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- <Fm>/var/lib/condor/execute/dir_4348/ds/sub-40/mri/msub-40_T1w.nii</Fm>
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- <fnames>.._4348/ds/sub-40/sub-40_T1w</fnames>
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- <parameter>
- <opts>
- <tpm>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
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- <extopts>
- <uhrlim>1.4</uhrlim>
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- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
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- <WMHC>2</WMHC>
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- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
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- <nproc>32</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
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- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
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- </darteltpm>
- <shootingtpm>
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- </shootingtpm>
- <shootingT1>
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- </shootingT1>
- <brainmask>
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- </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>
- <SRP>22</SRP>
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- <add_parahipp>0.1</add_parahipp>
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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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
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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>
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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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- <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>
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- <td>
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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>
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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/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>
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- <td>
- <item>gm</item>
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- </td>
- <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>
- </td>
- <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>
- <item>wm</item>
- </td>
- <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_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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- <tr>
- <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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- <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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- <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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- <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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- <td>Schaefer2018_100P_17N</td>
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- <td>1</td>
- <td>0</td>
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- <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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- <td>Schaefer2018_400P_17N</td>
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- <td>1</td>
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- <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>
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- <td>0</td>
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- <LAB>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- </shootingtpms>
- <templates>
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- </templates>
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- <tissue_mn>[1.40199995040894 93.6178894042969 214.237503051758 287.237030029297]</tissue_mn>
- <tissue_mnr>[0.00488098617643118 0.325925558805466 0.745856106281281 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[10.3910142364059 36.4179794243174 24.4330101350733 12.893149211794]</tissue_std>
- <tissue_stdr>[0.0363531894981861 0.127409085631371 0.0854794159531593 0.0451069623231888]</tissue_stdr>
- <contrast>73.3575897216797</contrast>
- <contrastr>0.25539043545723</contrastr>
- <NCR>0.141640365123749</NCR>
- <ICR>0.217432573437691</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999671594844 2.00000001113905 1.99999992075613]</res_vx_vol>
- <res_RMS>1.99999888261513</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[6.51440286636353 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>4.25247669219971</contrastr>
- <NCR>2.36434626579285</NCR>
- <ICR>0.999088704586029</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.20279642027948</SurfaceDefectArea>
- <SurfaceDefectNumber>1.9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.39228224754333</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.42427384853363</SurfacePositionRMSE>
- <IQR>2.23213876640028</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220711-085046</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.811185681117915</SurfaceDefectArea>
- <SurfaceDefectNumber>18</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0696141123771667</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0712136924266815</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.811185681117915</defect_size>
- <vol_abs_CGW>[179.762447838304 671.331988948618 506.352371244521 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.579591185792139</vol_abs_WMH>
- <vol_rel_WMH>0.000426971563351832</vol_rel_WMH>
- <surf_TSA>1924.9282704135</surf_TSA>
- <vol_TIV>1357.44680803144</vol_TIV>
- <vol_rel_CGW>[0.132426881683116 0.494554913663378 0.373018204653506 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.46514704047442 0.60452007521017]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.47120523452759 0.6745118364561 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.83433004091322 0.235773905356519 0.275206696188599;2.46833298283279 0.172658445680206 0.437664781017227;3.09143867418117 0.247595273095645 0.287128522794174]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.927324127117809 0.29354442529599 0.501276906238599;3.98893615461739 0.349937263225907 0.498723093761401]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.04301986166895</vol_TIV>
- <vol_rel_CGW>[0.5 6.73194888044859 4.54917752610463 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04269715633518</vol_rel_WMH>
- <surf_TSA>8.61642005518408</surf_TSA>
