: 78s</item>
      <item>Reduction of surface collisions with optimization: 72s</item>
      <item>Spherical mapping with areal smoothing 106s</item>
      <item>Spherical registration 292s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4514 0.5651 mm</item>
      <item>Surface intensity / position RMSE: 0.0671 / 0.0661</item>
      <item>Euler number / defect number / defect size: 16.0 / 7.5 / 0.40%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/surf/lh.thickness.sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/surf/rh.thickness.sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1946s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 28s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 105s</item>
      <item>ROI estimation of 'lpba40' atlas 30s</item>
      <item>ROI estimation of 'hammers' atlas 74s</item>
      <item>ROI estimation of 'thalamus' atlas 5s</item>
      <item>ROI estimation of 'ibsr' atlas 26s</item>
      <item>ROI estimation of 'aal3' atlas 43s</item>
      <item>ROI estimation of 'mori' atlas 62s</item>
      <item>ROI estimation of 'anatomy3' atlas 90s</item>
      <item>ROI estimation of 'julichbrain' atlas 118s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 42s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 51s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 193s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 282s</item>
      <item>Write results 283s</item>
      <item>1150s</item>
      <item>Quality check: 10s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/report/catreport_sub-wlsubj109_ses-nyu3t01_acq-highres_run-01_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 79 minute(s) and 51 second(s).</item>
      <item>Image Quality Rating (IQR): 86.32% (B)</item>
      <item>GM volume (GMV): 49.34% (708.89 / 1436.87 ml)</item>
      <item>GM thickness (GMT): 2.45 0.57 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_2945258/ds/sub-wlsubj109/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>