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- <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>
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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>
- <BVCstr>0.5</BVCstr>
- <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>
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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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- <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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- <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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- <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>
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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>
- <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>/var/lib/condor/execute/dir_2391280/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <item>csf</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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- <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>
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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>
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- <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>
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- <LASmyostr>0</LASmyostr>
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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_1_GS.nii</item>
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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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- </templates>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.764125658316591</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0682502090930939</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0705322176218033</SurfacePositionRMSE>
- <res_vx_vol>[1.00000002728649 1.00000002631383 1.00000001437573]</res_vx_vol>
- <res_vx_voli>[1.00000008650934 1.00000002527438 1.00000001434934]</res_vx_voli>
- <res_RMS>1.00000002265868</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[7.1710000038147 58.9080009460449 192.697998046875 319.424987792969]</tissue_mn>
- <tissue_mnr>[0.0224497150629759 0.184418886899948 0.603265285491943 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[11.9998411615009 32.4707875546333 37.1468925321091 22.7633716572927]</tissue_std>
- <tissue_stdr>[0.0384297445416451 0.103988379240036 0.118963703513145 0.0729001760482788]</tissue_stdr>
- <contrast>112.490028381348</contrast>
- <contrastr>0.352164149284363</contrastr>
- <res_ECR>0.354634821414948</res_ECR>
- <NCR>0.129843071103096</NCR>
- <ICR>0.330742985010147</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000005457299 2.00000005262766 2.00000002875146]</res_vx_vol>
- <res_RMS>2.00000004531737</res_RMS>
- <res_ECR>2.70732045173645</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>2.80087089538574</contrastr>
- <NCR>2.19499111175537</NCR>
- <ICR>1.28011655807495</ICR>
- <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
- <SurfaceDefectArea>1.19103141457915</SurfaceDefectArea>
- <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.36500418186188</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.41064429283142</SurfacePositionRMSE>
- <SIQR>2.4327938550728</SIQR>
- <IQR>2.11303364876748</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>20231031-000020</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.764125658316591</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0682502090930939</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0705322176218033</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>20</EC_abs>
- <defect_size>0.764125658316591</defect_size>
- <vol_abs_CGW>[192.966134143327 679.851124967378 483.273358995955 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.3970667167499</vol_abs_WMH>
- <vol_rel_WMH>0.000292802495237578</vol_rel_WMH>
- <surf_TSA>1926.66407230735</surf_TSA>
- <vol_TIV>1356.09061810666</vol_TIV>
- <vol_rel_CGW>[0.142295899379307 0.501331633660713 0.35637246695998 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.52418428523881 0.611194739492201]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.51668930053711 0.691896247984976 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.93946280956279 0.229233544896735 0.303666576071499;2.53721349728492 0.172669309171313 0.41039611157111;3.17182636456393 0.253240658261547 0.285937312357392]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.933367494739213 0.347987204107751 0.516071745693482;4.03546083485315 0.304451837953674 0.483928254306517]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.04579730038854</vol_TIV>
- <vol_rel_CGW>[0.5 6.85365721373407 4.25022390373528 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02928024952376</vol_rel_WMH>
- <surf_TSA>8.61660147848304</surf_TSA>
- <SQR>5.61986345171986</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.3367840586 0.382203658440028]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00133877689950168 0.00119084282778203 0.0321875624358654]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[820.479272116999 417.86291152985 316.401686967531 456.566437980271 1056.56252542431 8923.96080795928]</SPMvols0>
- <SPMvols1>[733.704786662065 395.754096976492 175.319578976337 361.744190725935 848.427769759875 9019.42058078422]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[67.4663009643555 211.870895385742 321.416595458984]</T3th>
- <Tth>
- <T3th>[-4.09611988067627 -4.09611797332764 2.8963451385498 67.4663009643555 211.870895385742 321.416595458984 448.391723632812 600.440734863281]</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>[0.0208641868084669 0.0728119164705276 0.0799911022186279 0 0]</dtc>
- <ll>[0.0812635967472927 0 0.0812635967472927 0;0.188942825665422 0.00977475531533414 0.198717580980757 2084.44702148438;0.188942825665422 0.00977475531533414 0.198717580980757 2084.44702148438]</ll>
- <rmsdtc>[0.0458883568644524 0.0952901169657707 0.105030201375484]</rmsdtc>
- <rmsgdt>[0.0328788906335831 0.042757410556078 0.0525485388934612]</rmsgdt>
- <rmsdt>0.105030201375484</rmsdt>
