CORR_cat12.8.1/IACAS/sub-0025466/ses-2/report/cat_sub-0025466_ses-2_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <Affine_shearing>[0.00759624214701597 0.0121774244424304 0.0355815037983082]</Affine_shearing>
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      <Affine0_shearing>[0.00759624214701597 0.0121774244424304 0.0355815037983082]</Affine0_shearing>
   </SPMpreprocessing>
   <filedata>
      <path>/var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2</path>
      <file>sub-0025466_ses-2_run-1_T1w</file>
      <fname>/var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/sub-0025466_ses-2_run-1_T1w.nii</fname>
      <F>/var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/sub-0025466_ses-2_run-1_T1w.nii</F>
      <Fm>/var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/mri/msub-0025466_ses-2_run-1_T1w.nii</Fm>
      <Fp0>/var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/mri/p0sub-0025466_ses-2_run-1_T1w.nii</Fp0>
      <fnames>..s/IACAS/sub-0025466/ses-2/sub-0025466_ses-2_run-1_T1w</fnames>
   </filedata>
   <parameter>
      <opts>
         <tpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
         </tpm>
         <ngaus>[1 1 2 3 4 2]</ngaus>
         <affreg>mni</affreg>
         <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
         <tol>0.0001</tol>
         <accstr>0.5</accstr>
         <biasstr>0.5</biasstr>
         <biasreg>0.001</biasreg>
         <biasfwhm>60</biasfwhm>
         <samp>3</samp>
         <redspmres>0</redspmres>
         <fwhm>1</fwhm>
         <biasacc>0</biasacc>
      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
         <BVCstr>0.5</BVCstr>
         <regstr>0.5</regstr>
         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
         <SLC>0</SLC>
         <mrf>1</mrf>
         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</nproc>
         <species>human</species>
         <APP>1070</APP>
         <setCOM>1</setCOM>
         <vox>1.5</vox>
         <bb>12</bb>
         <shootingsurf>Template_T1</shootingsurf>
         <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
         <darteltpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
         </darteltpm>
         <shootingtpm>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
         </shootingtpm>
         <shootingT1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
         </shootingT1>
         <brainmask>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
         </brainmask>
         <T1>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
         </T1>
         <cat12atlas>
            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
         </cat12atlas>
         <pbtres>0.5</pbtres>
         <SRP>22</SRP>
         <reduce_mesh>1</reduce_mesh>
         <vdist>2</vdist>
         <pbtlas>0</pbtlas>
         <thick_measure>1</thick_measure>
         <thick_limit>5</thick_limit>
         <close_parahipp>0</close_parahipp>
         <scale_cortex>0.7</scale_cortex>
         <add_parahipp>0.1</add_parahipp>
         <colormap>BCGWHw</colormap>
         <report/>
         <verb>2</verb>
         <ignoreErrors>1</ignoreErrors>
         <expertgui>1</expertgui>
         <subfolders>1</subfolders>
         <experimental>0</experimental>
         <print>2</print>
         <fontsize>10</fontsize>
         <send_info>1</send_info>
         <gifti_dat>1</gifti_dat>
         <atlas>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
               </td>
               <td>[false]</td>
            </tr>
            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
               <td>0</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
               <td>0</td>
               <td>
                  <item>csf</item>
                  <item>gm</item>
                  <item>wm</item>
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               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
               </td>
               <td>[false]</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/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>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
               <td>1</td>
               <td>
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               <td>[false]</td>
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            <tr>
               <td>/var/lib/condor/execute/dir_108989/ds/code/Tian_Subcortex_S2_7T.nii</td>
               <td>1</td>
               <td>
                  <item>gm</item>
                  <item>wm</item>
                  <item>csf</item>
               </td>
               <td>[false]</td>
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         </atlas>
