ds003826_ReproVBM/sub-82/report/cat_sub-82_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
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      <ll>-4.90936422348022</ll>
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      <Affine_rotation>[0.332953286931725 0.0256620567927068 -0.0156320852177129]</Affine_rotation>
      <Affine_scaling>[1.02004848642695 1.06086470701286 1.13678322207373]</Affine_scaling>
      <Affine_shearing>[0.00550349188492705 -0.00520769911936155 -0.0554885924918594]</Affine_shearing>
      <Affine0_translation>[3.18495609316597 12.7141306284889 -17.163928491193]</Affine0_translation>
      <Affine0_rotation>[0.332953286931725 0.0256620567927068 -0.0156320852177129]</Affine0_rotation>
      <Affine0_scaling>[1.02004848642695 1.06086470701286 1.13678322207373]</Affine0_scaling>
      <Affine0_shearing>[0.00550349188492705 -0.00520769911936155 -0.0554885924918594]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_28861/ds/sub-82</path>
      <file>sub-82_T1w</file>
      <fname>/var/lib/condor/execute/dir_28861/ds/sub-82/sub-82_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_28861/ds/sub-82/sub-82_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_28861/ds/sub-82/mri/msub-82_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_28861/ds/sub-82/mri/p0sub-82_T1w.nii</Fp0>
      <fnames>..28861/ds/sub-82/sub-82_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>32</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>
         </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>34</SurfaceEulerNumber>
      <SurfaceDefectArea>1.01822884944239</SurfaceDefectArea>
      <SurfaceDefectNumber>18</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>0.0699326321482658</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>0.0718117952346802</SurfacePositionRMSE>
      <res_vx_vol>[1.09999847412109 1 1]</res_vx_vol>
      <res_vx_voli>[1.09999847412109 1 1]</res_vx_voli>
      <res_RMS>1.03440750240073</res_RMS>
      <res_BB>0</res_BB>
      <tissue_mn>[2.77850008010864 22.8214168548584 90.2564315795898 143.398727416992]</tissue_mn>
      <tissue_mnr>[0.0193760450929403 0.159146577119827 0.629408895969391 1]</tissue_mnr>
      <tissue_weighting>T1</tissue_weighting>
      <tissue_std>[6.78129832847725 25.1450681363321 15.7941000952401 9.43429213020621]</tissue_std>
      <tissue_stdr>[0.0482242032885551 0.178815439343452 0.11231741309166 0.0670905783772469]</tissue_stdr>
      <contrast>51.3009834289551</contrast>
      <contrastr>0.357750624418259</contrastr>
      <NCR>0.139210373163223</NCR>
      <ICR>0.312377244234085</ICR>
   </qualitymeasures>
   <qualityratings>
      <res_vx_vol>[2.19999694824219 2 2]</res_vx_vol>
      <res_RMS>2.06881500480146</res_RMS>
      <res_BB>0.5</res_BB>
      <tissue_mn>[8.61485862731934 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>2.71707391738892</contrastr>
      <NCR>2.32946252822876</NCR>
      <ICR>1.23456656932831</ICR>
      <SurfaceEulerNumber>2.63265306122449</SurfaceEulerNumber>
      <SurfaceDefectArea>1.2545572123606</SurfaceDefectArea>
      <SurfaceDefectNumber>1.9</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.39865255355835</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.4362359046936</SurfacePositionRMSE>
      <IQR>2.22529253573518</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>20220703-105813</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>34</SurfaceEulerNumber>
         <SurfaceDefectArea>1.01822884944239</SurfaceDefectArea>
         <SurfaceDefectNumber>18</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0699326321482658</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0718117952346802</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>34</EC_abs>
      <defect_size>1.01822884944239</defect_size>
      <vol_abs_CGW>[439.746096666463 748.285626318419 525.677524524255 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.617043065628351</vol_abs_WMH>
      <vol_rel_WMH>0.000360062867446866</vol_rel_WMH>
      <surf_TSA>1979.95026370492</surf_TSA>
      <vol_TIV>1713.70924750914</vol_TIV>
      <vol_rel_CGW>[0.256604845486847 0.436646780897078 0.306748373616075 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.58874588314996 0.620093935382275]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.61160349845886 0.769747906004083 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.95412114999537 0.274210963503722 0.266983887081487;2.60694629342265 0.178689331418269 0.443207726003535;3.24499882233657 0.276801469148183 0.289808386914978]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.893492505885213 0.305591172070427 0.599308822117692;4.20733585509605 0.353369279431775 0.400691177882308]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>3.01843976675402</vol_TIV>
