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- <fnames>..99/ds/sub-sc006/sub-sc006_T1w</fnames>
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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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- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
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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>
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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>
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- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
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- <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>
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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>
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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>
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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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- <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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- <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>
- <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/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>
- <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_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>[false]</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>
- <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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- <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>
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- <td>0</td>
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- <PH>25</PH>
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- <regstr>0.5</regstr>
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- <optimal>[1 0.3]</optimal>
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- </shootingtpms>
- <templates>
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- </templates>
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- <tissue_mnr>[0 0.316390246152878 0.683729648590088 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[54944.1025426437 57910.5158328345 44678.9127936533 30117.8948114597]</tissue_std>
- <tissue_stdr>[0.120428256690502 0.126930147409439 0.0979286879301071 0.0660133734345436]</tissue_stdr>
- <contrast>144294.96875</contrast>
- <contrastr>0.316270381212234</contrastr>
- <NCR>0.105943158268929</NCR>
- <ICR>0.255565196275711</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999997392687 1.99999994068121 1.99999997336556]</res_vx_vol>
- <res_RMS>1.99999996265788</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[1.89584374427795 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>3.33927750587463</contrastr>
- <NCR>1.85189723968506</NCR>
- <ICR>1.09366369247437</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.28470979275584</SurfaceDefectArea>
- <SurfaceDefectNumber>1.375</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.46171593666077</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.66276752948761</SurfacePositionRMSE>
- <IQR>1.93577351023074</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>20220711-171628</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>1.13883917102335</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0730857998132706</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0831383764743805</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>1.13883917102335</defect_size>
- <vol_abs_CGW>[233.08177697607 730.716091995904 467.241863631403 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.610243066707543</vol_abs_WMH>
- <vol_rel_WMH>0.000426433349685809</vol_rel_WMH>
- <surf_TSA>1961.3779116429</surf_TSA>
- <vol_TIV>1431.03973260338</vol_TIV>
- <vol_rel_CGW>[0.162875824944457 0.510619010323753 0.32650516473179 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.62801115310981 0.631444999293128]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.67199635505676 0.789712209922243 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.96203172431942 0.278769904370993 0.25412856976409;2.64713424335318 0.184656092466837 0.431468501450289;3.28896346110154 0.274531219939531 0.314402928785621]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.853569721322655 0.334332363933824 0.645697272378025;4.1353575637199 0.267457843773717 0.354302727621975]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.02292003217404</vol_TIV>
- <vol_rel_CGW>[0.775068695123146 7.02045636357314 3.71381402176348 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04264333496858</vol_rel_WMH>
- <surf_TSA>8.6194827676418</surf_TSA>
- <SQR>5.74547570975686</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.617122745513916 3177 1138 4014.75877512058 0.364110200304099]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.347088813781738]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[862.312908155158 413.080430677068 351.203418222538 554.887688793195 2106.18376435704 6750.49137646988]</SPMvols0>
- <SPMvols1>[777.438741496477 387.356700317535 225.738871942596 792.856406380779 1579.42917819386 6722.95894435865]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[168639.125 338435.5 446817.28125]</T3th>
- <Tth>
- <T3th>[0 0 3998.35473632812 168639.125 338435.5 446817.28125 585906.375 867200.6875]</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>[0.0218124110251665 0.0735515505075455 0.0814669504761696 0 0]</dtc>
- <ll>[0.0832934736394558 0 0.0832934736394558 0;0.19254074920984 0.0102354051972351 0.202776154407075 2182.6796875;0.19254074920984 0.0102354051972351 0.202776154407075 2182.6796875]</ll>
- <rmsdtc>[0.0466758981347084 0.0994659438729286 0.110403381288052]</rmsdtc>
- <rmsgdt>[0.033149030059576 0.0465120933949947 0.057203259319067]</rmsgdt>
- <rmsdt>0.110403381288052</rmsdt>
