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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>
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- <NCstr>-Inf</NCstr>
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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>
- <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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- <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>
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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>
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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>
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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>/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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- <tr>
- <td>/var/lib/condor/execute/dir_1726829/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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- <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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- <TH>9</TH>
- <ON>11</ON>
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- <VT>15</VT>
- <NV>17</NV>
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- <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>
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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_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>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.390420088230897</SurfaceDefectArea>
- <SurfaceDefectNumber>7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0604712516069412</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0622770339250565</SurfacePositionRMSE>
- <res_vx_vol>[0.999900817871094 1 1]</res_vx_vol>
- <res_vx_voli>[0.999900817871094 1 1]</res_vx_voli>
- <res_RMS>0.999966940383411</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[3.71300005912781 15.9259996414185 172.337005615234 339.613006591797]</tissue_mn>
- <tissue_mnr>[0.0109330322593451 0.0468945503234863 0.507451117038727 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.6813383526759 33.170646513276 43.5540251194299 30.6902736813598]</tissue_std>
- <tissue_stdr>[0.00798254925757647 0.0987515524029732 0.129663661122322 0.0913672968745232]</tissue_stdr>
- <contrast>113.340621948242</contrast>
- <contrastr>0.333734631538391</contrastr>
- <res_ECR>0.386109530925751</res_ECR>
- <NCR>0.123906269669533</NCR>
- <ICR>0.369033455848694</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99980163574219 2 2]</res_vx_vol>
- <res_RMS>1.99993388076682</res_RMS>
- <res_ECR>2.86790561676025</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[8.62397956848145 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>3.0773138999939</contrastr>
- <NCR>2.10976552963257</NCR>
- <ICR>1.37508296966553</ICR>
- <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
- <SurfaceDefectArea>1.09760502205772</SurfaceDefectArea>
- <SurfaceDefectNumber>1.35</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.20942497253418</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.24554061889648</SurfacePositionRMSE>
- <SIQR>2.54166695707614</SIQR>
- <IQR>2.05995101933319</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>20231031-003605</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.390420088230897</SurfaceDefectArea>
- <SurfaceDefectNumber>7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0604712516069412</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0622770339250565</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>16</EC_abs>
- <defect_size>0.390420088230897</defect_size>
- <vol_abs_CGW>[249.563166907217 604.74899807108 426.572801130287 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.219993864650352</vol_abs_WMH>
- <vol_rel_WMH>0.000171751461271896</vol_rel_WMH>
- <surf_TSA>1690.41294667259</surf_TSA>
- <vol_TIV>1280.88496610858</vol_TIV>
- <vol_rel_CGW>[0.194836518118725 0.47213373103156 0.333029750849715 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.57140514414895 0.664448252814888]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55548357963562 0.822710301738049 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.94728529321036 0.268022161855703 0.324227300586639;2.61968222173592 0.195593353925475 0.430114117269358;3.3462697483669 0.298590449820979 0.245658582144004]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.862695648566569 0.287798959899565 0.531594333258376;4.36459449524497 0.332474740217681 0.468405666741624]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.33065386935704</vol_TIV>
- <vol_rel_CGW>[1.34907539724721 6.32926959467602 3.83099408853655 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01717514612719</vol_rel_WMH>
- <surf_TSA>8.48850183325888</surf_TSA>
- <SQR>5.18742591760877</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11533.192 0.462721086418247]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00145508965943009 0.00122277019545436 0.0251194052398205]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[752.075706013758 366.502085152959 407.256015239491 477.456569555485 821.168550597815 9207.3366277379]</SPMvols0>
- <SPMvols1>[657.143432336635 343.486328915405 233.900242112163 365.658055148465 680.533872977133 9252.99827101871]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[25.0065994262695 189.910705566406 349.967712402344]</T3th>
- <Tth>
- <T3th>[-3.80578994750977 -3.8057906627655 1.71535694599152 25.0065994262695 189.910705566406 349.967712402344 512.4482421875 768.440979003906]</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>[0.0199809037148952 0.07167137414217 0.0791171118617058 0 0]</dtc>
- <ll>[0.0843817751710059 0 0.0843817751710059 0;0.197823752303656 0.0107760091646522 0.208599761468308 2297.96240234375;0.197823752303656 0.0107760091646522 0.208599761468308 2297.96240234375]</ll>
- <rmsdtc>[0.0455210320651531 0.0949334278702736 0.106936603784561]</rmsdtc>
