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- <opts>
- <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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- <biasfwhm>60</biasfwhm>
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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>
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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
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- <SLC>0</SLC>
- <mrf>1</mrf>
- <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>
- <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>
- <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>
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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>
- <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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- <td>[false]</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>
- <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>
- <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/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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- <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>
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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>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <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_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_1726829/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</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>
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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>
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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>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.15470153175907</SurfaceDefectArea>
- <SurfaceDefectNumber>6.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.060332216322422</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0605324432253838</SurfacePositionRMSE>
- <res_vx_vol>[0.999893188476562 1 1]</res_vx_vol>
- <res_vx_voli>[0.999893188476562 1 1]</res_vx_voli>
- <res_RMS>0.999964397426533</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[3.4909999370575 13.0719995498657 159.055999755859 317.386993408203]</tissue_mn>
- <tissue_mnr>[0.010999190621078 0.0411863103508949 0.501142144203186 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.57546120967218 30.0483860462154 40.4681068373766 29.1071556709994]</tissue_std>
- <tissue_stdr>[0.00820482335984707 0.0957272052764893 0.128922030329704 0.0927286595106125]</tissue_stdr>
- <contrast>105.515991210938</contrast>
- <contrastr>0.332452148199081</contrastr>
- <res_ECR>0.388297259807587</res_ECR>
- <NCR>0.10349940508604</NCR>
- <ICR>0.331940710544586</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99978637695312 2 2]</res_vx_vol>
- <res_RMS>1.99992879485307</res_RMS>
- <res_ECR>2.87906742095947</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[8.62389755249023 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>3.09655094146729</contrastr>
- <NCR>1.81681609153748</NCR>
- <ICR>1.28308701515198</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.03867538293977</SurfaceDefectArea>
- <SurfaceDefectNumber>1.325</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.20664429664612</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.21064889431</SurfacePositionRMSE>
- <SIQR>2.53371299229443</SIQR>
- <IQR>1.92341330103904</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>20231031-015115</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.15470153175907</SurfaceDefectArea>
- <SurfaceDefectNumber>6.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.060332216322422</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0605324432253838</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.15470153175907</defect_size>
- <vol_abs_CGW>[262.623475201775 593.461012596938 427.647270405309 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.220066687909295</vol_abs_WMH>
- <vol_rel_WMH>0.000171427314548309</vol_rel_WMH>
- <surf_TSA>1680.5463568297</surf_TSA>
- <vol_TIV>1283.73175820402</vol_TIV>
- <vol_rel_CGW>[0.204578155462316 0.462293628559293 0.333128215978391 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.5477111738583 0.662232669285646]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.52235341072083 0.841227966695998 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.93095096762756 0.270203272435359 0.33054051668334;2.59293010729694 0.194716575998721 0.430765609368564;3.33877892338511 0.308945293242782 0.238693873948096]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.842343385512164 0.276058722050632 0.525194494314782;4.40407946484198 0.355841509735819 0.474805505685218]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.31536543577437</vol_TIV>
- <vol_rel_CGW>[1.52403296448125 6.15254361636661 3.83276249961191 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01714273145483</vol_rel_WMH>
- <surf_TSA>8.47359711406137</surf_TSA>
- <SQR>5.04547099767533</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11533.104 0.468132226392909]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00142961659003049 0.00120199588127434 0.0577674023807049]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[757.459627117202 366.713159957886 432.812118681066 427.645545099416 835.014758136884 9218.45923361421]</SPMvols0>
- <SPMvols1>[657.753634866512 342.816073499074 241.135845083259 367.543526157693 686.856365243171 9237.36228492306]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[25.2649993896484 173.218597412109 325.468505859375]</T3th>
- <Tth>
- <T3th>[-3.32342004776001 -3.32342195510864 1.66874587535858 25.2649993896484 173.218597412109 325.468505859375 475.570251464844 736.586853027344]</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>[0.0226972084492445 0.0808005109429359 0.0899798050522804 0 0]</dtc>
- <ll>[0.0856743820575105 0 0.0856743820575105 0;0.195675761759782 0.0118299280466581 0.20750568980644 2522.70849609375;0.195675761759782 0.0118299280466581 0.20750568980644 2522.70849609375]</ll>
- <rmsdtc>[0.0492073819041252 0.10689514875412 0.119462586939335]</rmsdtc>
- <rmsgdt>[0.0348284542560577 0.0489789098501205 0.0603191889822483]</rmsgdt>
