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- <opts>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <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>
- <nproc>1</nproc>
- <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>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <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>
- <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>
- <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>
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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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- <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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- <td>[false]</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>
- <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>
- <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_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_1726780/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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- <tr>
- <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>
- </tr>
- <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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- <TH>9</TH>
- <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>
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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>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.438823926563006</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.065004974603653</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0674196407198906</SurfacePositionRMSE>
- <res_vx_vol>[0.999900817871094 1 1]</res_vx_vol>
- <res_vx_voli>[0.999900817871094 1 1]</res_vx_voli>
- <res_RMS>0.999966940383411</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 18.0170001983643 180.647994995117 356.463012695312]</tissue_mn>
- <tissue_mnr>[0 0.0505438148975372 0.506779074668884 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.44647487683011 39.5301616018115 44.1885844061773 31.8713018785278]</tissue_std>
- <tissue_stdr>[0.00966853462159634 0.110895551741123 0.123964011669159 0.0894098430871964]</tissue_stdr>
- <contrast>119.304298400879</contrast>
- <contrastr>0.334689140319824</contrastr>
- <res_ECR>0.367298424243927</res_ECR>
- <NCR>0.128948777914047</NCR>
- <ICR>0.299370557069778</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99980163574219 2 2]</res_vx_vol>
- <res_RMS>1.99993388076682</res_RMS>
- <res_ECR>2.77193069458008</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>3.06299614906311</contrastr>
- <NCR>2.18215298652649</NCR>
- <ICR>1.20230793952942</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.10970598164075</SurfaceDefectArea>
- <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30009949207306</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.34839272499084</SurfacePositionRMSE>
- <SIQR>2.477302056016</SIQR>
- <IQR>2.10468789003676</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>20231031-004622</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.438823926563006</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.065004974603653</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0674196407198906</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.438823926563006</defect_size>
- <vol_abs_CGW>[281.177795695885 781.292592247069 606.947670176547 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.06561194691378</vol_abs_WMH>
- <vol_rel_WMH>0.000638313418098594</vol_rel_WMH>
- <surf_TSA>2230.23417264871</surf_TSA>
- <vol_TIV>1669.4180581195</vol_TIV>
- <vol_rel_CGW>[0.168428629562456 0.46800295974224 0.363568410695304 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.43961508836625 0.611401468513221]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.4018611907959 0.719938549250183 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.87569884904555 0.23065181061355 0.327218319021598;2.4572196454816 0.173621194241745 0.424130830759484;3.13870970094064 0.265822293605262 0.248650850218919]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.908420981453641 0.317065936609094 0.493808567603748;4.06826906653475 0.355263841470962 0.506191432396252]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.54725230073667</vol_TIV>
- <vol_rel_CGW>[0.874795789555608 6.25508189192241 4.37946139898175 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06383134180986</vol_rel_WMH>
- <surf_TSA>8.62394426611993</surf_TSA>
- <SQR>5.15121044342465</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11533.192 0.418026518911368]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0012282463721931 0.000933525443542749 0.0445854179561138]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[976.435486619927 517.607590818278 640.788729101622 484.690671598517 1207.04726276464 8392.41886495529]</SPMvols0>
- <SPMvols1>[808.487353568732 486.612724083605 331.447048605496 407.808791781048 1104.52618889435 8394.41026742416]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[44.8508987426758 196.082397460938 366.075714111328]</T3th>
- <Tth>
- <T3th>[-4.23443984985352 -4.2344388961792 2.87236428260803 44.8508987426758 196.082397460938 366.075714111328 526.688110351562 909.790893554688]</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>[0.018964784219861 0.0674229264259338 0.0738778486847878 0 0]</dtc>
- <ll>[0.0838330144069347 0 0.0838330144069347 0;0.206407544707336 0.00883896153371016 0.215246506241046 1884.89086914062;0.206407544707336 0.00883896153371016 0.215246506241046 1884.89086914062]</ll>
- <rmsdtc>[0.0460165813565254 0.0883123651146889 0.0990944281220436]</rmsdtc>
- <rmsgdt>[0.0336474999785423 0.0446666479110718 0.055672213435173]</rmsgdt>
- <rmsdt>0.0990944281220436</rmsdt>
- <dt>0.0738778486847878</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>[0.00784257054328918 0.026953861117363 0.0373541340231895 0.0450781956315041 0.0513877272605896 0.0566678941249847]</dtc>