         <satlas>
            <tr>
               <td>Desikan</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <tr>
               <td>Destrieux</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
               <td>0</td>
               <td>1</td>
            </tr>
            <tr>
               <td>HCP</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_100P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_200P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
               <td>0</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_400P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
            <tr>
               <td>Schaefer2018_600P_17N</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
               <td>1</td>
               <td>0</td>
            </tr>
         </satlas>
         <LAB>
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            <CT>1</CT>
            <CB>3</CB>
            <BG>5</BG>
            <BV>7</BV>
            <TH>9</TH>
            <ON>11</ON>
            <MB>13</MB>
            <BS>13</BS>
            <VT>15</VT>
            <NV>17</NV>
            <HC>19</HC>
            <HD>21</HD>
            <HI>23</HI>
            <PH>25</PH>
            <LE>27</LE>
         </LAB>
         <new_release>0</new_release>
         <lazy>0</lazy>
         <affmod>0</affmod>
         <regmethod>
            <shooting>
               <shootingtpm>
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               <regstr>0.5</regstr>
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         <restypes>
            <optimal>[1 0.3]</optimal>
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         <LASmyostr>0</LASmyostr>
         <pbtmethod>pbt2x</pbtmethod>
         <darteltpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
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         </darteltpms>
         <shootingtpms>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
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         <templates>
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            <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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         <AMAPframing>1</AMAPframing>
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      <res_vx_voli>[1 1 1]</res_vx_voli>
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      <contrast>576.822021484375</contrast>
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      <ICR>0.407111018896103</ICR>
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      <contrastr>4.68749380111694</contrastr>
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      <SurfaceDefectArea>1.35397441359809</SurfaceDefectArea>
      <SurfaceDefectNumber>3.05</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.47334742546082</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.67901253700256</SurfacePositionRMSE>
      <SIQR>3.38340049798387</SIQR>
      <IQR>3.55854937411879</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>20231031-005058</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>52</SurfaceEulerNumber>
         <SurfaceDefectArea>1.41589765439238</SurfaceDefectArea>
         <SurfaceDefectNumber>41</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0736673697829247</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0839506238698959</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>52</EC_abs>
      <defect_size>1.41589765439238</defect_size>
      <vol_abs_CGW>[323.146839215686 707.008909803921 665.169160784314 0 0]</vol_abs_CGW>
      <vol_abs_WMH>1.45890196078431</vol_abs_WMH>
      <vol_rel_WMH>0.000860544166105038</vol_rel_WMH>
      <surf_TSA>2273.28443682559</surf_TSA>
      <vol_TIV>1695.32490980392</vol_TIV>
      <vol_rel_CGW>[0.190610565176596 0.417034460896167 0.392354973927237 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.22549710124142 0.663239219735913]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.21661615371704 0.766556085718743 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.50220886637475 0.293008728505045 0.287172471850994;2.21485931360542 0.199512273332082 0.431193473529135;2.93268765439002 0.286027955407968 0.281634054619871]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.667813567806561 0.154830419420778 0.481322314049587;3.94524464051081 0.37782859885888 0.518677685950413]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>2.81883139796677</vol_TIV>
      <vol_rel_CGW>[1.27317825389001 5.33969936954323 4.89646145702653 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.0860544166105</vol_rel_WMH>