      <vol_rel_CGW>[2.4584203571632 5.69193212818029 3.35898659511628 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.03600628674469</vol_rel_WMH>
      <surf_TSA>8.62055482058122</surf_TSA>
      <SQR>4.66386440133748</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0.228380488510356 46 15 9484.17584388733 0.576618749004599]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.0272339545190334 0.0329149812459946 0.0992286875844002]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[891.367371369904 480.164932363592 618.307119169018 715.932893942081 2209.29718083143 8068.86212990546]</SPMvols0>
      <SPMvols1>[779.672620426552 455.103917323423 470.248502197744 700.993085646446 1469.45092398269 8415.85375837489]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[34.4365997314453 95.1912002563477 147.81689453125]</T3th>
            <Tth>
               <T3th>[0 0 4.84920930862427 34.4365997314453 95.1912002563477 147.81689453125 204.507049560547 569.531188964844]</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>[0.0169624593108892 0.064034104347229 0.070454329252243 0 0]</dtc>
         <ll>[0.084439928315076 0 0.084439928315076 0;0.207271085924604 0.00953924698846824 0.216810332913072 2034.22534179688;0.207271085924604 0.00953924698846824 0.216810332913072 2034.22534179688]</ll>
         <rmsdtc>[0.0387314446270466 0.0883780270814896 0.0992098897695541]</rmsdtc>
         <rmsgdt>[0.028006112203002 0.0432687141001225 0.054332260042429]</rmsgdt>
         <rmsdt>0.0992098897695541</rmsdt>
         <dt>0.070454329252243</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>[0.00849942583590746 0.0337597392499447 0.04639932513237 0.0546078532934189 0.0612129531800747 0.0689544752240181]</dtc>
         <ll>[0.0856535586877226 0 0.0856535586877226 0;0.223496703296703 0.0150141674297924 0.238510870726496 7685.376953125;0.206196997027978 0.0170293242079818 0.22322632123596 12256.208984375;0.18596668732472 0.0193187336862823 0.205285421011002 20830.849609375;0.16923630122108 0.0226912419548827 0.191927543175963 39694.9921875;0.16923630122108 0.0226912419548827 0.191927543175963 39694.9921875]</ll>
         <rmsdtc>[0.0105528468266129 0.0392359867691994 0.061329048126936 0.0864290595054626 0.111585326492786 0.119141846895218]</rmsdtc>
         <rmsgdt>[0.00321235414594412 0.0128110302612185 0.0287100169807673 0.0503914952278137 0.0714385509490967 0.0780084282159805]</rmsgdt>
         <rmsdt>0.119141846895218</rmsdt>
         <dt>0.0689544752240181</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_28861/ds/sub-82/sub-82_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 91s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 10s</item>
      <item>Initial correction 8s</item>
      <item>Refine background 4s</item>
      <item>Final correction 6s</item>
      <item>Final scaling 8s</item>
      <item>48s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 12s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 66s</item>
      <item>SPM preprocessing 1 (estimate 2): 53s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 15s</item>
      <item>Update Segmentation 19s</item>
      <item>Update Skull-Stripping 40s</item>
      <item>Update probability maps 9s</item>
      <item>83s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 21s</item>
      <item>Fast Optimized Shooting registration 32s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 14s</item>
      <item>Estimate local tissue thresholds (WM) 20s</item>
      <item>Estimate local tissue thresholds (GM) 27s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 32s</item>
      <item>102s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 18s</item>
      <item>Blood vessel detection 10s</item>
      <item>WMH detection (WMHCstr=0.48 &gt; WMHCstr'=0.17) 24s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>72s</item>
      <item>Blood vessel correction (BVCstr=0.50): 1s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 0.05]</item>
      <item>Final cleanup (gcutstr=0.24):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</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 | 0.0857 0.0000 0.0857 | 32.0000</item>
