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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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- <WMHC>2</WMHC>
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- <SLC>0</SLC>
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- <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>
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- <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>
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- <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>
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- <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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <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>
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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/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</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/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</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/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</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>
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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>
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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>
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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/anatomy3.nii</td>
- <td>1</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/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <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>
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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/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <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>
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- <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>
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- <td>[false]</td>
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- <td>/var/lib/condor/execute/dir_2926811/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <satlas>
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- <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>
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- <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>
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- <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>
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- <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>
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- <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>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- </darteltpms>
- <shootingtpms>
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- </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>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>38</SurfaceEulerNumber>
- <SurfaceDefectArea>0.828874485257212</SurfaceDefectArea>
- <SurfaceDefectNumber>18</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0650045424699783</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0673841089010239</SurfacePositionRMSE>
- <res_vx_vol>[0.999999993868342 0.999999993868342 1]</res_vx_vol>
- <res_vx_voli>[0.999999994121909 0.999999994121909 1]</res_vx_voli>
- <res_RMS>0.999999995912228</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[4.42000007629395 110.98999786377 263.798004150391 378.636993408203]</tissue_mn>
- <tissue_mnr>[0.0116734504699707 0.293130367994308 0.696704268455505 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.69944508568266 45.9014981986583 35.9401626246702 22.9586539788181]</tissue_std>
- <tissue_stdr>[0.0205748155713081 0.122660115361214 0.0960409715771675 0.0613511800765991]</tissue_stdr>
- <contrast>116.19539642334</contrast>
- <contrastr>0.306878089904785</contrastr>
- <res_ECR>0.299558877944946</res_ECR>
- <NCR>0.151062712073326</NCR>
- <ICR>0.314320921897888</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999998773668 1.99999998773668 2]</res_vx_vol>
- <res_RMS>1.99999999182446</res_RMS>
- <res_ECR>2.42632079124451</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.4801619052887</contrastr>
- <NCR>2.49960827827454</NCR>
- <ICR>1.23938727378845</ICR>
- <SurfaceEulerNumber>2.83673469387755</SurfaceEulerNumber>
- <SurfaceDefectArea>1.2072186213143</SurfaceDefectArea>
- <SurfaceDefectNumber>1.9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30009078979492</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.34768223762512</SurfacePositionRMSE>
