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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
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- <NCstr>-Inf</NCstr>
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- <WMHC>2</WMHC>
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- <SLC>0</SLC>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
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- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
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- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
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- <reduce_mesh>1</reduce_mesh>
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- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
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- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <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>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <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>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
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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>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <tr>
- <td>/var/lib/condor/execute/dir_3515445/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <td>[false]</td>
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- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
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- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
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- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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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>28</SurfaceEulerNumber>
- <SurfaceDefectArea>0.971358046346244</SurfaceDefectArea>
- <SurfaceDefectNumber>17</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.066293016076088</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0723280310630798</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>177.299957275391</res_BB>
- <tissue_mn>[2.14400005340576 827.544006347656 2531.28393554688 3215.80590820312]</tissue_mn>
- <tissue_mnr>[0.000666706939227879 0.257336437702179 0.787138283252716 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[90.5204740504293 451.119582317636 353.744495903953 210.623799894828]</tissue_std>
- <tissue_stdr>[0.0281673930585384 0.140375554561615 0.110075205564499 0.0655401274561882]</tissue_stdr>
- <contrast>684.978698730469</contrast>
- <contrastr>0.213003739714622</contrastr>
- <res_ECR>0.0818526148796082</res_ECR>
- <NCR>0.159229889512062</NCR>
- <ICR>0.559230446815491</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>1.3155745267868</res_ECR>
- <res_BB>10.5</res_BB>
- <tissue_mn>[8.43329429626465 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>4.88827705383301</contrastr>
- <NCR>2.61685180664062</NCR>
- <ICR>1.8468017578125</ICR>
- <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.24283951158656</SurfaceDefectArea>
- <SurfaceDefectNumber>1.85</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.32586026191711</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.4465606212616</SurfacePositionRMSE>
- <SIQR>2.31374343954481</SIQR>
- <IQR>2.4329241047072</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>20231030-235444</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>28</SurfaceEulerNumber>
- <SurfaceDefectArea>0.971358046346244</SurfaceDefectArea>
- <SurfaceDefectNumber>17</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.066293016076088</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0723280310630798</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>28</EC_abs>
- <defect_size>0.971358046346244</defect_size>
- <vol_abs_CGW>[248.365576470588 560.612141176471 492.293254901961 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.496047058823529</vol_abs_WMH>
- <vol_rel_WMH>0.000381201970448813</vol_rel_WMH>
- <surf_TSA>1787.03649593279</surf_TSA>
- <vol_TIV>1301.27097254902</vol_TIV>
- <vol_rel_CGW>[0.190863841359707 0.430818909360826 0.378317249279466 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.31800376239874 0.665464101581707]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.33719038963318 0.76614893477736 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.55504655681657 0.306780333845475 0.255745441344838;2.31740735765705 0.199226679753399 0.459586439920695;3.01211860949671 0.294286726390122 0.284668118734467]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.701550871446416 0.142165864336966 0.486832882747572;4.0023970615573 0.32236631104158 0.513167117252428]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.2287309650269</vol_TIV>
- <vol_rel_CGW>[1.27772703591428 5.58726489512979 4.6443471494157 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03812019704488</vol_rel_WMH>
- <surf_TSA>8.5786405954354</surf_TSA>
- <SQR>4.68786488350888</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 12320.768 0.323433342569028]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00144401099532843 0.00130768702365458 0.0135254552587867]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[689.033882352941 486.608462745098 395.305219607843 596.691407843137 878.010756862745 9751.26465490196]</SPMvols0>
- <SPMvols1>[575.414996078431 442.261023529412 241.14888627451 455.284392156863 746.977352941176 9859.80657647059]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[982.862915039062 2532.28466796875 3235.853515625]</T3th>
- <Tth>
- <T3th>[-41.1609306335449 -41.1609268188477 13.5488538742065 982.862915039062 2532.28466796875 3235.853515625 4362.3486328125 7347.52490234375]</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>[0.0227716378867626 0.0853525474667549 0.0947819650173187 0 0]</dtc>
- <ll>[0.0871263483420712 0 0.0871263483420712 0;0.196174923826953 0.01249947725367 0.208674401080623 2665.48852539062;0.196174923826953 0.01249947725367 0.208674401080623 2665.48852539062]</ll>
- <rmsdtc>[0.0485758073627949 0.110651195049286 0.122051209211349]</rmsdtc>
- <rmsgdt>[0.0345938839018345 0.0487694665789604 0.0594272315502167]</rmsgdt>
- <rmsdt>0.122051209211349</rmsdt>
