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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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- <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>
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- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
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- <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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- <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>
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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>
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- <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>
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- <item>csf</item>
- <item>gm</item>
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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>/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>
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- <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>
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- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_2613681/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <td>[false]</td>
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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>
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- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
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- <PH>25</PH>
- <LE>27</LE>
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- <shootingtpm>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <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>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.737246199662499</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0719515532255173</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0721598342061043</SurfacePositionRMSE>
- <res_vx_vol>[0.9375 0.9375 1]</res_vx_vol>
- <res_vx_voli>[0.9375 0.9375 1]</res_vx_voli>
- <res_RMS>0.958786124916988</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 8.70100021362305 45.2000007629395 89.7959976196289]</tissue_mn>
- <tissue_mnr>[0 0.0968974158167839 0.503363192081451 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[0.494864087455646 9.00266078255021 11.4841772615139 8.06992011354284]</tissue_std>
- <tissue_stdr>[0.00551098166033626 0.100256815552711 0.12789186835289 0.0898694843053818]</tissue_stdr>
- <contrast>29.9923973083496</contrast>
- <contrastr>0.334005951881409</contrastr>
- <res_ECR>0.311288058757782</res_ECR>
- <NCR>0.190141528844833</NCR>
- <ICR>0.304819613695145</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.875 1.875 2]</res_vx_vol>
- <res_RMS>1.91757224983398</res_RMS>
- <res_ECR>2.48616337776184</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[7.53818530974821 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.07324409484863</contrastr>
- <NCR>3.06060194969177</NCR>
- <ICR>1.21582245826721</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.18431154991562</SurfaceDefectArea>
- <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.43903112411499</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.44319665431976</SurfacePositionRMSE>
- <SIQR>2.73315089614232</SIQR>
- <IQR>2.81482913379551</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>20231031-000841</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.737246199662499</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0719515532255173</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0721598342061043</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.737246199662499</defect_size>
- <vol_abs_CGW>[195.015434283088 716.295241268382 483.200735294118 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.354733455882353</vol_abs_WMH>
- <vol_rel_WMH>0.000254378309939575</vol_rel_WMH>
- <surf_TSA>2037.67785545543</surf_TSA>
- <vol_TIV>1394.51141084559</vol_TIV>
- <vol_rel_CGW>[0.139844989984583 0.513653194730076 0.346501815285341 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.46266270914611 0.614872388595116]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.43262815475464 0.75914662281278 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.88628800303817 0.239234939205869 0.321568251648569;2.47943537944397 0.174798608715253 0.423381228176303;3.14635216635858 0.272200772644268 0.255050520175129]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.866636600459391 0.3378372302619 0.474949716584385;4.14460348983312 0.368719193113693 0.525050283415615]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00071768507308</vol_TIV>
- <vol_rel_CGW>[0.5 7.07494961799706 4.07294926877408 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02543783099396</vol_rel_WMH>
- <surf_TSA>8.62256105975049</surf_TSA>
- <SQR>5.79432817797619</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 12672 0.48807047958287]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0013958013150841 0.00135745701845735 0.053688183426857]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[873.571771599265 420.537625229779 332.950798483456 527.211214384191 1433.82803079044 9663.76789522059]</SPMvols0>
- <SPMvols1>[764.111081112132 397.272111672794 171.967203584559 385.511405101103 1081.51678883272 9871.68698644302]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[10.1597995758057 50.4323997497559 90.5623016357422]</T3th>
- <Tth>
- <T3th>[-1.04370999336243 -1.04370808601379 0.215195953845978 10.1597995758057 50.4323997497559 90.5623016357422 130.763549804688 176.492492675781]</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>[0.0222959890961647 0.0774392485618591 0.0853679999709129 0 0]</dtc>
- <ll>[0.0823024888666404 0 0.0823024888666404 0;0.191833111418395 0.0100134795739585 0.201846590992354 2135.3544921875;0.191833111418395 0.0100134795739585 0.201846590992354 2135.3544921875]</ll>
- <rmsdtc>[0.04648457467556 0.100453950464725 0.110420018434525]</rmsdtc>
- <rmsgdt>[0.0327209010720253 0.0442642569541931 0.0544370301067829]</rmsgdt>
- <rmsdt>0.110420018434525</rmsdt>