- <SIQR>2.36949963775877</SIQR>
- <IQR>2.3370755491743</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>20231031-002626</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>38</SurfaceEulerNumber>
- <SurfaceDefectArea>0.828874485257212</SurfaceDefectArea>
- <SurfaceDefectNumber>18</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0650045424699783</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0673841089010239</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>38</EC_abs>
- <defect_size>0.828874485257212</defect_size>
- <vol_abs_CGW>[288.037475045152 697.978709441494 497.768025520698 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.581505875516652</vol_abs_WMH>
- <vol_rel_WMH>0.000391907308080718</vol_rel_WMH>
- <surf_TSA>1956.70724375203</surf_TSA>
- <vol_TIV>1483.78421000734</vol_TIV>
- <vol_rel_CGW>[0.19412356129853 0.470404459579766 0.335471979121704 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50463622926026 0.653522690711865]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.4864227771759 0.815102480081303 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.86944886639706 0.268916774442127 0.315659412397857;2.53110115947542 0.190148713277231 0.42953041506646;3.2384886765184 0.295490725893903 0.254810172535682]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.838471081498599 0.266560906519928 0.49319330999611;4.29545739034644 0.356233240040417 0.50680669000389]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.16542549689836</vol_TIV>
- <vol_rel_CGW>[1.33627085665464 6.29821227693545 3.87485594686968 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03919073080807</vol_rel_WMH>
- <surf_TSA>8.61916795690559</surf_TSA>
- <SQR>5.16356057224135</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.3358585508 0.34403292790548]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00138097815215588 0.00126603082753718 0.00840575154870749]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[839.161641115055 440.350665411393 530.055327101907 392.861375773607 862.034542806942 8938.22375374414]</SPMvols0>
- <SPMvols1>[715.315936688655 410.533422624675 328.721168684514 316.319878634227 758.144073440062 9005.32746668075]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[137.712097167969 279.015899658203 366.542999267578]</T3th>
- <Tth>
- <T3th>[-5.29822015762329 -5.29822254180908 3.31917834281921 137.712097167969 279.015899658203 366.542999267578 480.958435058594 957.430969238281]</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>[0.0204924419522285 0.0744409710168839 0.0827193036675453 0 0]</dtc>
- <ll>[0.0865156243161327 0 0.0865156243161327 0;0.205413323776776 0.011168573798538 0.216581897575314 2381.67602539062;0.205413323776776 0.011168573798538 0.216581897575314 2381.67602539062]</ll>
- <rmsdtc>[0.0479655377566814 0.100858844816685 0.113230541348457]</rmsdtc>
- <rmsgdt>[0.0346688106656075 0.0481060147285461 0.0599612295627594]</rmsgdt>
- <rmsdt>0.113230541348457</rmsdt>
- <dt>0.0827193036675453</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>[0.00902314018458128 0.0338673256337643 0.0457927472889423 0.0541953667998314 0.0606934875249863 0.0682549104094505]</dtc>
- <ll>[0.0851734725421853 0 0.0851734725421853 0;0.223560546398046 0.0148238858363858 0.238384432234432 7587.9765625;0.206536585988562 0.0171159066925381 0.2236524926811 12318.5234375;0.185644397934844 0.0197546959829013 0.205399093917745 21300.935546875;0.16799348459116 0.0233131660855471 0.191306650676707 40782.95703125;0.16799348459116 0.0233131660855471 0.191306650676707 40782.95703125]</ll>
- <rmsdtc>[0.0107897566631436 0.0385783649981022 0.059186939150095 0.0842938795685768 0.111063793301582 0.116806603968143]</rmsdtc>
- <rmsgdt>[0.00322323595173657 0.0125366747379303 0.0287451017647982 0.0509130991995335 0.075437568128109 0.0773890912532806]</rmsgdt>
- <rmsdt>0.116806603968143</rmsdt>
- <dt>0.0682549104094505</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025663/ses-2/sub-0025663_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 31s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>24s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 5s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 47s</item>
- <item>SPM preprocessing 1 (estimate 2): 44s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 11s</item>
- <item>Update Segmentation 13s</item>
- <item>Update Skull-Stripping 27s</item>
- <item>Update probability maps 6s</item>
- <item>57s</item>
- <item>Global intensity correction: 10s</item>
- <item>SANLM denoising after intensity normalization (medium): 16s</item>
- <item>Fast Optimized Shooting registration 22s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.11) 9s</item>
