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- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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- <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_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>
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- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
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- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
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- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
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- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <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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- <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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- <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>
- <td>
- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_3499898/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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- <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>
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- <MB>13</MB>
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- <VT>15</VT>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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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_1_GS.nii</item>
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- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <SurfaceEulerNumber>42</SurfaceEulerNumber>
- <SurfaceDefectArea>1.3432613449351</SurfaceDefectArea>
- <SurfaceDefectNumber>26.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.071809396147728</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0758583471179008</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>178.430587768555</res_BB>
- <tissue_mn>[9.99600028991699 40.2690010070801 169.824005126953 306.652008056641]</tissue_mn>
- <tissue_mnr>[0.0325972102582455 0.131318241357803 0.553800404071808 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[6.95319823474023 37.3365592294182 38.6511086440696 26.6224223159096]</tissue_std>
- <tissue_stdr>[0.0234385896474123 0.125858098268509 0.130289316177368 0.0897417291998863]</tissue_stdr>
- <contrast>104.594833374023</contrast>
- <contrastr>0.3410864174366</contrastr>
- <res_ECR>0.39129239320755</res_ECR>
- <NCR>0.159337103366852</NCR>
- <ICR>0.379550516605377</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.89434885978699</res_ECR>
- <res_BB>10.5</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>2.96703696250916</contrastr>
- <NCR>2.61839079856873</NCR>
- <ICR>1.40116691589355</ICR>
- <SurfaceEulerNumber>3.04081632653061</SurfaceEulerNumber>
- <SurfaceDefectArea>1.33581533623378</SurfaceDefectArea>
- <SurfaceDefectNumber>2.325</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.4361879825592</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.51716685295105</SurfacePositionRMSE>
- <SIQR>2.65425993888407</SIQR>
- <IQR>2.43420600247476</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>20231031-005139</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>42</SurfaceEulerNumber>
- <SurfaceDefectArea>1.3432613449351</SurfaceDefectArea>
- <SurfaceDefectNumber>26.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.071809396147728</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0758583471179008</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>42</EC_abs>
- <defect_size>1.3432613449351</defect_size>
- <vol_abs_CGW>[255.879435294118 762.565294117647 487.807090196078 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.266796078431373</vol_abs_WMH>
- <vol_rel_WMH>0.000177125813199571</vol_rel_WMH>
- <surf_TSA>1986.28024000421</surf_TSA>
- <vol_TIV>1506.25181960784</vol_TIV>
- <vol_rel_CGW>[0.169878258046345 0.5062668035921 0.323854938361555 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.69005162930414 0.681655794519112]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.70987343788147 0.828806576675373 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.9972872366567 0.278882624206549 0.285577309702762;2.71668352197515 0.20113138526812 0.417815718660109;3.42849141819439 0.298113290832169 0.296606971637128]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.891485140357267 0.306438857344513 0.579944767165032;4.38508894167312 0.295209444874027 0.420055232834968]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.26428184613498</vol_TIV>
- <vol_rel_CGW>[0.90083078387832 6.94229173117996 3.66621656540149 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01771258131996</vol_rel_WMH>
- <surf_TSA>8.62086217670831</surf_TSA>
- <SQR>5.68144797597759</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.336 0.512504276009963]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0493877567350864 0.0481504276394844 0.261458337306976]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[911.687984313725 438.439964705882 397.969682352941 441.73622745098 2003.98749411765 8181.49034509804]</SPMvols0>
- <SPMvols1>[799.764062745098 409.644819607843 213.646290196078 501.758443137255 1372.0863254902 8237.65135294118]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[44.6976013183594 184.843399047852 300.163391113281]</T3th>
- <Tth>
- <T3th>[-2.60253000259399 -2.60252618789673 14.8953504562378 44.6976013183594 184.843399047852 300.163391113281 427.896301269531 1164.39379882812]</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>[0.0226867012679577 0.0859162881970406 0.0960885211825371 0 0]</dtc>
- <ll>[0.0865846155356674 0 0.0865846155356674 0;0.193106679927831 0.0123495889597294 0.20545626888756 2633.52514648438;0.193106679927831 0.0123495889597294 0.20545626888756 2633.52514648438]</ll>
- <rmsdtc>[0.0514942109584808 0.113752014935017 0.126790851354599]</rmsdtc>
- <rmsgdt>[0.0368057936429977 0.0527076050639153 0.065097764134407]</rmsgdt>
- <rmsdt>0.126790851354599</rmsdt>
- <dt>0.0960885211825371</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>[0.0108916237950325 0.0417870283126831 0.0594545751810074 0.0686122328042984 0.07523363083601 0.0852916911244392]</dtc>
