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- <Fm>/var/lib/condor/execute/dir_17509/ds/sub-025/mri/msub-025_T1w.nii</Fm>
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- <parameter>
- <opts>
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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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- <NCstr>-Inf</NCstr>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
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- <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>
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- </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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- <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>
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- <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>
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- <td>
- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
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- <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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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
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- <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>
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- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </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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- <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/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>
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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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- <regstr>0.5</regstr>
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- <optimal>[1 0.3]</optimal>
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- <templates>
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- <tissue_mn>[11.3579998016357 316.163757324219 867.35302734375 1248.15270996094]</tissue_mn>
- <tissue_mnr>[0.00909984763711691 0.253305345773697 0.694909393787384 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[21.1577223377438 153.534998485225 114.631710392568 64.1337891812499]</tissue_std>
- <tissue_stdr>[0.0171068999916315 0.124139443039894 0.0926845148205757 0.0518548376858234]</tissue_stdr>
- <contrast>384.296752929688</contrast>
- <contrastr>0.30789241194725</contrastr>
- <NCR>0.101951651275158</NCR>
- <ICR>0.282995015382767</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.60000008959255 1.60156242243701 1.60156250740083]</res_vx_vol>
- <res_RMS>1.60104184254821</res_RMS>
- <res_BB>0.5</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>3.46494722366333</contrastr>
- <NCR>1.79459738731384</NCR>
- <ICR>1.16169404983521</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.17769504725139</SurfaceDefectArea>
- <SurfaceDefectNumber>2.25</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.42015480995178</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.41627407073975</SurfacePositionRMSE>
- <IQR>1.71654521065214</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>20220710-034519</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.710780189005546</SurfaceDefectArea>
- <SurfaceDefectNumber>25</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0710077434778214</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0708137005567551</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.710780189005546</defect_size>
- <vol_abs_CGW>[175.390028951736 758.956325219859 558.052673317157 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.0281757098732</vol_abs_WMH>
- <vol_rel_WMH>0.00068894155714059</vol_rel_WMH>
- <surf_TSA>2100.44671571881</surf_TSA>
- <vol_TIV>1492.39902748875</vol_TIV>
- <vol_rel_CGW>[0.117522208016219 0.508547855660928 0.373929936322853 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.62621410094946 0.584615471067518]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.63591885566711 0.715594773866567 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.07417004970199 0.234078186840522 0.300237609337874;2.65346181469544 0.16558656407404 0.408884623611778;3.24794279892195 0.24766065811424 0.290877767050349]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.961754183842635 0.433937639282294 0.570403092214246;4.10279911056787 0.314585056833853 0.429596907785754]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.20071836723421</vol_TIV>
- <vol_rel_CGW>[0.5 6.98325890195632 4.56555201729262 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06889415571406</vol_rel_WMH>
- <surf_TSA>8.62347196166173</surf_TSA>
- <SQR>5.73415435124295</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.232874989509583 1 1 6602.43025075042 0.314798246311314]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0077561354264617 0 0.113611795008183]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[889.884084240394 507.536468449575 250.865156376155 622.266210685505 1875.71567103825 5036.91236624672]</SPMvols0>
- <SPMvols1>[809.264249874679 484.538513420436 154.895307114777 503.216050703747 1451.29611816416 5203.66493343947]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[405.337799072266 894.094482421875 1224.2021484375]</T3th>
- <Tth>
- <T3th>[0 0 18.8674907684326 405.337799072266 894.094482421875 1224.2021484375 1633.63427734375 3131.17749023438]</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>[0.0192317552864552 0.0619006752967834 0.0667122006416321 0 0]</dtc>
- <ll>[0.0804256333881209 0 0.0804256333881209 0;0.187894640277986 0.00925053382406429 0.19714517410205 1972.65783691406;0.187894640277986 0.00925053382406429 0.19714517410205 1972.65783691406]</ll>
- <rmsdtc>[0.0437702275812626 0.0779542997479439 0.0859894752502441]</rmsdtc>
- <rmsgdt>[0.0316491723060608 0.0376001819968224 0.0463277585804462]</rmsgdt>
- <rmsdt>0.0859894752502441</rmsdt>
- <dt>0.0667122006416321</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>[0.00906555075198412 0.0326938182115555 0.0444617532193661 0.0523971207439899 0.0588453896343708 0.0656230077147484]</dtc>