- <rmsgdt>[0.0325200334191322 0.0460585318505764 0.0572104454040527]</rmsgdt>
- <rmsdt>0.106936603784561</rmsdt>
- <dt>0.0791171118617058</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>[0.00884355138987303 0.0333710312843323 0.0467591062188148 0.0564890839159489 0.0632737204432487 0.0705661252140999]</dtc>
- <ll>[0.0859330288175069 0 0.0859330288175069 0;0.222641178266178 0.0151714524191087 0.237812630685287 7765.88720703125;0.203483411593804 0.0179242391943757 0.22140765078818 12900.2900390625;0.180676104336383 0.0204806821411944 0.201156786477577 22083.74609375;0.162781253983616 0.023246273050665 0.186027527034281 40665.9375;0.162781253983616 0.023246273050665 0.186027527034281 40665.9375]</ll>
- <rmsdtc>[0.0103599140420556 0.0372262448072433 0.0585092641413212 0.0850858837366104 0.108778856694698 0.115154556930065]</rmsdtc>
- <rmsgdt>[0.00311630149371922 0.0125252241268754 0.0288119316101074 0.0500048361718655 0.0672661662101746 0.0730126723647118]</rmsgdt>
- <rmsdt>0.115154556930065</rmsdt>
- <dt>0.0705661252140999</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027250/ses-2/sub-0027250_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 51s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 5s</item>
- <item>43s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 17s</item>
- <item>Use initial fine affine registration. 7s</item>
- <item>Use previous fine affine registration. 64s</item>
- <item>SPM preprocessing 1 (estimate 2): 65s</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 10s</item>
- <item>101s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 29s</item>
- <item>Fast Optimized Shooting registration 41s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 16s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 33s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 50s</item>
- <item>132s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 14s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 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>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.99 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 | 0.0859 0.0000 0.0859 | 32.0000</item>
- <item>2 | 2.50 | 0.0833 0.0012 0.0844 | 29.4886</item>
- <item>3 | 2.50 | 0.0825 0.0018 0.0843 | 26.9772</item>
- <item>4 | 2.50 | 0.0821 0.0020 0.0841 | 24.6107</item>
- <item>5 | 2.50 | 0.0818 0.0021 0.0839 | 22.6548</item>
- <item>6 | 2.50 | 0.0815 0.0022 0.0837 | 20.6989</item>
- <item>7 | 2.50 | 0.0812 0.0023 0.0836 | 18.9688</item>
- <item>8 | 2.50 | 0.0809 0.0024 0.0834 | 17.4455</item>
- <item>9 | 2.50 | 0.0807 0.0025 0.0832 | 15.9223</item>
- <item>10 | 2.50 | 0.0803 0.0026 0.0829 | 14.6627</item>
- <item>11 | 2.50 | 0.0800 0.0027 0.0827 | 13.4764</item>
- <item>12 | 2.50 | 0.0797 0.0027 0.0825 | 12.3015</item>
- <item>13 | 2.50 | 0.0794 0.0028 0.0822 | 11.3776</item>
- <item>14 | 2.50 | 0.0791 0.0029 0.0820 | 10.4537</item>
- <item>15 | 2.25 | 0.0785 0.0030 0.0815 | 9.5920</item>
- <item>16 | 2.25 | 0.0754 0.0045 0.0799 | 8.8725</item>
- <item>17 | 2.25 | 0.0742 0.0051 0.0793 | 8.1530</item>
- <item>29 | 2.00 | 0.0762 0.0023 0.0785 | 3.3283</item>
- <item>30 | 2.00 | 0.0700 0.0049 0.0749 | 3.1221</item>
- <item>31 | 2.00 | 0.0678 0.0060 0.0738 | 2.9160</item>
- <item>43 | 1.75 | 0.0667 0.0034 0.0701 | 1.5785</item>
- <item>44 | 1.75 | 0.0618 0.0060 0.0678 | 1.5194</item>
- <item>45 | 1.75 | 0.0602 0.0068 0.0671 | 1.4626</item>
- <item>57 | 1.50 | 0.0586 0.0050 0.0635 | 1.0900</item>
- <item>58 | 1.50 | 0.0553 0.0071 0.0624 | 1.0730</item>
- <item>59 | 1.50 | 0.0543 0.0077 0.0620 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 210s</item>
- <item>Prepare output 13s</item>
- <item>224s</item>
- <item>Jacobian determinant (RMS): 0.010 0.037 0.059 0.085 0.109 | 0.115155</item>
- <item>Template Matching: 0.086 0.223 0.203 0.181 0.163 | 0.162781</item>
- <item>Write result maps: 46s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 50s</item>
- <item>102s</item>
- <item>Create initial surface 87s</item>
- <item>Topology correction: 83s</item>
- <item>Surface refinement: 100s</item>
- <item>Reduction of surface collisions with optimization: 62s</item>
- <item>Spherical mapping with areal smoothing 88s</item>
- <item>Spherical registration 323s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 33s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 49s</item>
- <item>105s</item>
- <item>Create initial surface 85s</item>
- <item>Topology correction: 82s</item>
- <item>Surface refinement: 75s</item>
- <item>Reduction of surface collisions with optimization: 61s</item>
- <item>Spherical mapping with areal smoothing 89s</item>
- <item>Spherical registration 319s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5714 0.6644 mm</item>
- <item>Surface intensity / position RMSE: 0.0605 / 0.0623</item>
- <item>Euler number / defect number / defect size: 16.0 / 7.0 / 0.39%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/surf/lh.thickness.sub-0027250_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/surf/rh.thickness.sub-0027250_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/sub-0027250_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1764s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 34s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 15s</item>
- <item>ROI estimation of 'mori' atlas 22s</item>
- <item>ROI estimation of 'anatomy3' atlas 31s</item>
- <item>ROI estimation of 'julichbrain' atlas 42s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 123s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s</item>
- <item>Write results 13s</item>
- <item>460s</item>
- <item>Quality check: 16s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/report/catreport_sub-0027250_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 55 minute(s) and 21 second(s).</item>
- <item>Image Quality Rating (IQR): 84.40% (B)</item>
- <item>GM volume (GMV): 47.21% (604.75 / 1280.88 ml)</item>
- <item>GM thickness (GMT): 2.57 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|