      <surf_TSA>8.62397491122334</surf_TSA>
      <SQR>4.59362391691582</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 12320.768 0.307137831915441]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00150094437412918 0.00140550010837615 0.0730696693062782]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[918.381462745098 645.372231372549 549.099180392157 895.63622745098 1273.57952941176 8725.58447843137]</SPMvols0>
      <SPMvols1>[735.056494117647 582.299207843137 327.736329411765 628.315756862745 1052.54656470588 8994.93143137255]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[821.256225585938 1949.98364257812 2534.11645507812]</T3th>
            <Tth>
               <T3th>[-31.8359107971191 -31.8359107971191 20.5649681091309 821.256225585938 1949.98364257812 2534.11645507812 3390.54663085938 5257.93798828125]</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>[0.020664906129241 0.0770562961697578 0.0848327949643135 0 0]</dtc>
         <ll>[0.086073717817205 0 0.086073717817205 0;0.203333750492384 0.0108857813144789 0.214219531806863 2321.37109375;0.203333750492384 0.0108857813144789 0.214219531806863 2321.37109375]</ll>
         <rmsdtc>[0.043889757245779 0.0997144654393196 0.110347345471382]</rmsdtc>
         <rmsgdt>[0.031250137835741 0.0463932044804096 0.0565971732139587]</rmsgdt>
         <rmsdt>0.110347345471382</rmsdt>
         <dt>0.0848327949643135</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>[0.00963896233588457 0.0449002683162689 0.0537521541118622 0.0631779879331589 0.0703328177332878 0.0792207345366478]</dtc>
         <ll>[0.0883171807620978 0 0.0883171807620978 0;0.223544108669109 0.017791556013431 0.24133566468254 9107.052734375;0.21101628585462 0.0191429354945103 0.23015922134913 13777.400390625;0.190599925158031 0.0206967722429962 0.211296697401027 22316.75;0.173928232323608 0.0239012830743709 0.197829515397979 41811.78125;0.173928232323608 0.0239012830743709 0.197829515397979 41811.78125]</ll>
         <rmsdtc>[0.0112627698108554 0.0422870367765427 0.0683392733335495 0.0909083113074303 0.115307934582233 0.123344630002975]</rmsdtc>
         <rmsgdt>[0.00348140927962959 0.0136891631409526 0.0301289316266775 0.0509032346308231 0.0705805793404579 0.0769849568605423]</rmsgdt>
         <rmsdt>0.123344630002975</rmsdt>
         <dt>0.0792207345366478</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025466/ses-2/sub-0025466_ses-2_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 42s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 8s</item>
      <item>Estimate background 8s</item>
      <item>Initial correction 9s</item>
      <item>Refine background 4s</item>
      <item>Final correction 7s</item>
      <item>Final scaling 7s</item>
      <item>51s</item>
      <item>Correct center-of-mass 5s</item>
      <item>Affine registration 12s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 107s</item>
      <item>SPM preprocessing 1 (estimate 2): 106s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 23s</item>
      <item>Update Segmentation 25s</item>
      <item>Update Skull-Stripping 54s</item>
      <item>Update probability maps 11s</item>
      <item>112s</item>
      <item>Global intensity correction: 21s</item>
      <item>SANLM denoising after intensity normalization (medium): 33s</item>
      <item>Fast Optimized Shooting registration 43s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 5s</item>
      <item>Prepare partitions 3s</item>
      <item>Prepare segments (LASmod = 1.00) 19s</item>
      <item>Estimate local tissue thresholds (WM) 26s</item>
      <item>Estimate local tissue thresholds (GM) 37s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 59s</item>
      <item>155s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 10s</item>
      <item>Major structures 5s</item>
      <item>Ventricle detection 19s</item>
      <item>Blood vessel detection 14s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.10) 33s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 5s</item>
      <item>Final corrections 6s</item>
      <item>94s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 44s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 6s</item>
      <item>Level 1 cleanup (brain masking) 4s</item>
      <item>Level 2 cleanup (CSF correction) 2s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
      <item>16s</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 | 0.0883 0.0000 0.0883 | 32.0000</item>
      <item>2 | 2.50 | 0.0855 0.0012 0.0867 | 29.4886</item>
      <item>3 | 2.50 | 0.0847 0.0018 0.0865 | 26.9772</item>
      <item>4 | 2.50 | 0.0843 0.0021 0.0864 | 24.6107</item>
      <item>5 | 2.50 | 0.0840 0.0022 0.0862 | 22.6548</item>