- <dt>0.0799911022186279</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>[0.00984660349786282 0.0361648797988892 0.0495615452528 0.0567788071930408 0.0625307261943817 0.069836713373661]</dtc>
- <ll>[0.0822706846523661 0 0.0822706846523661 0;0.21355844017094 0.0139365918803419 0.227495032051282 7133.79296875;0.191756954517918 0.016403889572322 0.20816084409024 11806.076171875;0.172346790744821 0.0180639319496843 0.190410722694506 19477.83203125;0.156270668355672 0.0206359910278257 0.176906659383498 36099.6328125;0.156270668355672 0.0206359910278257 0.176906659383498 36099.6328125]</ll>
- <rmsdtc>[0.0115029504522681 0.0415919870138168 0.0607372522354126 0.0831464529037476 0.104650259017944 0.111125431954861]</rmsdtc>
- <rmsgdt>[0.00329815153963864 0.0127222817391157 0.027460228651762 0.0462979190051556 0.0633845627307892 0.0689518675208092]</rmsgdt>
- <rmsdt>0.111125431954861</rmsdt>
- <dt>0.069836713373661</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025922/ses-2/sub-0025922_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 36s</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 3s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 58s</item>
- <item>SPM preprocessing 1 (estimate 2): 48s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 15s</item>
- <item>Update Skull-Stripping 34s</item>
- <item>Update probability maps 8s</item>
- <item>70s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 20s</item>
- <item>Fast Optimized Shooting registration 26s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.08) 10s</item>
- <item>Estimate local tissue thresholds (WM) 14s</item>
- <item>Estimate local tissue thresholds (GM) 20s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 30s</item>
- <item>81s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 9s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 4s</item>
- <item>45s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 25s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 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>8s</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 | 0.0823 0.0000 0.0823 | 32.0000</item>
- <item>2 | 2.50 | 0.0796 0.0012 0.0808 | 29.4886</item>
- <item>3 | 2.50 | 0.0788 0.0018 0.0806 | 26.9772</item>
- <item>4 | 2.50 | 0.0784 0.0021 0.0804 | 24.6107</item>
- <item>5 | 2.50 | 0.0781 0.0022 0.0803 | 22.6548</item>
- <item>6 | 2.50 | 0.0778 0.0023 0.0801 | 20.6989</item>
- <item>7 | 2.50 | 0.0775 0.0024 0.0799 | 18.9688</item>
- <item>8 | 2.50 | 0.0772 0.0025 0.0797 | 17.4455</item>
- <item>9 | 2.50 | 0.0769 0.0026 0.0795 | 15.9223</item>
- <item>10 | 2.50 | 0.0766 0.0027 0.0793 | 14.6627</item>
- <item>11 | 2.50 | 0.0762 0.0028 0.0790 | 13.4764</item>
- <item>12 | 2.50 | 0.0759 0.0029 0.0788 | 12.3015</item>
- <item>13 | 2.50 | 0.0756 0.0030 0.0785 | 11.3776</item>
- <item>14 | 2.50 | 0.0752 0.0030 0.0783 | 10.4537</item>
- <item>15 | 2.25 | 0.0743 0.0031 0.0774 | 9.5920</item>
- <item>16 | 2.25 | 0.0712 0.0046 0.0758 | 8.8725</item>
- <item>29 | 2.00 | 0.0720 0.0021 0.0741 | 3.3283</item>
- <item>30 | 2.00 | 0.0660 0.0045 0.0705 | 3.1221</item>
- <item>31 | 2.00 | 0.0639 0.0055 0.0694 | 2.9160</item>
- <item>43 | 1.75 | 0.0629 0.0032 0.0660 | 1.5785</item>
- <item>44 | 1.75 | 0.0588 0.0053 0.0641 | 1.5194</item>
- <item>45 | 1.75 | 0.0574 0.0060 0.0635 | 1.4626</item>
- <item>57 | 1.50 | 0.0559 0.0044 0.0603 | 1.0900</item>
- <item>58 | 1.50 | 0.0530 0.0063 0.0593 | 1.0730</item>
- <item>59 | 1.50 | 0.0521 0.0069 0.0590 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 157s</item>
- <item>Prepare output 8s</item>
- <item>165s</item>
- <item>Jacobian determinant (RMS): 0.012 0.042 0.061 0.083 0.105 | 0.111125</item>
- <item>Template Matching: 0.082 0.214 0.192 0.172 0.156 | 0.156271</item>
- <item>Write result maps: 35s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 20s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 31s</item>
- <item>66s</item>
- <item>Create initial surface 57s</item>
- <item>Topology correction: 72s</item>
- <item>Surface refinement: 57s</item>
- <item>Reduction of surface collisions with optimization: 52s</item>
- <item>Spherical mapping with areal smoothing 65s</item>
- <item>Spherical registration 232s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 18s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 31s</item>
- <item>63s</item>
- <item>Create initial surface 57s</item>
- <item>Topology correction: 72s</item>
- <item>Surface refinement: 72s</item>
- <item>Reduction of surface collisions with optimization: 52s</item>
- <item>Spherical mapping with areal smoothing 64s</item>
- <item>Spherical registration 213s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5241 0.6109 mm</item>
- <item>Surface intensity / position RMSE: 0.0683 / 0.0705</item>
- <item>Euler number / defect number / defect size: 20.0 / 13.0 / 0.76%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/surf/lh.thickness.sub-0025922_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/surf/rh.thickness.sub-0025922_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/sub-0025922_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1266s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 11s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 50s</item>
- <item>ROI estimation of 'lpba40' atlas 18s</item>
- <item>ROI estimation of 'hammers' atlas 46s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 17s</item>
- <item>ROI estimation of 'aal3' atlas 31s</item>
- <item>ROI estimation of 'mori' atlas 53s</item>
- <item>ROI estimation of 'anatomy3' atlas 77s</item>
- <item>ROI estimation of 'julichbrain' atlas 102s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 81s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 158s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 224s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 18s</item>
- <item>Write results 19s</item>
- <item>933s</item>
- <item>Quality check: 12s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/report/catreport_sub-0025922_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 49 minute(s) and 21 second(s).</item>
- <item>Image Quality Rating (IQR): 83.87% (B)</item>
- <item>GM volume (GMV): 50.13% (679.85 / 1356.09 ml)</item>
- <item>GM thickness (GMT): 2.52 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2391280/ds/BNU_2/sub-0025922/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|