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- <filedata>
- <path>/var/lib/condor/execute/dir_21556/ds/sub-season129</path>
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- <F>/var/lib/condor/execute/dir_21556/ds/sub-season129/sub-season129_ses-3_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_21556/ds/sub-season129/mri/msub-season129_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_21556/ds/sub-season129/mri/p0sub-season129_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season129/..son129_ses-3_acq-MPrageHiRes_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <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>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <accstr>0.5</accstr>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
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- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <extopts>
- <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>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>32</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>
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- </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>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</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/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</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/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_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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- </atlas>
- <satlas>
- <tr>
- <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>
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- <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>
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- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
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- <PH>25</PH>
- <LE>27</LE>
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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- </darteltpms>
- <shootingtpms>
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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_3_GS.nii</item>
- <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>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.131102010287254</SurfaceDefectArea>
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- <SurfaceIntensityRMSE>0.0651634633541107</SurfaceIntensityRMSE>
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- <res_RMS>0.876669894272699</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.3509998321533 304.757446289062 764.680969238281 1112.677734375]</tissue_mn>
- <tissue_mnr>[0.0093027837574482 0.273895531892776 0.6872438788414 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[19.3256444823708 121.96517131855 101.15580452638 60.3176489689092]</tissue_std>
- <tissue_stdr>[0.0175316836684942 0.11064338684082 0.0917657166719437 0.0547184832394123]</tissue_stdr>
- <contrast>351.264495849609</contrast>
- <contrastr>0.315692931413651</contrastr>
- <NCR>0.0994341447949409</NCR>
- <ICR>0.264881372451782</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.76000033750929 1.75000007323593 1.74999994226592]</res_vx_vol>
- <res_RMS>1.7533397885454</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62400054931641 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>3.34793925285339</contrastr>
- <NCR>1.75845742225647</NCR>
- <ICR>1.11676931381226</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.03277550257181</SurfaceDefectArea>
- <SurfaceDefectNumber>1.675</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30326926708221</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.28480613231659</SurfacePositionRMSE>
- <IQR>1.75591165622767</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_BB>brain next to the image boundary</res_BB>
- <tissue_mn>mean within the tissue classes</tissue_mn>
- <tissue_std>standard deviation within the tissue classes</tissue_std>
- <contrast>contrast between tissue classes</contrast>
- <contrastr>contrast between tissue classes</contrastr>
- <NCR>noise to contrast ratio</NCR>
- <ICR>inhomogeneity to contrast ratio</ICR>
- <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
- <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
- <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
- <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
- </qualitymeasures>
- <subjectmeasures>
- <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
- <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
- <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