- <dt>0.0853679999709129</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>[0.0105854673311114 0.0387682840228081 0.0534301772713661 0.0610316768288612 0.0673081800341606 0.075514167547226]</dtc>
- <ll>[0.0821296089401917 0 0.0821296089401917 0;0.215066697191697 0.0135787345467033 0.2286454317384 6950.61474609375;0.195314671007292 0.0161232529578672 0.211437923965159 11604.0986328125;0.176425002805415 0.0181549756954878 0.194579978500902 19576.001953125;0.160328132743934 0.0213270054342948 0.181655138178229 37308.4609375;0.160328132743934 0.0213270054342948 0.181655138178229 37308.4609375]</ll>
- <rmsdtc>[0.0121472794562578 0.043654877692461 0.0638882368803024 0.0876983404159546 0.110565386712551 0.117153026163578]</rmsdtc>
- <rmsgdt>[0.00337971234694123 0.0128558240830898 0.0279154349118471 0.048384677618742 0.0669708549976349 0.0725065991282463]</rmsgdt>
- <rmsdt>0.117153026163578</rmsdt>
- <dt>0.075514167547226</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025349/ses-1/sub-0025349_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 41s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 9s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>46s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 14s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 81s</item>
- <item>SPM preprocessing 1 (estimate 2): 79s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 20s</item>
- <item>Update Segmentation 21s</item>
- <item>Update Skull-Stripping 49s</item>
- <item>Update probability maps 11s</item>
- <item>101s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 26s</item>
- <item>Fast Optimized Shooting registration 35s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 15s</item>
- <item>Estimate local tissue thresholds (WM) 21s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 49s</item>
- <item>127s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 15s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 26s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>74s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>13s</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 | 0.0821 0.0000 0.0821 | 32.0000</item>
- <item>2 | 2.50 | 0.0795 0.0012 0.0806 | 29.4886</item>
- <item>3 | 2.50 | 0.0787 0.0018 0.0805 | 26.9772</item>
- <item>4 | 2.50 | 0.0783 0.0020 0.0803 | 24.6107</item>
- <item>5 | 2.50 | 0.0780 0.0022 0.0802 | 22.6548</item>
- <item>6 | 2.50 | 0.0777 0.0023 0.0800 | 20.6989</item>
- <item>7 | 2.50 | 0.0774 0.0024 0.0798 | 18.9688</item>
- <item>8 | 2.50 | 0.0771 0.0025 0.0796 | 17.4455</item>
- <item>9 | 2.50 | 0.0768 0.0025 0.0794 | 15.9223</item>
- <item>10 | 2.50 | 0.0765 0.0027 0.0792 | 14.6627</item>
- <item>11 | 2.50 | 0.0762 0.0027 0.0789 | 13.4764</item>
- <item>12 | 2.50 | 0.0759 0.0028 0.0787 | 12.3015</item>
- <item>13 | 2.50 | 0.0755 0.0029 0.0785 | 11.3776</item>
- <item>14 | 2.50 | 0.0752 0.0030 0.0782 | 10.4537</item>
- <item>15 | 2.25 | 0.0746 0.0031 0.0776 | 9.5920</item>
- <item>16 | 2.25 | 0.0717 0.0045 0.0762 | 8.8725</item>
- <item>29 | 2.00 | 0.0729 0.0021 0.0750 | 3.3283</item>
- <item>30 | 2.00 | 0.0671 0.0044 0.0715 | 3.1221</item>
- <item>31 | 2.00 | 0.0651 0.0054 0.0705 | 2.9160</item>
- <item>43 | 1.75 | 0.0643 0.0031 0.0674 | 1.5785</item>
- <item>44 | 1.75 | 0.0602 0.0053 0.0655 | 1.5194</item>
- <item>45 | 1.75 | 0.0588 0.0061 0.0649 | 1.4626</item>
- <item>57 | 1.50 | 0.0576 0.0044 0.0620 | 1.0900</item>
- <item>58 | 1.50 | 0.0545 0.0064 0.0609 | 1.0730</item>
- <item>59 | 1.50 | 0.0534 0.0071 0.0606 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 175s</item>
- <item>Prepare output 11s</item>
- <item>187s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.111 | 0.117153</item>
- <item>Template Matching: 0.082 0.215 0.195 0.176 0.160 | 0.160328</item>
- <item>Write result maps: 40s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 26s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 44s</item>
- <item>91s</item>
- <item>Create initial surface 84s</item>
- <item>Topology correction: 97s</item>
- <item>Surface refinement: 74s</item>
- <item>Reduction of surface collisions with optimization: 74s</item>
- <item>Spherical mapping with areal smoothing 81s</item>
- <item>Spherical registration 294s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 43s</item>
- <item>91s</item>
- <item>Create initial surface 80s</item>
- <item>Topology correction: 96s</item>
- <item>Surface refinement: 86s</item>
- <item>Reduction of surface collisions with optimization: 73s</item>
- <item>Spherical mapping with areal smoothing 83s</item>
- <item>Spherical registration 304s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4628 0.6146 mm</item>
- <item>Surface intensity / position RMSE: 0.0720 / 0.0722</item>
- <item>Euler number / defect number / defect size: 18.0 / 15.0 / 0.74%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/surf/lh.thickness.sub-0025349_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/surf/rh.thickness.sub-0025349_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/sub-0025349_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1717s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 59s</item>
- <item>ROI estimation of 'lpba40' atlas 18s</item>
- <item>ROI estimation of 'hammers' atlas 43s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 16s</item>
- <item>ROI estimation of 'aal3' atlas 25s</item>
- <item>ROI estimation of 'mori' atlas 44s</item>
- <item>ROI estimation of 'anatomy3' atlas 67s</item>
- <item>ROI estimation of 'julichbrain' atlas 81s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 55s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 94s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 127s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 11s</item>
- <item>681s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/report/catreport_sub-0025349_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 57 minute(s) and 5 second(s).</item>
- <item>Image Quality Rating (IQR): 76.85% (C+)</item>
- <item>GM volume (GMV): 51.37% (716.30 / 1394.51 ml)</item>
- <item>GM thickness (GMT): 2.46 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2613681/ds/LMU_1/sub-0025349/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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