- <dt>0.0947819650173187</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>[0.0113511001691222 0.0485251843929291 0.0638396218419075 0.0729618892073631 0.0791030377149582 0.0900538489222527]</dtc>
- <ll>[0.0890391352416114 0 0.0890391352416114 0;0.222367399267399 0.021309571504884 0.243676970772283 10907.8369140625;0.202606563458717 0.0219252604470608 0.224531823905778 15779.873046875;0.179322317907726 0.0229068875652433 0.20222920547297 24699.85546875;0.161628649277762 0.0254523096360483 0.18708095891381 44525.07421875;0.161628649277762 0.0254523096360483 0.18708095891381 44525.07421875]</ll>
- <rmsdtc>[0.0134230079129338 0.0509187579154968 0.0794878378510475 0.106061972677708 0.130057036876678 0.137395724654198]</rmsdtc>
- <rmsgdt>[0.00388148101046681 0.0153870396316051 0.0325393527746201 0.0543238744139671 0.0740667060017586 0.0798442512750626]</rmsgdt>
- <rmsdt>0.137395724654198</rmsdt>
- <dt>0.0900538489222527</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025467/ses-1/sub-0025467_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 21s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 4s</item>
- <item>26s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 9s</item>
- <item>Use initial fine affine registration. 47s</item>
- <item>SPM preprocessing 1 (estimate 2): 50s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 15s</item>
- <item>Update Skull-Stripping 36s</item>
- <item>Update probability maps 8s</item>
- <item>72s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 17s</item>
- <item>Fast Optimized Shooting registration 27s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 10s</item>
- <item>Estimate local tissue thresholds (WM) 14s</item>
- <item>Estimate local tissue thresholds (GM) 19s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 34s</item>
- <item>86s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 7s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 14s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 4s</item>
- <item>43s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s</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) 3s</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>8s</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 | 0.0890 0.0000 0.0890 | 32.0000</item>
- <item>2 | 2.50 | 0.0855 0.0015 0.0869 | 29.4886</item>
- <item>3 | 2.50 | 0.0844 0.0023 0.0866 | 26.9772</item>
- <item>4 | 2.50 | 0.0838 0.0026 0.0864 | 24.6107</item>
- <item>5 | 2.50 | 0.0834 0.0028 0.0862 | 22.6548</item>
- <item>6 | 2.50 | 0.0830 0.0029 0.0859 | 20.6989</item>
- <item>7 | 2.50 | 0.0826 0.0031 0.0857 | 18.9688</item>
- <item>8 | 2.50 | 0.0822 0.0032 0.0854 | 17.4455</item>
- <item>9 | 2.50 | 0.0818 0.0033 0.0851 | 15.9223</item>
- <item>10 | 2.50 | 0.0813 0.0035 0.0848 | 14.6627</item>
- <item>11 | 2.50 | 0.0809 0.0036 0.0845 | 13.4764</item>
- <item>12 | 2.50 | 0.0804 0.0037 0.0841 | 12.3015</item>
- <item>13 | 2.50 | 0.0799 0.0039 0.0838 | 11.3776</item>
- <item>14 | 2.50 | 0.0795 0.0040 0.0834 | 10.4537</item>
- <item>15 | 2.25 | 0.0807 0.0041 0.0848 | 9.5920</item>
- <item>16 | 2.25 | 0.0768 0.0061 0.0828 | 8.8725</item>
- <item>17 | 2.25 | 0.0751 0.0068 0.0819 | 8.1530</item>
- <item>18 | 2.25 | 0.0741 0.0071 0.0812 | 7.5234</item>
- <item>29 | 2.00 | 0.0762 0.0034 0.0796 | 3.3283</item>
- <item>30 | 2.00 | 0.0698 0.0062 0.0760 | 3.1221</item>
- <item>31 | 2.00 | 0.0675 0.0073 0.0748 | 2.9160</item>
- <item>43 | 1.75 | 0.0662 0.0042 0.0704 | 1.5785</item>
- <item>44 | 1.75 | 0.0614 0.0067 0.0682 | 1.5194</item>
- <item>45 | 1.75 | 0.0598 0.0076 0.0674 | 1.4626</item>
- <item>57 | 1.50 | 0.0584 0.0056 0.0640 | 1.0900</item>
- <item>58 | 1.50 | 0.0550 0.0078 0.0628 | 1.0730</item>
- <item>59 | 1.50 | 0.0539 0.0085 0.0624 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 146s</item>
- <item>Prepare output 8s</item>
- <item>154s</item>
- <item>Jacobian determinant (RMS): 0.013 0.051 0.079 0.106 0.130 | 0.137396</item>
- <item>Template Matching: 0.089 0.222 0.203 0.179 0.162 | 0.161629</item>
- <item>Write result maps: 32s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 29s</item>
- <item>81s</item>
- <item>Create initial surface 59s</item>
- <item>Topology correction: 67s</item>
- <item>Surface refinement: 53s</item>
- <item>Reduction of surface collisions with optimization: 41s</item>
- <item>Spherical mapping with areal smoothing 56s</item>
- <item>Spherical registration 221s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 26s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 28s</item>
- <item>67s</item>
- <item>Create initial surface 54s</item>
- <item>Topology correction: 65s</item>
- <item>Surface refinement: 50s</item>
- <item>Reduction of surface collisions with optimization: 43s</item>
- <item>Spherical mapping with areal smoothing 58s</item>
- <item>Spherical registration 211s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3176 0.6647 mm</item>
- <item>Surface intensity / position RMSE: 0.0663 / 0.0723</item>
- <item>Euler number / defect number / defect size: 28.0 / 17.0 / 0.97%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/surf/lh.thickness.sub-0025467_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/surf/rh.thickness.sub-0025467_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/sub-0025467_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1196s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 27s</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 19s</item>
- <item>ROI estimation of 'anatomy3' atlas 33s</item>
- <item>ROI estimation of 'julichbrain' atlas 50s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 78s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 189s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 254s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 18s</item>
- <item>Write results 19s</item>
- <item>751s</item>
- <item>Quality check: 11s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/report/catreport_sub-0025467_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 46 minute(s) and 21 second(s).</item>
- <item>Image Quality Rating (IQR): 80.67% (B-)</item>
- <item>GM volume (GMV): 43.08% (560.61 / 1301.27 ml)</item>
- <item>GM thickness (GMT): 2.32 0.67 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3515445/ds/IACAS/sub-0025467/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|