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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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- <WMHC>2</WMHC>
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- <SLC>0</SLC>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <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>
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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>
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- <reduce_mesh>1</reduce_mesh>
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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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <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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- <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>
- <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/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>
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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/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_92055/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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- <satlas>
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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>
- <BV>7</BV>
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- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <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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- <LASmyostr>0</LASmyostr>
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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_1_GS.nii</item>
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- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.46080700776894</SurfaceDefectArea>
- <SurfaceDefectNumber>7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0615805462002754</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0621420443058014</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>189.552017211914</res_BB>
- <tissue_mn>[7.03000020980835 70.7419967651367 208.667999267578 340.230010986328]</tissue_mn>
- <tissue_mnr>[0.0206624921411276 0.207924038171768 0.613314509391785 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[4.79958836139412 36.6568504850816 38.1526417227139 24.9578509427771]</tissue_std>
- <tissue_stdr>[0.0144045259803534 0.110014550387859 0.114503718912601 0.0749035105109215]</tissue_stdr>
- <contrast>120.565452575684</contrast>
- <contrastr>0.354364544153214</contrastr>
- <res_ECR>0.376297175884247</res_ECR>
- <NCR>0.144304305315018</NCR>
- <ICR>0.31567907333374</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.81784272193909</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>2.76786518096924</contrastr>
- <NCR>2.40258836746216</NCR>
- <ICR>1.242755651474</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11520175194224</SurfaceDefectArea>
- <SurfaceDefectNumber>1.35</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.23161089420319</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.24284088611603</SurfacePositionRMSE>
- <SIQR>2.5486798347298</SIQR>
- <IQR>2.26106976492313</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>20231031-004020</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.46080700776894</SurfaceDefectArea>
- <SurfaceDefectNumber>7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0615805462002754</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0621420443058014</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.46080700776894</defect_size>
- <vol_abs_CGW>[283.347137254902 716.854482352941 527.754866666667 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.408725490196078</vol_abs_WMH>
- <vol_rel_WMH>0.000267498121751255</vol_rel_WMH>
- <surf_TSA>2091.24260648347</surf_TSA>
- <vol_TIV>1527.95648627451</vol_TIV>
- <vol_rel_CGW>[0.185441889085313 0.469158964140915 0.345399146773772 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50657260248076 0.596659286268077]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.50624084472656 0.725328901059574 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92893864220907 0.23802500359064 0.292780598854662;2.5281432821683 0.167959393441888 0.440441857310521;3.14897607280478 0.263125090064276 0.266777543834817]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.912351778884249 0.330929822614937 0.521245964575517;4.11034447325151 0.373146018487534 0.478754035424483]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.38027214186902</vol_TIV>
- <vol_rel_CGW>[1.18035001949197 6.27584346517448 4.05314559579332 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02674981217513</vol_rel_WMH>
- <surf_TSA>8.62338622035984</surf_TSA>
- <SQR>5.15133302326396</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11141.12 0.356248493418536]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00146424630656838 0.00121899414807558 0.0359685458242893]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[876.527094117647 463.083180392157 496.449192156863 502.516960784314 959.761831372549 8395.33199215686]</SPMvols0>
- <SPMvols1>[763.551650980392 435.700384313726 284.169325490196 442.498901960784 836.595466666667 8379.45983137255]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[82.9602966308594 227.918197631836 337.839904785156]</T3th>
- <Tth>
- <T3th>[-4.65846014022827 -4.65846109390259 3.50691437721252 82.9602966308594 227.918197631836 337.839904785156 465.279724121094 825.258178710938]</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>[0.0195431839674711 0.0733532607555389 0.0807426050305367 0 0]</dtc>
- <ll>[0.0843363956910889 0 0.0843363956910889 0;0.196437968497946 0.0107261524910257 0.207164120988972 2287.33056640625;0.196437968497946 0.0107261524910257 0.207164120988972 2287.33056640625]</ll>
- <rmsdtc>[0.047125767916441 0.0963740646839142 0.107093974947929]</rmsdtc>
- <rmsgdt>[0.0345513634383678 0.0458367429673672 0.0559484921395779]</rmsgdt>
- <rmsdt>0.107093974947929</rmsdt>
