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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>
- <LASstr>0.5</LASstr>
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- <regstr>0.5</regstr>
- <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>
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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>
- <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>
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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>
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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>
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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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- <tr>
- <td>/var/lib/condor/execute/dir_2390666/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>
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- <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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- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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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>
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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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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>24</SurfaceEulerNumber>
- <SurfaceDefectArea>0.712335414266196</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0708301737904549</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0690265446901321</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>189.937759399414</res_BB>
- <tissue_mn>[9.03600025177002 52.5470008850098 206.376007080078 340.726013183594]</tissue_mn>
- <tissue_mnr>[0.0265198424458504 0.154220685362816 0.605694890022278 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[4.63128879236701 37.3453732293858 39.0645436564021 24.8742295559013]</tissue_std>
- <tissue_stdr>[0.0139627028256655 0.112591192126274 0.11777425557375 0.0749924033880234]</tissue_stdr>
- <contrast>120.045936584473</contrast>
- <contrastr>0.352323949337006</contrastr>
- <res_ECR>0.411783397197723</res_ECR>
- <NCR>0.11899247020483</NCR>
- <ICR>0.315573424100876</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.99889469146729</res_ECR>
- <res_BB>10.5</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>2.79847407341003</contrastr>
- <NCR>2.03922581672668</NCR>
- <ICR>1.24249362945557</ICR>
- <SurfaceEulerNumber>2.12244897959184</SurfaceEulerNumber>
- <SurfaceDefectArea>1.17808385356655</SurfaceDefectArea>
- <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.41660344600677</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.380530834198</SurfacePositionRMSE>
- <SIQR>2.64083985626992</SIQR>
- <IQR>2.02027892485284</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>20231031-000218</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>24</SurfaceEulerNumber>
- <SurfaceDefectArea>0.712335414266196</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0708301737904549</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0690265446901321</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>24</EC_abs>
- <defect_size>0.712335414266196</defect_size>
- <vol_abs_CGW>[242.065117647059 752.106611764706 587.796682352941 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.24330196078431</vol_abs_WMH>
- <vol_rel_WMH>0.000785920851224453</vol_rel_WMH>
- <surf_TSA>2145.52494361274</surf_TSA>
- <vol_TIV>1581.96841176471</vol_TIV>
- <vol_rel_CGW>[0.153015139775789 0.475424544618891 0.37156031560532 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50512684314057 0.654124522010501]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.51283502578735 0.772880814492259 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.81714971758726 0.275826968785168 0.283149795486399;2.5146525952433 0.1903106763846 0.432819427361918;3.20352514254513 0.276756245439239 0.284030777151683]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.868754642245971 0.246026383618791 0.548568507157464;4.21149501637631 0.379971580310442 0.451431492842536]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.74946094436815</vol_TIV>
- <vol_rel_CGW>[0.597973056318043 6.3883718501956 4.52299417394612 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.07859208512245</vol_rel_WMH>
- <surf_TSA>8.62375160177397</surf_TSA>
- <SQR>5.26432401658758</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.336 0.381612992201865]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00157105503603816 0.00134730199351907 0.0478870905935764]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[930.366654901961 510.191109803922 401.211545098039 563.845615686275 1195.1583372549 8667.14216078431]</SPMvols0>
- <SPMvols1>[805.569309803922 478.529996078431 223.565619607843 408.38682745098 765.977 8853.33438823529]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[68.002197265625 225.023193359375 341.512603759766]</T3th>
- <Tth>
- <T3th>[-3.90482997894287 -3.90483331680298 4.34620666503906 68.002197265625 225.023193359375 341.512603759766 478.267822265625 724.322082519531]</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>[0.0208485089242458 0.0713587924838066 0.0780730843544006 0 0]</dtc>
- <ll>[0.0821995363086641 0 0.0821995363086641 0;0.194867210800336 0.00959141114178826 0.204458621942124 2045.34924316406;0.194867210800336 0.00959141114178826 0.204458621942124 2045.34924316406]</ll>
- <rmsdtc>[0.0459946766495705 0.0918018072843552 0.101699523627758]</rmsdtc>
- <rmsgdt>[0.0330923199653625 0.0434657335281372 0.0537137351930141]</rmsgdt>
- <rmsdt>0.101699523627758</rmsdt>
- <dt>0.0780730843544006</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>[0.00900632329285145 0.0323265120387077 0.0445888228714466 0.0520174913108349 0.0581600591540337 0.0642185434699059]</dtc>