- <surf_TSA>total surface area</surf_TSA>
- </subjectmeasures>
- </ratings_help>
- <software>
- <version_segment>1639</version_segment>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>1980</revision_cat>
- <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
- <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
- <qamethod>cat12</qamethod>
- <date>20220712-165916</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.131102010287254</SurfaceDefectArea>
- <SurfaceDefectNumber>13.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0651634633541107</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0642403066158295</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.131102010287254</defect_size>
- <vol_abs_CGW>[224.289330471361 680.650553128724 471.084509832958 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.579641767408977</vol_abs_WMH>
- <vol_rel_WMH>0.000421243816734112</vol_rel_WMH>
- <surf_TSA>1909.00397479977</surf_TSA>
- <vol_TIV>1376.02439343304</vol_TIV>
- <vol_rel_CGW>[0.162998077317351 0.494650063165355 0.342351859517293 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.56227924581758 0.592842321926667]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55543375015259 0.763316364985756 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.00217039000827 0.242155874418809 0.297497234060661;2.57814900246778 0.165296930968471 0.427925185432501;3.19103320487476 0.261720753849122 0.274577580506838]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.904149895378969 0.384585296873061 0.537169517884915;4.2147454441021 0.400040231477014 0.462830482115086]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.01368302446583</vol_TIV>
- <vol_rel_CGW>[0.777264319636342 6.73365774363066 3.99841701719277 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04212438167341</vol_rel_WMH>
- <surf_TSA>8.61455225462411</surf_TSA>
- <SQR>5.51711996032065</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.342088971819196 1 1 6507.19738550516 0.332002854087158]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00547702796757221 0 0.15945690870285]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[806.373032561737 417.438764925453 316.290137742761 446.924884445949 2175.59955669833 6181.71077937476]</SPMvols0>
- <SPMvols1>[725.74253550294 396.323533658271 203.020465679781 344.884106406837 1321.62364413155 6899.13438200685]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[361.308685302734 797.2548828125 1100.06481933594]</T3th>
- <Tth>
- <T3th>[0 0 14.9114665985107 361.308685302734 797.2548828125 1100.06481933594 1469.44287109375 2560.64379882812]</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>[0.0213332716375589 0.0728474855422974 0.0798874273896217 0 0]</dtc>
- <ll>[0.0822150454420049 0 0.0822150454420049 0;0.191044160584156 0.0095733605942377 0.200617521178393 2041.5;0.191044160584156 0.0095733605942377 0.200617521178393 2041.5]</ll>
- <rmsdtc>[0.0462425090372562 0.09447231143713 0.104050785303116]</rmsdtc>
- <rmsgdt>[0.0330986604094505 0.0417820401489735 0.0512457825243473]</rmsgdt>
- <rmsdt>0.104050785303116</rmsdt>
- <dt>0.0798874273896217</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>[0.0102289458736777 0.0367313027381897 0.0505435988306999 0.0581050217151642 0.0643587112426758 0.0720409527420998]</dtc>
- <ll>[0.0833759793587577 0 0.0833759793587577 0;0.214931059218559 0.0136158844627595 0.228546943681319 6969.630859375;0.194761845710506 0.0159281486031913 0.210689994313698 11463.6796875;0.175019049576545 0.0179268238324838 0.192945873409029 19329.9921875;0.157975780902997 0.0207718939516496 0.178747674854646 36337.375;0.157975780902997 0.0207718939516496 0.178747674854646 36337.375]</ll>
- <rmsdtc>[0.0118997497484088 0.042020034044981 0.0611301623284817 0.083996869623661 0.106241211295128 0.11356807500124]</rmsdtc>
- <rmsgdt>[0.00327152735553682 0.012421602383256 0.0272421110421419 0.0473973639309406 0.0650224760174751 0.0705485939979553]</rmsgdt>
- <rmsdt>0.11356807500124</rmsdt>
- <dt>0.0720409527420998</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season129_ses-3_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 39s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 9s</item>
- <item>Initial correction 18s</item>
- <item>Refine background 4s</item>
- <item>Final correction 13s</item>
- <item>Final scaling 9s</item>
- <item>68s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 14s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 101s</item>
- <item>SPM preprocessing 1 (estimate 2): 84s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 25s</item>
- <item>Update Skull-Stripping 53s</item>