- <rmsdt>0.119462586939335</rmsdt>
- <dt>0.0899798050522804</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>[0.0107237035408616 0.0411013029515743 0.0565267838537693 0.0662772282958031 0.0729770436882973 0.0822017043828964]</dtc>
- <ll>[0.0876149433484199 0 0.0876149433484199 0;0.223775091575092 0.0175360023656899 0.241311093940781 8976.2412109375;0.203071853741497 0.0195391321133488 0.222610985854845 14062.5478515625;0.179959796206338 0.0214045597956731 0.201364356002011 23079.9375;0.161855733233944 0.0240302325345428 0.185885965768487 42037.359375;0.161855733233944 0.0240302325345428 0.185885965768487 42037.359375]</ll>
- <rmsdtc>[0.0123847797513008 0.0448241606354713 0.0687799155712128 0.0959276556968689 0.11960194259882 0.126214027404785]</rmsdtc>
- <rmsgdt>[0.00342095666565001 0.0137430746108294 0.0306103471666574 0.0520943440496922 0.0692975372076035 0.0748066604137421]</rmsgdt>
- <rmsdt>0.126214027404785</rmsdt>
- <dt>0.0822017043828964</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027250/ses-1/sub-0027250_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 53s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>43s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 13s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 15s</item>
- <item>Use initial fine affine registration. 71s</item>
- <item>SPM preprocessing 1 (estimate 2): 60s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 20s</item>
- <item>Update Segmentation 20s</item>
- <item>Update Skull-Stripping 47s</item>
- <item>Update probability maps 10s</item>
- <item>96s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 29s</item>
- <item>Fast Optimized Shooting registration 38s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 15s</item>
- <item>Estimate local tissue thresholds (WM) 21s</item>
- <item>Estimate local tissue thresholds (GM) 32s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 49s</item>
- <item>127s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 13s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 23s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 5s</item>
- <item>67s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 36s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.37 0.05,0.68 0.08,0.99 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) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>12s</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 | 0.0876 0.0000 0.0876 | 32.0000</item>
- <item>2 | 2.50 | 0.0844 0.0013 0.0858 | 29.4886</item>
- <item>3 | 2.50 | 0.0835 0.0020 0.0855 | 26.9772</item>
- <item>4 | 2.50 | 0.0830 0.0023 0.0853 | 24.6107</item>
- <item>5 | 2.50 | 0.0827 0.0025 0.0851 | 22.6548</item>
- <item>6 | 2.50 | 0.0824 0.0026 0.0849 | 20.6989</item>
- <item>7 | 2.50 | 0.0820 0.0027 0.0847 | 18.9688</item>
- <item>8 | 2.50 | 0.0817 0.0028 0.0845 | 17.4455</item>
- <item>9 | 2.50 | 0.0813 0.0029 0.0842 | 15.9223</item>
- <item>10 | 2.50 | 0.0810 0.0030 0.0840 | 14.6627</item>
- <item>11 | 2.50 | 0.0806 0.0031 0.0837 | 13.4764</item>
- <item>12 | 2.50 | 0.0802 0.0032 0.0834 | 12.3015</item>
- <item>13 | 2.50 | 0.0798 0.0033 0.0832 | 11.3776</item>
- <item>14 | 2.50 | 0.0795 0.0034 0.0829 | 10.4537</item>
- <item>15 | 2.25 | 0.0794 0.0035 0.0829 | 9.5920</item>
- <item>16 | 2.25 | 0.0760 0.0052 0.0812 | 8.8725</item>
- <item>17 | 2.25 | 0.0746 0.0058 0.0804 | 8.1530</item>
- <item>29 | 2.00 | 0.0764 0.0027 0.0791 | 3.3283</item>
- <item>30 | 2.00 | 0.0700 0.0054 0.0754 | 3.1221</item>
- <item>31 | 2.00 | 0.0677 0.0065 0.0742 | 2.9160</item>
- <item>43 | 1.75 | 0.0664 0.0037 0.0702 | 1.5785</item>
- <item>44 | 1.75 | 0.0616 0.0063 0.0679 | 1.5194</item>
- <item>45 | 1.75 | 0.0600 0.0071 0.0671 | 1.4626</item>
- <item>57 | 1.50 | 0.0583 0.0052 0.0636 | 1.0900</item>
- <item>58 | 1.50 | 0.0550 0.0074 0.0624 | 1.0730</item>
- <item>59 | 1.50 | 0.0540 0.0080 0.0620 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 196s</item>
- <item>Prepare output 13s</item>
- <item>209s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.069 0.096 0.120 | 0.126214</item>
- <item>Template Matching: 0.088 0.224 0.203 0.180 0.162 | 0.161856</item>
- <item>Write result maps: 39s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 36s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 50s</item>
- <item>109s</item>
- <item>Create initial surface 91s</item>
- <item>Topology correction: 86s</item>
- <item>Surface refinement: 100s</item>
- <item>Reduction of surface collisions with optimization: 62s</item>
- <item>Spherical mapping with areal smoothing 93s</item>
- <item>Spherical registration 363s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 50s</item>
- <item>104s</item>
- <item>Create initial surface 89s</item>
- <item>Topology correction: 84s</item>
- <item>Surface refinement: 99s</item>
- <item>Reduction of surface collisions with optimization: 60s</item>
- <item>Spherical mapping with areal smoothing 85s</item>
- <item>Spherical registration 357s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5477 0.6622 mm</item>
- <item>Surface intensity / position RMSE: 0.0603 / 0.0605</item>
- <item>Euler number / defect number / defect size: 8.0 / 6.5 / 0.15%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/surf/lh.thickness.sub-0027250_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/surf/rh.thickness.sub-0027250_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/sub-0027250_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1881s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 35s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 24s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 14s</item>
- <item>ROI estimation of 'mori' atlas 21s</item>
- <item>ROI estimation of 'anatomy3' atlas 29s</item>
- <item>ROI estimation of 'julichbrain' atlas 40s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>402s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/report/catreport_sub-0027250_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 55 minute(s) and 6 second(s).</item>
- <item>Image Quality Rating (IQR): 85.77% (B)</item>
- <item>GM volume (GMV): 46.23% (593.46 / 1283.73 ml)</item>
- <item>GM thickness (GMT): 2.55 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1726829/ds/IBA_TRT/sub-0027250/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|