      <item>2 | 2.50 | 0.0829 0.0012 0.0842 | 29.4886</item>
      <item>3 | 2.50 | 0.0822 0.0018 0.0840 | 26.9772</item>
      <item>4 | 2.50 | 0.0818 0.0020 0.0838 | 24.6107</item>
      <item>5 | 2.50 | 0.0815 0.0022 0.0837 | 22.6548</item>
      <item>6 | 2.50 | 0.0812 0.0023 0.0835 | 20.6989</item>
      <item>7 | 2.50 | 0.0809 0.0024 0.0833 | 18.9688</item>
      <item>8 | 2.50 | 0.0807 0.0025 0.0831 | 17.4455</item>
      <item>9 | 2.50 | 0.0804 0.0025 0.0829 | 15.9223</item>
      <item>10 | 2.50 | 0.0801 0.0026 0.0827 | 14.6627</item>
      <item>11 | 2.50 | 0.0798 0.0027 0.0825 | 13.4764</item>
      <item>12 | 2.50 | 0.0795 0.0028 0.0822 | 12.3015</item>
      <item>13 | 2.50 | 0.0791 0.0029 0.0820 | 11.3776</item>
      <item>14 | 2.50 | 0.0788 0.0029 0.0817 | 10.4537</item>
      <item>15 | 2.25 | 0.0788 0.0030 0.0818 | 9.5920</item>
      <item>16 | 2.25 | 0.0757 0.0045 0.0802 | 8.8725</item>
      <item>17 | 2.25 | 0.0745 0.0050 0.0795 | 8.1530</item>
      <item>29 | 2.00 | 0.0763 0.0023 0.0786 | 3.3283</item>
      <item>30 | 2.00 | 0.0706 0.0047 0.0754 | 3.1221</item>
      <item>31 | 2.00 | 0.0687 0.0057 0.0744 | 2.9160</item>
      <item>43 | 1.75 | 0.0679 0.0032 0.0711 | 1.5785</item>
      <item>44 | 1.75 | 0.0634 0.0056 0.0691 | 1.5194</item>
      <item>45 | 1.75 | 0.0620 0.0064 0.0684 | 1.4626</item>
      <item>57 | 1.50 | 0.0608 0.0047 0.0655 | 1.0900</item>
      <item>58 | 1.50 | 0.0575 0.0069 0.0643 | 1.0730</item>
      <item>59 | 1.50 | 0.0564 0.0076 0.0640 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 163s</item>
      <item>Prepare output 10s</item>
      <item>173s</item>
      <item>Jacobian determinant (RMS): 0.011 0.039 0.061 0.086 0.112 | 0.119142</item>
      <item>Template Matching: 0.086 0.223 0.206 0.186 0.169 | 0.169236</item>
      <item>Write result maps: 23s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 55s</item>
      <item>CSF distance: 18s</item>
      <item>PBT2x thickness: 49s</item>
      <item>128s</item>
      <item>Create initial surface 86s</item>
      <item>Topology correction: 95s</item>
      <item>Surface refinement: 82s</item>
      <item>Reduction of surface collisions with optimization: 70s</item>
      <item>Spherical mapping with areal smoothing 87s</item>
      <item>Spherical registration 304s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 48s</item>
      <item>CSF distance: 17s</item>
      <item>PBT2x thickness: 47s</item>
      <item>117s</item>
      <item>Create initial surface 83s</item>
      <item>Topology correction: 89s</item>
      <item>Surface refinement: 70s</item>
      <item>Reduction of surface collisions with optimization: 65s</item>
      <item>Spherical mapping with areal smoothing 78s</item>
      <item>Spherical registration 279s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.5888 0.6199 mm</item>
      <item>Surface intensity / position RMSE: 0.0699 / 0.0718</item>
      <item>Euler number / defect number / defect size: 34.0 / 18.0 / 1.02%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28861/ds/sub-82/surf/lh.thickness.sub-82_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_28861/ds/sub-82/surf/rh.thickness.sub-82_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_28861/ds/sub-82/sub-82_T1w.nii</item>
      <item>Surface ROI estimation: 7s</item>
      <item>Surface and thickness estimation takes: 1726s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 11s</item>
      <item>ROI estimation of 'mori' atlas 16s</item>
      <item>ROI estimation of 'anatomy3' atlas 23s</item>
      <item>ROI estimation of 'julichbrain' atlas 31s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 49s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 73s</item>
      <item>Write results 73s</item>
      <item>307s</item>
      <item>Quality check: 5s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_28861/ds/sub-82/report/catreport_sub-82_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 49 minute(s) and 21 second(s).</item>
      <item>Image Quality Rating (IQR): 82.75% (B-)</item>
      <item>GM volume (GMV): 43.66% (748.29 / 1713.71 ml)</item>
      <item>GM thickness (GMT): 2.59 0.62 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_28861/ds/sub-82/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_28861/ds/sub-82/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_28861/ds/sub-82/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>