- <ll>[0.0828002933888077 0 0.0828002933888077 0;0.214362347374847 0.0144367578601954 0.228799105235043 7389.8154296875;0.195063963085234 0.0168735815723859 0.21193754465762 12144.119140625;0.174664141445758 0.0193829894179066 0.194047130863664 20900.134765625;0.157224431689888 0.0227769120211873 0.180001343711075 39844.859375;0.157224431689888 0.0227769120211873 0.180001343711075 39844.859375]</ll>
- <rmsdtc>[0.010567307472229 0.0371580272912979 0.0540918596088886 0.0771144479513168 0.101331919431686 0.108961746096611]</rmsdtc>
- <rmsgdt>[0.00328112440183759 0.0124450186267495 0.0277526937425137 0.0491618365049362 0.0696396380662918 0.075952410697937]</rmsgdt>
- <rmsdt>0.108961746096611</rmsdt>
- <dt>0.0656230077147484</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_17509/ds/sub-025/sub-025_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 84s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 7s</item>
- <item>Final scaling 11s</item>
- <item>49s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 94s</item>
- <item>SPM preprocessing 1 (estimate 2): 50s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 25s</item>
- <item>Update Skull-Stripping 50s</item>
- <item>Update probability maps 10s</item>
- <item>104s</item>
- <item>Global intensity correction: 17s</item>
- <item>SANLM denoising after intensity normalization (medium): 24s</item>
- <item>Fast Optimized Shooting registration 31s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 19s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 38s</item>
- <item>125s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 21s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 42s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 5s</item>
- <item>107s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 6s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>16s</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 | 0.0828 0.0000 0.0828 | 32.0000</item>
- <item>2 | 2.50 | 0.0796 0.0013 0.0809 | 29.4886</item>
- <item>3 | 2.50 | 0.0787 0.0020 0.0807 | 26.9772</item>
- <item>4 | 2.50 | 0.0783 0.0022 0.0805 | 24.6107</item>
- <item>5 | 2.50 | 0.0780 0.0024 0.0803 | 22.6548</item>
- <item>6 | 2.50 | 0.0777 0.0025 0.0801 | 20.6989</item>
- <item>7 | 2.50 | 0.0774 0.0026 0.0799 | 18.9688</item>
- <item>8 | 2.50 | 0.0770 0.0027 0.0797 | 17.4455</item>
- <item>9 | 2.50 | 0.0767 0.0027 0.0794 | 15.9223</item>
- <item>10 | 2.50 | 0.0763 0.0028 0.0792 | 14.6627</item>
- <item>11 | 2.50 | 0.0760 0.0029 0.0789 | 13.4764</item>
- <item>12 | 2.50 | 0.0757 0.0030 0.0786 | 12.3015</item>
- <item>13 | 2.50 | 0.0753 0.0031 0.0784 | 11.3776</item>
- <item>14 | 2.50 | 0.0750 0.0031 0.0781 | 10.4537</item>
- <item>15 | 2.25 | 0.0747 0.0032 0.0779 | 9.5920</item>
- <item>16 | 2.25 | 0.0715 0.0048 0.0763 | 8.8725</item>
- <item>29 | 2.00 | 0.0733 0.0022 0.0755 | 3.3283</item>
- <item>30 | 2.00 | 0.0671 0.0046 0.0718 | 3.1221</item>
- <item>31 | 2.00 | 0.0650 0.0056 0.0706 | 2.9160</item>
- <item>43 | 1.75 | 0.0643 0.0032 0.0675 | 1.5785</item>
- <item>44 | 1.75 | 0.0598 0.0056 0.0654 | 1.5194</item>
- <item>45 | 1.75 | 0.0582 0.0065 0.0647 | 1.4626</item>
- <item>57 | 1.50 | 0.0569 0.0047 0.0616 | 1.0900</item>
- <item>58 | 1.50 | 0.0535 0.0069 0.0604 | 1.0730</item>
- <item>59 | 1.50 | 0.0524 0.0076 0.0600 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 133s</item>
- <item>Prepare output 10s</item>
- <item>143s</item>
- <item>Jacobian determinant (RMS): 0.011 0.037 0.054 0.077 0.101 | 0.108962</item>
- <item>Template Matching: 0.083 0.214 0.195 0.175 0.157 | 0.157224</item>
- <item>Write result maps: 27s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 26s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 36s</item>
- <item>79s</item>
- <item>Create initial surface 60s</item>
- <item>Topology correction: 67s</item>
- <item>Surface refinement: 52s</item>
- <item>Reduction of surface collisions with optimization: 50s</item>
- <item>Spherical mapping with areal smoothing 64s</item>
- <item>Spherical registration 177s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 22s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 35s</item>
- <item>74s</item>
- <item>Create initial surface 58s</item>
- <item>Topology correction: 68s</item>
- <item>Surface refinement: 53s</item>
- <item>Reduction of surface collisions with optimization: 49s</item>
- <item>Spherical mapping with areal smoothing 62s</item>
- <item>Spherical registration 178s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6262 0.5845 mm</item>
- <item>Surface intensity / position RMSE: 0.0710 / 0.0708</item>
- <item>Euler number / defect number / defect size: 30.0 / 25.0 / 0.71%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_17509/ds/sub-025/surf/lh.thickness.sub-025_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_17509/ds/sub-025/surf/rh.thickness.sub-025_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_17509/ds/sub-025/sub-025_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1174s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 16s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 59s</item>
- <item>ROI estimation of 'lpba40' atlas 17s</item>
- <item>ROI estimation of 'hammers' atlas 41s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 14s</item>
- <item>ROI estimation of 'aal3' atlas 25s</item>
- <item>ROI estimation of 'mori' atlas 38s</item>
- <item>ROI estimation of 'anatomy3' atlas 56s</item>
- <item>ROI estimation of 'julichbrain' atlas 77s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 99s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 137s</item>
- <item>Write results 138s</item>
- <item>640s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_17509/ds/sub-025/report/catreport_sub-025_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 47 minute(s) and 23 second(s).</item>
- <item>Image Quality Rating (IQR): 87.83% (B+)</item>
- <item>GM volume (GMV): 50.85% (758.96 / 1492.40 ml)</item>
- <item>GM thickness (GMT): 2.63 0.58 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_17509/ds/sub-025/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_17509/ds/sub-025/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_17509/ds/sub-025/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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