- <item>Update probability maps 11s</item>
- <item>110s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 12s</item>
- <item>Fast Optimized Shooting registration 35s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 6s</item>
- <item>Prepare segments (LASmod = 1.00) 19s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 32s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 32s</item>
- <item>121s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 25s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 38s</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>102s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</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 | 0.0834 0.0000 0.0834 | 32.0000</item>
- <item>2 | 2.50 | 0.0805 0.0013 0.0818 | 29.4886</item>
- <item>3 | 2.50 | 0.0797 0.0019 0.0816 | 26.9772</item>
- <item>4 | 2.50 | 0.0793 0.0021 0.0814 | 24.6107</item>
- <item>5 | 2.50 | 0.0789 0.0023 0.0812 | 22.6548</item>
- <item>6 | 2.50 | 0.0787 0.0024 0.0810 | 20.6989</item>
- <item>7 | 2.50 | 0.0784 0.0025 0.0808 | 18.9688</item>
- <item>8 | 2.50 | 0.0781 0.0026 0.0806 | 17.4455</item>
- <item>9 | 2.50 | 0.0778 0.0026 0.0804 | 15.9223</item>
- <item>10 | 2.50 | 0.0774 0.0028 0.0802 | 14.6627</item>
- <item>11 | 2.50 | 0.0771 0.0028 0.0799 | 13.4764</item>
- <item>12 | 2.50 | 0.0768 0.0029 0.0797 | 12.3015</item>
- <item>13 | 2.50 | 0.0764 0.0030 0.0794 | 11.3776</item>
- <item>14 | 2.50 | 0.0761 0.0030 0.0792 | 10.4537</item>
- <item>15 | 2.25 | 0.0746 0.0031 0.0777 | 9.5920</item>
- <item>16 | 2.25 | 0.0716 0.0045 0.0762 | 8.8725</item>
- <item>29 | 2.00 | 0.0726 0.0020 0.0746 | 3.3283</item>
- <item>30 | 2.00 | 0.0669 0.0044 0.0712 | 3.1221</item>
- <item>31 | 2.00 | 0.0649 0.0053 0.0702 | 2.9160</item>
- <item>43 | 1.75 | 0.0639 0.0031 0.0669 | 1.5785</item>
- <item>44 | 1.75 | 0.0598 0.0052 0.0650 | 1.5194</item>
- <item>45 | 1.75 | 0.0583 0.0060 0.0643 | 1.4626</item>
- <item>57 | 1.50 | 0.0566 0.0044 0.0610 | 1.0900</item>
- <item>58 | 1.50 | 0.0537 0.0063 0.0599 | 1.0730</item>
- <item>59 | 1.50 | 0.0527 0.0069 0.0596 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 157s</item>
- <item>Prepare output 11s</item>
- <item>168s</item>
- <item>Jacobian determinant (RMS): 0.012 0.042 0.061 0.084 0.106 | 0.113568</item>
- <item>Template Matching: 0.083 0.215 0.195 0.175 0.158 | 0.157976</item>
- <item>Write result maps: 27s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 42s</item>
- <item>93s</item>
- <item>Create initial surface 80s</item>
- <item>Topology correction: 91s</item>
- <item>Surface refinement: 65s</item>
- <item>Reduction of surface collisions with optimization: 63s</item>
- <item>Spherical mapping with areal smoothing 82s</item>
- <item>Spherical registration 301s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 43s</item>
- <item>102s</item>
- <item>Create initial surface 79s</item>
- <item>Topology correction: 86s</item>
- <item>Surface refinement: 67s</item>
- <item>Reduction of surface collisions with optimization: 62s</item>
- <item>Spherical mapping with areal smoothing 76s</item>
- <item>Spherical registration 276s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5623 0.5926 mm</item>
- <item>Surface intensity / position RMSE: 0.0652 / 0.0642</item>
- <item>Euler number / defect number / defect size: 8.0 / 13.5 / 0.13%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_21556/ds/sub-season129/surf/lh.thickness.sub-season129_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_21556/ds/sub-season129/surf/rh.thickness.sub-season129_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_21556/ds/sub-season129/sub-season129_ses-3_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1613s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 34s</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 20s</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 28s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 95s</item>
- <item>Write results 95s</item>
- <item>395s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_21556/ds/sub-season129/report/catreport_sub-season129_ses-3_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 51 minute(s) and 41 second(s).</item>
- <item>Image Quality Rating (IQR): 87.44% (B+)</item>
- <item>GM volume (GMV): 49.47% (680.65 / 1376.02 ml)</item>
- <item>GM thickness (GMT): 2.56 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_21556/ds/sub-season129/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_21556/ds/sub-season129/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_21556/ds/sub-season129/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|