- <SQR>5.53452457811318</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.393122586337003 513 6 6124.92673412702 0.282284437157756]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00441252673044801 0 0.37595722079277]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[818.755690968569 450.444660993 266.980533082131 479.707227651582 2973.8860291953 5631.26455730758]</SPMvols0>
- <SPMvols1>[714.035784067612 418.936329469613 167.149814068062 1434.77638827425 2587.19970451625 4770.47405833446]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[114.366203308105 217.245300292969 277.414794921875]</T3th>
- <Tth>
- <T3th>[0 41.0002593994141 4.53242206573486 114.366203308105 217.245300292969 277.414794921875 358.939086914062 591.232666015625]</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>[0.0214090012013912 0.0758746191859245 0.0834368094801903 0 0]</dtc>
- <ll>[0.0813174757207571 0 0.0813174757207571 0;0.189809224471038 0.00997406866799454 0.199783293139033 2126.9501953125;0.189809224471038 0.00997406866799454 0.199783293139033 2126.9501953125]</ll>
- <rmsdtc>[0.0445604026317596 0.0982838794589043 0.108102455735207]</rmsdtc>
- <rmsgdt>[0.0313649959862232 0.0416485257446766 0.0506135635077953]</rmsgdt>
- <rmsdt>0.108102455735207</rmsdt>
- <dt>0.0834368094801903</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>[0.00991968996822834 0.0366826914250851 0.0515639670193195 0.0589436106383801 0.0646635293960571 0.0724878162145615]</dtc>
- <ll>[0.0817387200555287 0 0.0817387200555287 0;0.216521352258852 0.0133599196810134 0.229881271939866 6838.60888671875;0.196376402123349 0.0162758299934557 0.212652232116805 11713.91015625;0.176725121305199 0.0181680409430552 0.194893162248255 19590.08984375;0.160264877214604 0.0210914116354732 0.181356288850078 36896.32421875;0.160264877214604 0.0210914116354732 0.181356288850078 36896.32421875]</ll>
- <rmsdtc>[0.0116115529090166 0.0424637869000435 0.0626709833741188 0.0858538895845413 0.106974646449089 0.113944135606289]</rmsdtc>
- <rmsgdt>[0.00329216476529837 0.0126347607001662 0.0276019796729088 0.0479192212224007 0.0650925859808922 0.0704175978899002]</rmsgdt>
- <rmsdt>0.113944135606289</rmsdt>
- <dt>0.0724878162145615</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_4348/ds/sub-40/sub-40_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 23s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>36s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 70s</item>
- <item>SPM preprocessing 1 (estimate 2): 56s</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 7s</item>
- <item>73s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 7s</item>
- <item>Fast Optimized Shooting registration 29s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 12s</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) 24s</item>
- <item>81s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 15s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s</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>66s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 34s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>11s</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 | 0.0817 0.0000 0.0817 | 32.0000</item>
- <item>2 | 2.50 | 0.0793 0.0011 0.0804 | 29.4886</item>
- <item>3 | 2.50 | 0.0786 0.0017 0.0803 | 26.9772</item>
- <item>4 | 2.50 | 0.0782 0.0019 0.0801 | 24.6107</item>
- <item>5 | 2.50 | 0.0779 0.0021 0.0800 | 22.6548</item>
- <item>6 | 2.50 | 0.0777 0.0022 0.0798 | 20.6989</item>
- <item>7 | 2.50 | 0.0774 0.0023 0.0797 | 18.9688</item>
- <item>8 | 2.50 | 0.0771 0.0024 0.0795 | 17.4455</item>
- <item>9 | 2.50 | 0.0768 0.0024 0.0793 | 15.9223</item>
- <item>10 | 2.50 | 0.0765 0.0026 0.0791 | 14.6627</item>
- <item>11 | 2.50 | 0.0762 0.0026 0.0789 | 13.4764</item>
- <item>12 | 2.50 | 0.0759 0.0027 0.0786 | 12.3015</item>
- <item>13 | 2.50 | 0.0756 0.0028 0.0784 | 11.3776</item>
- <item>14 | 2.50 | 0.0753 0.0029 0.0782 | 10.4537</item>
- <item>15 | 2.25 | 0.0752 0.0030 0.0781 | 9.5920</item>
- <item>16 | 2.25 | 0.0722 0.0045 0.0766 | 8.8725</item>
- <item>29 | 2.00 | 0.0737 0.0020 0.0758 | 3.3283</item>
- <item>30 | 2.00 | 0.0677 0.0044 0.0721 | 3.1221</item>
- <item>31 | 2.00 | 0.0655 0.0054 0.0709 | 2.9160</item>
- <item>43 | 1.75 | 0.0645 0.0032 0.0677 | 1.5785</item>
- <item>44 | 1.75 | 0.0604 0.0053 0.0657 | 1.5194</item>
- <item>45 | 1.75 | 0.0589 0.0061 0.0650 | 1.4626</item>
- <item>57 | 1.50 | 0.0576 0.0045 0.0620 | 1.0900</item>
- <item>58 | 1.50 | 0.0545 0.0064 0.0609 | 1.0730</item>
- <item>59 | 1.50 | 0.0534 0.0070 0.0605 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 162s</item>
- <item>Prepare output 9s</item>
- <item>172s</item>
- <item>Jacobian determinant (RMS): 0.012 0.042 0.063 0.086 0.107 | 0.113944</item>
- <item>Template Matching: 0.082 0.217 0.196 0.177 0.160 | 0.160265</item>
- <item>Write result maps: 21s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 25s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 42s</item>
- <item>87s</item>
- <item>Create initial surface 82s</item>
- <item>Topology correction: 90s</item>
- <item>Surface refinement: 69s</item>
- <item>Reduction of surface collisions with optimization: 65s</item>
- <item>Spherical mapping with areal smoothing 80s</item>
- <item>Spherical registration 294s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 28s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 41s</item>
- <item>88s</item>
- <item>Create initial surface 79s</item>
- <item>Topology correction: 93s</item>
- <item>Surface refinement: 87s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 79s</item>
- <item>Spherical registration 304s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4651 0.6043 mm</item>
- <item>Surface intensity / position RMSE: 0.0696 / 0.0712</item>
- <item>Euler number / defect number / defect size: 30.0 / 18.0 / 0.81%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4348/ds/sub-40/surf/lh.thickness.sub-40_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4348/ds/sub-40/surf/rh.thickness.sub-40_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4348/ds/sub-40/sub-40_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1652s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 18s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 22s</item>
- <item>ROI estimation of 'julichbrain' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s</item>
- <item>Write results 79s</item>
- <item>299s</item>
- <item>Quality check: 5s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_4348/ds/sub-40/report/catreport_sub-40_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 46 minute(s) and 36 second(s).</item>
- <item>Image Quality Rating (IQR): 82.68% (B-)</item>
- <item>GM volume (GMV): 49.46% (671.33 / 1357.45 ml)</item>
- <item>GM thickness (GMT): 2.47 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_4348/ds/sub-40/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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