      <item>6 | 2.50 | 0.0837 0.0023 0.0860 | 20.6989</item>
      <item>7 | 2.50 | 0.0834 0.0025 0.0858 | 18.9688</item>
      <item>8 | 2.50 | 0.0831 0.0026 0.0856 | 17.4455</item>
      <item>9 | 2.50 | 0.0827 0.0027 0.0854 | 15.9223</item>
      <item>10 | 2.50 | 0.0824 0.0028 0.0852 | 14.6627</item>
      <item>11 | 2.50 | 0.0821 0.0029 0.0849 | 13.4764</item>
      <item>12 | 2.50 | 0.0817 0.0029 0.0847 | 12.3015</item>
      <item>13 | 2.50 | 0.0814 0.0031 0.0844 | 11.3776</item>
      <item>14 | 2.50 | 0.0810 0.0031 0.0841 | 10.4537</item>
      <item>15 | 2.25 | 0.0817 0.0032 0.0849 | 9.5920</item>
      <item>16 | 2.25 | 0.0785 0.0048 0.0833 | 8.8725</item>
      <item>17 | 2.25 | 0.0771 0.0054 0.0825 | 8.1530</item>
      <item>18 | 2.25 | 0.0763 0.0057 0.0820 | 7.5234</item>
      <item>19 | 2.25 | 0.0756 0.0059 0.0815 | 6.9630</item>
      <item>20 | 2.25 | 0.0751 0.0059 0.0809 | 6.4027</item>
      <item>21 | 2.25 | 0.0745 0.0059 0.0804 | 5.9447</item>
      <item>29 | 2.00 | 0.0766 0.0035 0.0800 | 3.3283</item>
      <item>30 | 2.00 | 0.0720 0.0056 0.0776 | 3.1221</item>
      <item>31 | 2.00 | 0.0703 0.0064 0.0767 | 2.9160</item>
      <item>43 | 1.75 | 0.0696 0.0036 0.0732 | 1.5785</item>
      <item>44 | 1.75 | 0.0651 0.0060 0.0711 | 1.5194</item>
      <item>45 | 1.75 | 0.0635 0.0069 0.0704 | 1.4626</item>
      <item>57 | 1.50 | 0.0625 0.0050 0.0675 | 1.0900</item>
      <item>58 | 1.50 | 0.0591 0.0072 0.0663 | 1.0730</item>
      <item>59 | 1.50 | 0.0580 0.0080 0.0659 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 234s</item>
      <item>Prepare output 15s</item>
      <item>248s</item>
      <item>Jacobian determinant (RMS): 0.011 0.042 0.068 0.091 0.115 | 0.123345</item>
      <item>Template Matching: 0.088 0.224 0.211 0.191 0.174 | 0.173928</item>
      <item>Write result maps: 61s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 115s</item>
      <item>CSF distance: 23s</item>
      <item>PBT2x thickness: 65s</item>
      <item>212s</item>
      <item>Create initial surface 124s</item>
      <item>Topology correction: 133s</item>
      <item>Surface refinement: 117s</item>
      <item>Reduction of surface collisions with optimization: 100s</item>
      <item>Spherical mapping with areal smoothing 128s</item>
      <item>Spherical registration 366s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 76s</item>
      <item>CSF distance: 22s</item>
      <item>PBT2x thickness: 66s</item>
      <item>174s</item>
      <item>Create initial surface 121s</item>
      <item>Topology correction: 139s</item>
      <item>Surface refinement: 131s</item>
      <item>Reduction of surface collisions with optimization: 110s</item>
      <item>Spherical mapping with areal smoothing 144s</item>
      <item>Spherical registration 383s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.2254 0.6629 mm</item>
      <item>Surface intensity / position RMSE: 0.0737 / 0.0840</item>
      <item>Euler number / defect number / defect size: 52.0 / 41.0 / 1.42%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/surf/lh.thickness.sub-0025466_ses-2_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/surf/rh.thickness.sub-0025466_ses-2_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/sub-0025466_ses-2_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 12s</item>
      <item>Surface and thickness estimation takes: 2518s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 22s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 86s</item>
      <item>ROI estimation of 'lpba40' atlas 24s</item>
      <item>ROI estimation of 'hammers' atlas 55s</item>
      <item>ROI estimation of 'thalamus' atlas 4s</item>
      <item>ROI estimation of 'ibsr' atlas 25s</item>
      <item>ROI estimation of 'aal3' atlas 46s</item>
      <item>ROI estimation of 'mori' atlas 56s</item>
      <item>ROI estimation of 'anatomy3' atlas 42s</item>
      <item>ROI estimation of 'julichbrain' atlas 46s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 78s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 114s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
      <item>Write results 11s</item>
      <item>660s</item>
      <item>Quality check: 16s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/report/catreport_sub-0025466_ses-2_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 74 minute(s) and 28 second(s).</item>
      <item>Image Quality Rating (IQR): 69.41% (D+)</item>
      <item>GM volume (GMV): 41.70% (707.01 / 1695.32 ml)</item>
      <item>GM thickness (GMT): 2.23 0.66 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_108989/ds/IACAS/sub-0025466/ses-2/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>