- <item>Estimate local tissue thresholds (WM) 12s</item>
- <item>Estimate local tissue thresholds (GM) 17s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 30s</item>
- <item>74s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 6s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 13s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 3s</item>
- <item>39s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s</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) 3s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>7s</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 | 0.0852 0.0000 0.0852 | 32.0000</item>
- <item>2 | 2.50 | 0.0826 0.0012 0.0838 | 29.4886</item>
- <item>3 | 2.50 | 0.0818 0.0018 0.0836 | 26.9772</item>
- <item>4 | 2.50 | 0.0815 0.0020 0.0834 | 24.6107</item>
- <item>5 | 2.50 | 0.0811 0.0021 0.0833 | 22.6548</item>
- <item>6 | 2.50 | 0.0809 0.0022 0.0831 | 20.6989</item>
- <item>7 | 2.50 | 0.0806 0.0023 0.0829 | 18.9688</item>
- <item>8 | 2.50 | 0.0803 0.0024 0.0827 | 17.4455</item>
- <item>9 | 2.50 | 0.0800 0.0025 0.0825 | 15.9223</item>
- <item>10 | 2.50 | 0.0797 0.0026 0.0823 | 14.6627</item>
- <item>11 | 2.50 | 0.0794 0.0027 0.0820 | 13.4764</item>
- <item>12 | 2.50 | 0.0790 0.0027 0.0818 | 12.3015</item>
- <item>13 | 2.50 | 0.0787 0.0029 0.0816 | 11.3776</item>
- <item>14 | 2.50 | 0.0784 0.0029 0.0813 | 10.4537</item>
- <item>15 | 2.25 | 0.0786 0.0030 0.0816 | 9.5920</item>
- <item>16 | 2.25 | 0.0757 0.0044 0.0801 | 8.8725</item>
- <item>17 | 2.25 | 0.0745 0.0049 0.0795 | 8.1530</item>
- <item>29 | 2.00 | 0.0766 0.0023 0.0789 | 3.3283</item>
- <item>30 | 2.00 | 0.0708 0.0047 0.0756 | 3.1221</item>
- <item>31 | 2.00 | 0.0688 0.0057 0.0746 | 2.9160</item>
- <item>43 | 1.75 | 0.0680 0.0033 0.0712 | 1.5785</item>
- <item>44 | 1.75 | 0.0634 0.0057 0.0691 | 1.5194</item>
- <item>45 | 1.75 | 0.0619 0.0066 0.0685 | 1.4626</item>
- <item>57 | 1.50 | 0.0606 0.0048 0.0654 | 1.0900</item>
- <item>58 | 1.50 | 0.0572 0.0071 0.0642 | 1.0730</item>
- <item>59 | 1.50 | 0.0560 0.0078 0.0638 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 115s</item>
- <item>Prepare output 7s</item>
- <item>122s</item>
- <item>Jacobian determinant (RMS): 0.011 0.039 0.059 0.084 0.111 | 0.116807</item>
- <item>Template Matching: 0.085 0.224 0.207 0.186 0.168 | 0.167993</item>
- <item>Write result maps: 24s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 24s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 30s</item>
- <item>67s</item>
- <item>Create initial surface 53s</item>
- <item>Topology correction: 65s</item>
- <item>Surface refinement: 69s</item>
- <item>Reduction of surface collisions with optimization: 44s</item>
- <item>Spherical mapping with areal smoothing 60s</item>
- <item>Spherical registration 183s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 19s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 28s</item>
- <item>60s</item>
- <item>Create initial surface 49s</item>
- <item>Topology correction: 62s</item>
- <item>Surface refinement: 45s</item>
- <item>Reduction of surface collisions with optimization: 43s</item>
- <item>Spherical mapping with areal smoothing 103s</item>
- <item>Spherical registration 186s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5046 0.6534 mm</item>
- <item>Surface intensity / position RMSE: 0.0650 / 0.0674</item>
- <item>Euler number / defect number / defect size: 38.0 / 18.0 / 0.83%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/surf/lh.thickness.sub-0025663_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/surf/rh.thickness.sub-0025663_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/sub-0025663_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1153s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 21s</item>
- <item>ROI estimation of 'lpba40' atlas 6s</item>
- <item>ROI estimation of 'hammers' atlas 15s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 5s</item>
- <item>ROI estimation of 'aal3' atlas 8s</item>
- <item>ROI estimation of 'mori' atlas 13s</item>
- <item>ROI estimation of 'anatomy3' atlas 18s</item>
- <item>ROI estimation of 'julichbrain' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 59s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 6s</item>
- <item>248s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/report/catreport_sub-0025663_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 34 minute(s) and 6 second(s).</item>
- <item>Image Quality Rating (IQR): 81.63% (B-)</item>
- <item>GM volume (GMV): 47.04% (697.98 / 1483.78 ml)</item>
- <item>GM thickness (GMT): 2.50 0.65 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2926811/ds/SWU_4/sub-0025663/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|