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- <tpm>
- <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>
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- <restype>optimal</restype>
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- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
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- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
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- <vox>1.5</vox>
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- <shootingsurf>Template_T1</shootingsurf>
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- <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>
- <vdist>2</vdist>
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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>
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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>
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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/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
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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/suit.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/ibsr.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/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>
- <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>
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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_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>
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- <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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- <td>/var/lib/condor/execute/dir_912710/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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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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- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
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- <shootingtpm>
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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>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.165179836001839</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0575902089476585</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0585145503282547</SurfacePositionRMSE>
- <res_vx_vol>[0.999999996983206 1.00000000500754 1.00000000178441]</res_vx_vol>
- <res_vx_voli>[0.99999993554981 1.00000000478011 0.999999999076223]</res_vx_voli>
- <res_RMS>1.00000000125839</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 123.980003356934 313.490997314453 419.384002685547]</tissue_mn>
- <tissue_mnr>[0 0.295624077320099 0.747503459453583 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.27361153109778 48.4385868860532 39.5716913978405 21.2772907580508]</tissue_std>
- <tissue_stdr>[0.0173435602337122 0.115499369800091 0.0943567007780075 0.0507346279919147]</tissue_stdr>
- <contrast>105.893013000488</contrast>
- <contrastr>0.252496540546417</contrastr>
- <res_ECR>0.173864543437958</res_ECR>
- <NCR>0.143862545490265</NCR>
- <ICR>0.554800510406494</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999999396641 2.00000001001508 2.00000000356882]</res_vx_vol>
- <res_RMS>2.00000000251677</res_RMS>
- <res_ECR>1.78502321243286</res_ECR>
- <res_BB>1</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>4.29588508605957</contrastr>
- <NCR>2.39624667167664</NCR>
- <ICR>1.83581471443176</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.04129495900046</SurfaceDefectArea>
- <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.15180420875549</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.17029094696045</SurfacePositionRMSE>
- <SIQR>2.16464060675299</SIQR>
- <IQR>2.25622830107753</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>20231031-051646</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.165179836001839</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0575902089476585</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0585145503282547</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.165179836001839</defect_size>
- <vol_abs_CGW>[363.192577992761 672.39090435528 607.15666517082 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.82819204608554</vol_abs_WMH>
- <vol_rel_WMH>0.00111289180388437</vol_rel_WMH>
- <surf_TSA>2052.14795326643</surf_TSA>
- <vol_TIV>1642.74014751886</vol_TIV>
- <vol_rel_CGW>[0.221089487915246 0.409310568911849 0.369599943172905 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.36412073770318 0.58714433367326]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.35840964317322 0.681620460479293 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.79587035942185 0.22838603355171 0.297509178054252;2.39134426486749 0.165362970091923 0.459756781562309;3.00975677065353 0.253564762816538 0.242734040383439]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.876727666088065 0.281143445465866 0.495012799011387;3.93636914088038 0.35316694883529 0.504987200988613]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.28216929628162</vol_TIV>
- <vol_rel_CGW>[1.82057269962726 5.20098004511224 4.48778633572027 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.11128918038844</vol_rel_WMH>
- <surf_TSA>8.62285235008236</surf_TSA>
- <SQR>4.39815566241789</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.3360435439 0.385345344327208]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00175784202292562 0.00150685699190944 0.326571613550186]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[825.377518614643 550.218323522894 636.712428085804 3401.80575857735 1020.54782835715 6148.52793724089]</SPMvols0>
- <SPMvols1>[682.454844921938 511.307757253185 394.291968265191 4372.49544877912 953.204263810304 4621.8800650405]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[155.368896484375 322.743011474609 418.890289306641]</T3th>
- <Tth>
- <T3th>[-8.13967037200928 -8.13966751098633 6.49228858947754 155.368896484375 322.743011474609 418.890289306641 550.651000976562 1324.79113769531]</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>[0.0189002975821495 0.0766230747103691 0.0847130939364433 0 0]</dtc>