- <ll>[0.0858178321964078 0 0.0858178321964078 0;0.220547893772894 0.0162231227106227 0.236771016483516 8304.2109375;0.196918068442655 0.0190653911846857 0.215983459627341 13721.5908203125;0.174978084147599 0.0207033637355649 0.195681447883164 22323.857421875;0.15825409808655 0.0234579517577356 0.181712049844285 41036.23828125;0.15825409808655 0.0234579517577356 0.181712049844285 41036.23828125]</ll>
- <rmsdtc>[0.0125941140577197 0.0471421889960766 0.0709446147084236 0.0991600304841995 0.123872429132462 0.130892470479012]</rmsdtc>
- <rmsgdt>[0.00350918923504651 0.0142644932493567 0.031489934772253 0.0535448417067528 0.0724692344665527 0.07817442715168]</rmsgdt>
- <rmsdt>0.130892470479012</rmsdt>
- <dt>0.0852916911244392</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027121/ses-3/sub-0027121_ses-3_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 169s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 9s</item>
- <item>Refine background 4s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 8s</item>
- <item>52s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 98s</item>
- <item>SPM preprocessing 1 (estimate 2): 82s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 24s</item>
- <item>Update Skull-Stripping 52s</item>
- <item>Update probability maps 11s</item>
- <item>108s</item>
- <item>Global intensity correction: 21s</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 3s</item>
- <item>Prepare segments (LASmod = 1.10) 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) 55s</item>
- <item>146s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 22s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 31s</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>91s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 43s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</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 | 0.0858 0.0000 0.0858 | 32.0000</item>
- <item>2 | 2.50 | 0.0821 0.0015 0.0836 | 29.4886</item>
- <item>3 | 2.50 | 0.0811 0.0022 0.0833 | 26.9772</item>
- <item>4 | 2.50 | 0.0805 0.0025 0.0831 | 24.6107</item>
- <item>5 | 2.50 | 0.0801 0.0027 0.0828 | 22.6548</item>
- <item>6 | 2.50 | 0.0798 0.0028 0.0826 | 20.6989</item>
- <item>7 | 2.50 | 0.0794 0.0029 0.0823 | 18.9688</item>
- <item>8 | 2.50 | 0.0790 0.0030 0.0821 | 17.4455</item>
- <item>9 | 2.50 | 0.0787 0.0031 0.0818 | 15.9223</item>
- <item>10 | 2.50 | 0.0782 0.0033 0.0815 | 14.6627</item>
- <item>11 | 2.50 | 0.0778 0.0034 0.0812 | 13.4764</item>
- <item>12 | 2.50 | 0.0774 0.0034 0.0809 | 12.3015</item>
- <item>13 | 2.50 | 0.0770 0.0036 0.0805 | 11.3776</item>
- <item>14 | 2.50 | 0.0766 0.0036 0.0802 | 10.4537</item>
- <item>15 | 2.25 | 0.0769 0.0037 0.0807 | 9.5920</item>
- <item>16 | 2.25 | 0.0735 0.0054 0.0789 | 8.8725</item>
- <item>29 | 2.00 | 0.0749 0.0025 0.0773 | 3.3283</item>
- <item>30 | 2.00 | 0.0680 0.0052 0.0733 | 3.1221</item>
- <item>31 | 2.00 | 0.0656 0.0064 0.0720 | 2.9160</item>
- <item>43 | 1.75 | 0.0645 0.0037 0.0682 | 1.5785</item>
- <item>44 | 1.75 | 0.0599 0.0061 0.0660 | 1.5194</item>
- <item>45 | 1.75 | 0.0583 0.0069 0.0652 | 1.4626</item>
- <item>57 | 1.50 | 0.0570 0.0051 0.0621 | 1.0900</item>
- <item>58 | 1.50 | 0.0538 0.0071 0.0610 | 1.0730</item>
- <item>59 | 1.50 | 0.0528 0.0078 0.0606 | 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): 0.013 0.047 0.071 0.099 0.124 | 0.130892</item>
- <item>Template Matching: 0.086 0.221 0.197 0.175 0.158 | 0.158254</item>
- <item>Write result maps: 63s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 63s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 62s</item>
- <item>154s</item>
- <item>Create initial surface 109s</item>
- <item>Topology correction: 119s</item>
- <item>Surface refinement: 99s</item>
- <item>Reduction of surface collisions with optimization: 85s</item>
- <item>Spherical mapping with areal smoothing 103s</item>
- <item>Spherical registration 322s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 42s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 62s</item>
- <item>132s</item>
- <item>Create initial surface 102s</item>
- <item>Topology correction: 115s</item>
- <item>Surface refinement: 89s</item>
- <item>Reduction of surface collisions with optimization: 79s</item>
- <item>Spherical mapping with areal smoothing 104s</item>
- <item>Spherical registration 329s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6900 0.6815 mm</item>
- <item>Surface intensity / position RMSE: 0.0718 / 0.0759</item>
- <item>Euler number / defect number / defect size: 42.0 / 26.5 / 1.34%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/surf/lh.thickness.sub-0027121_ses-3_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/surf/rh.thickness.sub-0027121_ses-3_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/sub-0027121_ses-3_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2065s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 15s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 57s</item>
- <item>ROI estimation of 'lpba40' atlas 17s</item>
- <item>ROI estimation of 'hammers' atlas 41s</item>
- <item>ROI estimation of 'thalamus' atlas 4s</item>
- <item>ROI estimation of 'ibsr' atlas 14s</item>
- <item>ROI estimation of 'aal3' atlas 26s</item>
- <item>ROI estimation of 'mori' atlas 38s</item>
- <item>ROI estimation of 'anatomy3' atlas 55s</item>
- <item>ROI estimation of 'julichbrain' atlas 74s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 55s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 108s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 117s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 11s</item>
- <item>663s</item>
- <item>Quality check: 15s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/report/catreport_sub-0027121_ses-3_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 67 minute(s) and 37 second(s).</item>
- <item>Image Quality Rating (IQR): 80.66% (B-)</item>
- <item>GM volume (GMV): 50.63% (762.57 / 1506.25 ml)</item>
- <item>GM thickness (GMT): 2.69 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3499898/ds/NYU_1/sub-0027121/ses-3/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|