- <dt>0.0814669504761696</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>[0.0104913590475917 0.0379877127707005 0.0514761470258236 0.0597658716142178 0.0665031746029854 0.0749223679304123]</dtc>
- <ll>[0.0839649373830701 0 0.0839649373830701 0;0.217215918803419 0.0141113467261905 0.231327265529609 7223.24560546875;0.195883496627818 0.0165162486978298 0.212399745325648 11886.9423828125;0.175932562702175 0.0184421955916503 0.194374758293826 19885.703125;0.159536643690553 0.0212103038058928 0.180746947496446 37104.30859375;0.159536643690553 0.0212103038058928 0.180746947496446 37104.30859375]</ll>
- <rmsdtc>[0.0121819283813238 0.0441963039338589 0.0650378689169884 0.0900896042585373 0.112879045307636 0.118945218622684]</rmsdtc>
- <rmsgdt>[0.00331148412078619 0.0130827026441693 0.0288444515317678 0.049108199775219 0.0665422901511192 0.0719271898269653]</rmsgdt>
- <rmsdt>0.118945218622684</rmsdt>
- <dt>0.0749223679304123</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_15299/ds/sub-sc006/sub-sc006_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 19s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>34s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 61s</item>
- <item>SPM preprocessing 1 (estimate 2): 50s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 39s</item>
- <item>Update probability maps 8s</item>
- <item>80s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 31s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.14) 14s</item>
- <item>Estimate local tissue thresholds (WM) 17s</item>
- <item>Estimate local tissue thresholds (GM) 23s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 22s</item>
- <item>84s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 12s</item>
- <item>Blood vessel detection 9s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 27s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>68s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 32s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 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 | 0.0840 0.0000 0.0840 | 32.0000</item>
- <item>2 | 2.50 | 0.0809 0.0013 0.0822 | 29.4886</item>
- <item>3 | 2.50 | 0.0800 0.0019 0.0820 | 26.9772</item>
- <item>4 | 2.50 | 0.0796 0.0022 0.0818 | 24.6107</item>
- <item>5 | 2.50 | 0.0793 0.0023 0.0816 | 22.6548</item>
- <item>6 | 2.50 | 0.0790 0.0024 0.0814 | 20.6989</item>
- <item>7 | 2.50 | 0.0787 0.0025 0.0812 | 18.9688</item>
- <item>8 | 2.50 | 0.0783 0.0026 0.0810 | 17.4455</item>
- <item>9 | 2.50 | 0.0780 0.0027 0.0807 | 15.9223</item>
- <item>10 | 2.50 | 0.0777 0.0028 0.0805 | 14.6627</item>
- <item>11 | 2.50 | 0.0774 0.0029 0.0803 | 13.4764</item>
- <item>12 | 2.50 | 0.0770 0.0029 0.0800 | 12.3015</item>
- <item>13 | 2.50 | 0.0767 0.0030 0.0797 | 11.3776</item>
- <item>14 | 2.50 | 0.0764 0.0031 0.0794 | 10.4537</item>
- <item>15 | 2.25 | 0.0756 0.0032 0.0787 | 9.5920</item>
- <item>16 | 2.25 | 0.0724 0.0047 0.0771 | 8.8725</item>
- <item>29 | 2.00 | 0.0733 0.0021 0.0754 | 3.3283</item>
- <item>30 | 2.00 | 0.0673 0.0046 0.0719 | 3.1221</item>
- <item>31 | 2.00 | 0.0653 0.0055 0.0708 | 2.9160</item>
- <item>43 | 1.75 | 0.0643 0.0032 0.0674 | 1.5785</item>
- <item>44 | 1.75 | 0.0600 0.0054 0.0654 | 1.5194</item>
- <item>45 | 1.75 | 0.0586 0.0061 0.0648 | 1.4626</item>
- <item>57 | 1.50 | 0.0572 0.0045 0.0617 | 1.0900</item>
- <item>58 | 1.50 | 0.0542 0.0064 0.0606 | 1.0730</item>
- <item>59 | 1.50 | 0.0532 0.0071 0.0602 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 163s</item>
- <item>Prepare output 10s</item>
- <item>173s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.065 0.090 0.113 | 0.118945</item>
- <item>Template Matching: 0.084 0.217 0.196 0.176 0.160 | 0.159537</item>
- <item>Write result maps: 22s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 44s</item>
- <item>97s</item>
- <item>Create initial surface 81s</item>
- <item>Topology correction: 96s</item>
- <item>Surface refinement: 88s</item>
- <item>Reduction of surface collisions with optimization: 70s</item>
- <item>Spherical mapping with areal smoothing 81s</item>
- <item>Spherical registration 299s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 44s</item>
- <item>95s</item>
- <item>Create initial surface 82s</item>
- <item>Topology correction: 94s</item>
- <item>Surface refinement: 73s</item>
- <item>Reduction of surface collisions with optimization: 77s</item>
- <item>Spherical mapping with areal smoothing 93s</item>
- <item>Spherical registration 305s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6278 0.6302 mm</item>
- <item>Surface intensity / position RMSE: 0.0731 / 0.0831</item>
- <item>Euler number / defect number / defect size: 14.0 / 7.5 / 1.14%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_15299/ds/sub-sc006/surf/lh.thickness.sub-sc006_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_15299/ds/sub-sc006/surf/rh.thickness.sub-sc006_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_15299/ds/sub-sc006/sub-sc006_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1724s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 28s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 12s</item>
- <item>ROI estimation of 'mori' atlas 18s</item>
- <item>ROI estimation of 'anatomy3' atlas 24s</item>
- <item>ROI estimation of 'julichbrain' atlas 34s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 76s</item>
- <item>Write results 77s</item>
- <item>326s</item>
- <item>Quality check: 5s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_15299/ds/sub-sc006/report/catreport_sub-sc006_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 47 minute(s) and 34 second(s).</item>
- <item>Image Quality Rating (IQR): 85.64% (B)</item>
- <item>GM volume (GMV): 51.06% (730.72 / 1431.04 ml)</item>
- <item>GM thickness (GMT): 2.63 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_15299/ds/sub-sc006/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_15299/ds/sub-sc006/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_15299/ds/sub-sc006/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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