- <ll>[0.0876784307472989 0 0.0876784307472989 0;0.20654624764945 0.0117063659722922 0.218252613621743 2496.35913085938;0.20654624764945 0.0117063659722922 0.218252613621743 2496.35913085938]</ll>
- <rmsdtc>[0.0448591820895672 0.10084368288517 0.11333392560482]</rmsdtc>
- <rmsgdt>[0.0325904078781605 0.0511356219649315 0.0631559565663338]</rmsgdt>
- <rmsdt>0.11333392560482</rmsdt>
- <dt>0.0847130939364433</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>[0.00818066485226154 0.034950990229845 0.0446093752980232 0.0532633401453495 0.0599597692489624 0.0670526623725891]</dtc>
- <ll>[0.0874129053268423 0 0.0874129053268423 0;0.224537683150183 0.01618067002442 0.240718353174603 8282.48046875;0.208593745657985 0.0180265167047722 0.226620262362758 12973.900390625;0.187632416727876 0.0200346469426314 0.207667063670507 21602.798828125;0.169734431815648 0.023154556105886 0.192888987921534 40505.4921875;0.169734431815648 0.023154556105886 0.192888987921534 40505.4921875]</ll>
- <rmsdtc>[0.00968642998486757 0.0358214862644672 0.0574740953743458 0.0809128731489182 0.104625828564167 0.112386986613274]</rmsdtc>
- <rmsgdt>[0.00326814665459096 0.0130819398909807 0.029227988794446 0.0495210625231266 0.0681986585259438 0.0745425447821617]</rmsgdt>
- <rmsdt>0.112386986613274</rmsdt>
- <dt>0.0670526623725891</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025997/ses-3/sub-0025997_ses-3_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 43s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>32s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 62s</item>
- <item>SPM preprocessing 1 (estimate 2): 50s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 35s</item>
- <item>Update probability maps 7s</item>
- <item>73s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 22s</item>
- <item>Fast Optimized Shooting registration 27s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.03) 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) 37s</item>
- <item>94s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 12s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.20) 20s</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>57s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>10s</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 | 0.0874 0.0000 0.0874 | 32.0000</item>
- <item>2 | 2.50 | 0.0849 0.0012 0.0861 | 29.4886</item>
- <item>3 | 2.50 | 0.0841 0.0018 0.0859 | 26.9772</item>
- <item>4 | 2.50 | 0.0837 0.0020 0.0857 | 24.6107</item>
- <item>5 | 2.50 | 0.0834 0.0022 0.0855 | 22.6548</item>
- <item>6 | 2.50 | 0.0831 0.0023 0.0853 | 20.6989</item>
- <item>7 | 2.50 | 0.0828 0.0024 0.0852 | 18.9688</item>
- <item>8 | 2.50 | 0.0825 0.0025 0.0850 | 17.4455</item>
- <item>9 | 2.50 | 0.0822 0.0025 0.0847 | 15.9223</item>
- <item>10 | 2.50 | 0.0819 0.0026 0.0845 | 14.6627</item>
- <item>11 | 2.50 | 0.0815 0.0027 0.0843 | 13.4764</item>
- <item>12 | 2.50 | 0.0812 0.0028 0.0840 | 12.3015</item>
- <item>13 | 2.50 | 0.0809 0.0029 0.0838 | 11.3776</item>
- <item>14 | 2.50 | 0.0806 0.0030 0.0835 | 10.4537</item>
- <item>15 | 2.25 | 0.0805 0.0030 0.0835 | 9.5920</item>
- <item>16 | 2.25 | 0.0774 0.0045 0.0819 | 8.8725</item>
- <item>17 | 2.25 | 0.0762 0.0051 0.0813 | 8.1530</item>
- <item>18 | 2.25 | 0.0755 0.0053 0.0807 | 7.5234</item>
- <item>19 | 2.25 | 0.0748 0.0054 0.0802 | 6.9630</item>
- <item>29 | 2.00 | 0.0766 0.0028 0.0794 | 3.3283</item>
- <item>30 | 2.00 | 0.0713 0.0051 0.0764 | 3.1221</item>
- <item>31 | 2.00 | 0.0695 0.0060 0.0755 | 2.9160</item>
- <item>43 | 1.75 | 0.0686 0.0034 0.0719 | 1.5785</item>
- <item>44 | 1.75 | 0.0640 0.0059 0.0699 | 1.5194</item>
- <item>45 | 1.75 | 0.0625 0.0067 0.0692 | 1.4626</item>
- <item>57 | 1.50 | 0.0609 0.0048 0.0658 | 1.0900</item>
- <item>58 | 1.50 | 0.0576 0.0070 0.0647 | 1.0730</item>
- <item>59 | 1.50 | 0.0566 0.0077 0.0643 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 141s</item>
- <item>Prepare output 9s</item>
- <item>149s</item>
- <item>Jacobian determinant (RMS): 0.010 0.036 0.057 0.081 0.105 | 0.112387</item>
- <item>Template Matching: 0.087 0.225 0.209 0.188 0.170 | 0.169734</item>
- <item>Write result maps: 28s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 56s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 38s</item>
- <item>113s</item>
- <item>Create initial surface 73s</item>
- <item>Topology correction: 83s</item>
- <item>Surface refinement: 90s</item>
- <item>Reduction of surface collisions with optimization: 57s</item>
- <item>Spherical mapping with areal smoothing 65s</item>
- <item>Spherical registration 256s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 44s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 39s</item>
- <item>101s</item>
- <item>Create initial surface 75s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 70s</item>
- <item>Reduction of surface collisions with optimization: 59s</item>
- <item>Spherical mapping with areal smoothing 67s</item>
- <item>Spherical registration 244s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3640 0.5870 mm</item>
- <item>Surface intensity / position RMSE: 0.0576 / 0.0585</item>
- <item>Euler number / defect number / defect size: 12.0 / 15.5 / 0.17%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/surf/lh.thickness.sub-0025997_ses-3_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/surf/rh.thickness.sub-0025997_ses-3_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/sub-0025997_ses-3_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1516s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 25s</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 21s</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 45s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>291s</item>
- <item>Quality check: 10s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/report/catreport_sub-0025997_ses-3_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 43 minute(s) and 18 second(s).</item>
- <item>Image Quality Rating (IQR): 82.44% (B-)</item>
- <item>GM volume (GMV): 40.93% (672.39 / 1642.74 ml)</item>
- <item>GM thickness (GMT): 2.36 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_912710/ds/XHCUMS/sub-0025997/ses-3/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|