- <dt>0.0807426050305367</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>[0.00900911912322044 0.0333918556571007 0.0478941015899181 0.0565233044326305 0.0631170123815536 0.0699590519070625]</dtc>
- <ll>[0.0844688438948323 0 0.0844688438948323 0;0.219775671550672 0.0138870917277167 0.233662763278388 7108.455078125;0.197787448312658 0.0170591864132806 0.214846634725939 12277.701171875;0.177499551945149 0.0189181053400719 0.196417657285221 20398.86328125;0.160252676275171 0.0216290970325886 0.18188177330776 37836.92578125;0.160252676275171 0.0216290970325886 0.18188177330776 37836.92578125]</ll>
- <rmsdtc>[0.0105997174978256 0.0388803742825985 0.0584290139377117 0.0813563317060471 0.102048590779305 0.108638189733028]</rmsdtc>
- <rmsgdt>[0.00328695704229176 0.0128677058964968 0.0269839391112328 0.0448479913175106 0.0604448243975639 0.0657031163573265]</rmsgdt>
- <rmsdt>0.108638189733028</rmsdt>
- <dt>0.0699590519070625</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025627/ses-1/sub-0025627_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 65s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>44s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 95s</item>
- <item>SPM preprocessing 1 (estimate 2): 106s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 49s</item>
- <item>Update probability maps 10s</item>
- <item>105s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 34s</item>
- <item>Fast Optimized Shooting registration 41s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.05) 17s</item>
- <item>Estimate local tissue thresholds (WM) 24s</item>
- <item>Estimate local tissue thresholds (GM) 37s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 51s</item>
- <item>141s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 16s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 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>83s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 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 | 0.0845 0.0000 0.0845 | 32.0000</item>
- <item>2 | 2.50 | 0.0818 0.0012 0.0830 | 29.4886</item>
- <item>3 | 2.50 | 0.0810 0.0018 0.0828 | 26.9772</item>
- <item>4 | 2.50 | 0.0806 0.0021 0.0826 | 24.6107</item>
- <item>5 | 2.50 | 0.0802 0.0022 0.0824 | 22.6548</item>
- <item>6 | 2.50 | 0.0799 0.0023 0.0822 | 20.6989</item>
- <item>7 | 2.50 | 0.0796 0.0024 0.0821 | 18.9688</item>
- <item>8 | 2.50 | 0.0793 0.0025 0.0819 | 17.4455</item>
- <item>9 | 2.50 | 0.0790 0.0026 0.0816 | 15.9223</item>
- <item>10 | 2.50 | 0.0787 0.0027 0.0814 | 14.6627</item>
- <item>11 | 2.50 | 0.0784 0.0028 0.0812 | 13.4764</item>
- <item>12 | 2.50 | 0.0780 0.0029 0.0809 | 12.3015</item>
- <item>13 | 2.50 | 0.0777 0.0030 0.0807 | 11.3776</item>
- <item>14 | 2.50 | 0.0774 0.0030 0.0804 | 10.4537</item>
- <item>15 | 2.25 | 0.0762 0.0031 0.0794 | 9.5920</item>
- <item>16 | 2.25 | 0.0733 0.0046 0.0779 | 8.8725</item>
- <item>29 | 2.00 | 0.0744 0.0021 0.0765 | 3.3283</item>
- <item>30 | 2.00 | 0.0680 0.0047 0.0727 | 3.1221</item>
- <item>31 | 2.00 | 0.0659 0.0057 0.0716 | 2.9160</item>
- <item>43 | 1.75 | 0.0649 0.0033 0.0682 | 1.5785</item>
- <item>44 | 1.75 | 0.0606 0.0055 0.0661 | 1.5194</item>
- <item>45 | 1.75 | 0.0592 0.0063 0.0655 | 1.4626</item>
- <item>57 | 1.50 | 0.0575 0.0046 0.0621 | 1.0900</item>
- <item>58 | 1.50 | 0.0544 0.0066 0.0610 | 1.0730</item>
- <item>59 | 1.50 | 0.0534 0.0072 0.0606 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 215s</item>
- <item>Prepare output 14s</item>
- <item>229s</item>
- <item>Jacobian determinant (RMS): 0.011 0.039 0.058 0.081 0.102 | 0.108638</item>
- <item>Template Matching: 0.084 0.220 0.198 0.177 0.160 | 0.160253</item>
- <item>Write result maps: 43s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 53s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 61s</item>
- <item>142s</item>
- <item>Create initial surface 107s</item>
- <item>Topology correction: 122s</item>
- <item>Surface refinement: 108s</item>
- <item>Reduction of surface collisions with optimization: 94s</item>
- <item>Spherical mapping with areal smoothing 123s</item>
- <item>Spherical registration 343s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 57s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 61s</item>
- <item>146s</item>
- <item>Create initial surface 105s</item>
- <item>Topology correction: 124s</item>
- <item>Surface refinement: 127s</item>
- <item>Reduction of surface collisions with optimization: 88s</item>
- <item>Spherical mapping with areal smoothing 121s</item>
- <item>Spherical registration 364s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5065 0.5966 mm</item>
- <item>Surface intensity / position RMSE: 0.0616 / 0.0621</item>
- <item>Euler number / defect number / defect size: 12.0 / 7.0 / 0.46%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/surf/lh.thickness.sub-0025627_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/surf/rh.thickness.sub-0025627_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/sub-0025627_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2238s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 11s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 36s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 15s</item>
- <item>ROI estimation of 'mori' atlas 22s</item>
- <item>ROI estimation of 'anatomy3' atlas 31s</item>
- <item>ROI estimation of 'julichbrain' atlas 44s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 70s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s</item>
- <item>Write results 12s</item>
- <item>445s</item>
- <item>Quality check: 16s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/report/catreport_sub-0025627_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 64 minute(s) and 46 second(s).</item>
- <item>Image Quality Rating (IQR): 82.39% (B-)</item>
- <item>GM volume (GMV): 46.92% (716.85 / 1527.96 ml)</item>
- <item>GM thickness (GMT): 2.51 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_92055/ds/JHNU/sub-0025627/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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