- <ll>[0.0828558011385555 0 0.0828558011385555 0;0.217336278998779 0.012745447954823 0.230081726953602 6524.076171875;0.199335875843393 0.0154555460964768 0.21479142193987 11123.5419921875;0.179592918693057 0.0180275963242577 0.197620515017315 19438.65234375;0.162691524380728 0.0212610301494324 0.183952554530161 37193.046875;0.162691524380728 0.0212610301494324 0.183952554530161 37193.046875]</ll>
- <rmsdtc>[0.0104083055630326 0.0366275645792484 0.0529487691819668 0.073401153087616 0.0945645421743393 0.101563490927219]</rmsdtc>
- <rmsgdt>[0.00325558870099485 0.0121192522346973 0.0256976541131735 0.0444838590919971 0.0620195604860783 0.0678899958729744]</rmsgdt>
- <rmsdt>0.101563490927219</rmsdt>
- <dt>0.0642185434699059</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025930/ses-2/sub-0025930_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 43s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 2s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>29s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 61s</item>
- <item>SPM preprocessing 1 (estimate 2): 46s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 16s</item>
- <item>Update Skull-Stripping 36s</item>
- <item>Update probability maps 8s</item>
- <item>74s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 23s</item>
- <item>Fast Optimized Shooting registration 26s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.03) 11s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 21s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 31s</item>
- <item>86s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 9s</item>
- <item>Blood vessel detection 7s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 18s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>51s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.04]</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>9s</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 | 0.0829 0.0000 0.0829 | 32.0000</item>
- <item>2 | 2.50 | 0.0802 0.0012 0.0814 | 29.4886</item>
- <item>3 | 2.50 | 0.0795 0.0018 0.0813 | 26.9772</item>
- <item>4 | 2.50 | 0.0791 0.0020 0.0811 | 24.6107</item>
- <item>5 | 2.50 | 0.0788 0.0021 0.0809 | 22.6548</item>
- <item>6 | 2.50 | 0.0785 0.0022 0.0808 | 20.6989</item>
- <item>7 | 2.50 | 0.0783 0.0023 0.0806 | 18.9688</item>
- <item>8 | 2.50 | 0.0780 0.0024 0.0804 | 17.4455</item>
- <item>9 | 2.50 | 0.0777 0.0025 0.0802 | 15.9223</item>
- <item>10 | 2.50 | 0.0774 0.0025 0.0800 | 14.6627</item>
- <item>11 | 2.50 | 0.0771 0.0026 0.0797 | 13.4764</item>
- <item>12 | 2.50 | 0.0768 0.0027 0.0795 | 12.3015</item>
- <item>13 | 2.50 | 0.0765 0.0028 0.0793 | 11.3776</item>
- <item>14 | 2.50 | 0.0762 0.0028 0.0790 | 10.4537</item>
- <item>15 | 2.25 | 0.0752 0.0029 0.0781 | 9.5920</item>
- <item>16 | 2.25 | 0.0724 0.0042 0.0767 | 8.8725</item>
- <item>29 | 2.00 | 0.0741 0.0019 0.0760 | 3.3283</item>
- <item>30 | 2.00 | 0.0684 0.0042 0.0726 | 3.1221</item>
- <item>31 | 2.00 | 0.0664 0.0052 0.0716 | 2.9160</item>
- <item>43 | 1.75 | 0.0656 0.0030 0.0686 | 1.5785</item>
- <item>44 | 1.75 | 0.0613 0.0052 0.0665 | 1.5194</item>
- <item>45 | 1.75 | 0.0599 0.0060 0.0659 | 1.4626</item>
- <item>57 | 1.50 | 0.0585 0.0044 0.0628 | 1.0900</item>
- <item>58 | 1.50 | 0.0553 0.0064 0.0617 | 1.0730</item>
- <item>59 | 1.50 | 0.0542 0.0071 0.0613 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 164s</item>
- <item>Prepare output 8s</item>
- <item>172s</item>
- <item>Jacobian determinant (RMS): 0.010 0.037 0.053 0.073 0.095 | 0.101563</item>
- <item>Template Matching: 0.083 0.217 0.199 0.180 0.163 | 0.162692</item>
- <item>Write result maps: 32s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 36s</item>
- <item>86s</item>
- <item>Create initial surface 67s</item>
- <item>Topology correction: 82s</item>
- <item>Surface refinement: 61s</item>
- <item>Reduction of surface collisions with optimization: 60s</item>
- <item>Spherical mapping with areal smoothing 68s</item>
- <item>Spherical registration 215s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 23s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 36s</item>
- <item>76s</item>
- <item>Create initial surface 67s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 59s</item>
- <item>Spherical mapping with areal smoothing 69s</item>
- <item>Spherical registration 239s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5051 0.6541 mm</item>
- <item>Surface intensity / position RMSE: 0.0708 / 0.0690</item>
- <item>Euler number / defect number / defect size: 24.0 / 15.0 / 0.71%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/surf/lh.thickness.sub-0025930_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/surf/rh.thickness.sub-0025930_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/sub-0025930_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1397s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 23s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 83s</item>
- <item>ROI estimation of 'lpba40' atlas 24s</item>
- <item>ROI estimation of 'hammers' atlas 58s</item>
- <item>ROI estimation of 'thalamus' atlas 5s</item>
- <item>ROI estimation of 'ibsr' atlas 21s</item>
- <item>ROI estimation of 'aal3' atlas 37s</item>
- <item>ROI estimation of 'mori' atlas 54s</item>
- <item>ROI estimation of 'anatomy3' atlas 75s</item>
- <item>ROI estimation of 'julichbrain' atlas 98s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 75s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 152s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 133s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>887s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/report/catreport_sub-0025930_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 50 minute(s) and 59 second(s).</item>
- <item>Image Quality Rating (IQR): 84.80% (B)</item>
- <item>GM volume (GMV): 47.54% (752.11 / 1581.97 ml)</item>
- <item>GM thickness (GMT): 2.51 0.65 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2390666/ds/BNU_2/sub-0025930/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|