- <ll>[0.0815375239179965 0 0.0815375239179965 0;0.219553098290598 0.00979184218559219 0.22934494047619 5012.19921875;0.204218123881497 0.0132980465406649 0.217516170422162 9570.763671875;0.18521536947542 0.0166536206193799 0.2018689900948 17957.1328125;0.16845910316557 0.0202738013175443 0.188732904483115 35466.03515625;0.16845910316557 0.0202738013175443 0.188732904483115 35466.03515625]</ll>
- <rmsdtc>[0.00907319597899914 0.030824176967144 0.0455918945372105 0.0671834871172905 0.0897777155041695 0.0965002104640007]</rmsdtc>
- <rmsgdt>[0.00285723269917071 0.0108419572934508 0.0242458377033472 0.0432049781084061 0.0610668808221817 0.0666103288531303]</rmsgdt>
- <rmsdt>0.0965002104640007</rmsdt>
- <dt>0.0566678941249847</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027237/ses-1/sub-0027237_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 61s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 4s</item>
- <item>Final correction 7s</item>
- <item>Final scaling 8s</item>
- <item>50s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 12s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 105s</item>
- <item>SPM preprocessing 1 (estimate 2): 82s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 22s</item>
- <item>Update Segmentation 24s</item>
- <item>Update Skull-Stripping 52s</item>
- <item>Update probability maps 10s</item>
- <item>109s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 32s</item>
- <item>Fast Optimized Shooting registration 42s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 18s</item>
- <item>Estimate local tissue thresholds (WM) 24s</item>
- <item>Estimate local tissue thresholds (GM) 38s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 52s</item>
- <item>144s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 23s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 30s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>92s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 45s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 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>15s</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 | 0.0815 0.0000 0.0815 | 32.0000</item>
- <item>2 | 2.50 | 0.0798 0.0009 0.0808 | 29.4886</item>
- <item>3 | 2.50 | 0.0793 0.0014 0.0807 | 26.9772</item>
- <item>4 | 2.50 | 0.0791 0.0015 0.0806 | 24.6107</item>
- <item>5 | 2.50 | 0.0788 0.0016 0.0805 | 22.6548</item>
- <item>6 | 2.50 | 0.0787 0.0017 0.0803 | 20.6989</item>
- <item>7 | 2.50 | 0.0785 0.0017 0.0802 | 18.9688</item>
- <item>8 | 2.50 | 0.0783 0.0018 0.0801 | 17.4455</item>
- <item>9 | 2.50 | 0.0781 0.0019 0.0799 | 15.9223</item>
- <item>10 | 2.50 | 0.0778 0.0019 0.0798 | 14.6627</item>
- <item>11 | 2.50 | 0.0776 0.0020 0.0796 | 13.4764</item>
- <item>12 | 2.50 | 0.0774 0.0020 0.0794 | 12.3015</item>
- <item>13 | 2.50 | 0.0772 0.0021 0.0793 | 11.3776</item>
- <item>14 | 2.50 | 0.0770 0.0021 0.0791 | 10.4537</item>
- <item>15 | 2.25 | 0.0754 0.0022 0.0776 | 9.5920</item>
- <item>16 | 2.25 | 0.0732 0.0033 0.0764 | 8.8725</item>
- <item>29 | 2.00 | 0.0750 0.0015 0.0765 | 3.3283</item>
- <item>30 | 2.00 | 0.0698 0.0035 0.0734 | 3.1221</item>
- <item>31 | 2.00 | 0.0681 0.0044 0.0725 | 2.9160</item>
- <item>43 | 1.75 | 0.0674 0.0025 0.0699 | 1.5785</item>
- <item>44 | 1.75 | 0.0632 0.0047 0.0679 | 1.5194</item>
- <item>45 | 1.75 | 0.0617 0.0056 0.0673 | 1.4626</item>
- <item>57 | 1.50 | 0.0605 0.0040 0.0644 | 1.0900</item>
- <item>58 | 1.50 | 0.0572 0.0061 0.0633 | 1.0730</item>
- <item>59 | 1.50 | 0.0562 0.0068 0.0629 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 216s</item>
- <item>Prepare output 14s</item>
- <item>230s</item>
- <item>Jacobian determinant (RMS): 0.009 0.031 0.046 0.067 0.090 | 0.096500</item>
- <item>Template Matching: 0.082 0.220 0.204 0.185 0.168 | 0.168459</item>
- <item>Write result maps: 41s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 66s</item>
- <item>143s</item>
- <item>Create initial surface 112s</item>
- <item>Topology correction: 129s</item>
- <item>Surface refinement: 96s</item>
- <item>Reduction of surface collisions with optimization: 97s</item>
- <item>Spherical mapping with areal smoothing 118s</item>
- <item>Spherical registration 331s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 43s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 65s</item>
- <item>137s</item>
- <item>Create initial surface 108s</item>
- <item>Topology correction: 126s</item>
- <item>Surface refinement: 132s</item>
- <item>Reduction of surface collisions with optimization: 92s</item>
- <item>Spherical mapping with areal smoothing 142s</item>
- <item>Spherical registration 371s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4397 0.6113 mm</item>
- <item>Surface intensity / position RMSE: 0.0650 / 0.0674</item>
- <item>Euler number / defect number / defect size: 18.0 / 15.5 / 0.44%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/surf/lh.thickness.sub-0027237_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/surf/rh.thickness.sub-0027237_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/sub-0027237_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 13s</item>
- <item>Surface and thickness estimation takes: 2261s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 43s</item>
- <item>ROI estimation of 'lpba40' atlas 12s</item>
- <item>ROI estimation of 'hammers' atlas 30s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 11s</item>
- <item>ROI estimation of 'aal3' atlas 17s</item>
- <item>ROI estimation of 'mori' atlas 24s</item>
- <item>ROI estimation of 'anatomy3' atlas 35s</item>
- <item>ROI estimation of 'julichbrain' atlas 48s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 71s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 104s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 10s</item>
- <item>470s</item>
- <item>Quality check: 15s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/report/catreport_sub-0027237_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 65 minute(s) and 23 second(s).</item>
- <item>Image Quality Rating (IQR): 83.95% (B)</item>
- <item>GM volume (GMV): 46.80% (781.29 / 1669.42 ml)</item>
- <item>GM thickness (GMT): 2.44 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1726780/ds/IBA_TRT/sub-0027237/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|