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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
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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>
- <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>
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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>
- <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>
- <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/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>
- <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/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>
- <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/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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- <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>
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- <item>gm</item>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/var/lib/condor/execute/dir_1682613/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <td>[false]</td>
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- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
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- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
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- <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>
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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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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>22</SurfaceEulerNumber>
- <SurfaceDefectArea>1.6514668892821</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0749340802431107</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.105693161487579</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>188.178802490234</res_BB>
- <tissue_mn>[5.17700004577637 74.3580017089844 220.018997192383 352.790008544922]</tissue_mn>
- <tissue_mnr>[0.0146744521334767 0.210771277546883 0.623654246330261 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[5.81362836791873 38.9702076079309 37.9024944131951 25.9686143019561]</tissue_std>
- <tissue_stdr>[0.0167244262993336 0.112108021974564 0.109036467969418 0.0747055336833]</tissue_stdr>
- <contrast>125.925994873047</contrast>
- <contrastr>0.356943190097809</contrastr>
- <res_ECR>0.389096438884735</res_ECR>
- <NCR>0.138456761837006</NCR>
- <ICR>0.29890301823616</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.88314485549927</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>2.72918558120728</contrastr>
- <NCR>2.31864428520203</NCR>
- <ICR>1.20114839076996</ICR>
- <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
- <SurfaceDefectArea>1.41286672232053</SurfaceDefectArea>
- <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.49868154525757</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.11386322975159</SurfacePositionRMSE>
- <SIQR>2.5787051058302</SIQR>
- <IQR>2.19845302836027</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>20231031-004408</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>22</SurfaceEulerNumber>
- <SurfaceDefectArea>1.6514668892821</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0749340802431107</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.105693161487579</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>22</EC_abs>
- <defect_size>1.6514668892821</defect_size>
- <vol_abs_CGW>[238.626909803922 741.370121568627 510.360031372549 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.318862745098039</vol_abs_WMH>
- <vol_rel_WMH>0.000213950571355514</vol_rel_WMH>
- <surf_TSA>2091.10125829725</surf_TSA>
- <vol_TIV>1490.3570627451</vol_TIV>
- <vol_rel_CGW>[0.160113918851361 0.497444632632594 0.342441448516045 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.47795539678442 0.64623250826104]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.5015664100647 0.84940685601778 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.86126676039898 0.298732818884017 0.284842494051354;2.5192256791886 0.184228485907946 0.43813407834456;3.19332017453313 0.298194249920819 0.277023427604086]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.679785823317548 0.292816965810379 0.652796842827728;4.16390415277191 0.311027471516805 0.347203157172272]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.19205634454231</vol_TIV>
- <vol_rel_CGW>[0.725465496612089 6.78384756883251 4.00002601501517 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02139505713555</vol_rel_WMH>
- <surf_TSA>8.62338480615237</surf_TSA>
- <SQR>5.55766419422278</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11141.12 0.387338988182391]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00148017064202577 0.00126538774929941 0.0305196158587933]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[905.161270588235 442.734654901961 446.332341176471 472.295647058824 904.897545098039 8431.74425098039]</SPMvols0>
- <SPMvols1>[791.078117647059 414.802745098039 249.396874509804 429.097792156863 840.115803921569 8416.6843254902]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[98.809196472168 238.22819519043 348.797607421875]</T3th>
- <Tth>
- <T3th>[-5.22525978088379 -5.225257396698 3.00956130027771 98.809196472168 238.22819519043 348.797607421875 473.791809082031 866.758422851562]</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>[0.019352039322257 0.0665379017591476 0.0728339999914169 0 0]</dtc>
- <ll>[0.0812203848824686 0 0.0812203848824686 0;0.196271898652039 0.0091507460604481 0.205422644712487 1951.37829589844;0.196271898652039 0.0091507460604481 0.205422644712487 1951.37829589844]</ll>
- <rmsdtc>[0.0410418920218945 0.0876451656222343 0.0977204442024231]</rmsdtc>
- <rmsgdt>[0.0293211005628109 0.0427350513637066 0.0527234822511673]</rmsgdt>
- <rmsdt>0.0977204442024231</rmsdt>
- <dt>0.0728339999914169</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>[0.00873597897589207 0.0305207222700119 0.0425174422562122 0.0506323017179966 0.0571558624505997 0.0636244043707848]</dtc>
- <ll>[0.0823031643973435 0 0.0823031643973435 0;0.220553556166056 0.0117368456196581 0.232290401785714 6007.7978515625;0.201810129433718 0.0149780656077535 0.216788195041471 10779.8935546875;0.182037889674405 0.0177708269863726 0.199808716660778 19161.78515625;0.165227479816824 0.0210965072694019 0.186323987086226 36905.23828125;0.165227479816824 0.0210965072694019 0.186323987086226 36905.23828125]</ll>
- <rmsdtc>[0.0101917283609509 0.0357791930437088 0.0539525747299194 0.0782444775104523 0.10230015963316 0.108453288674355]</rmsdtc>
- <rmsgdt>[0.00319821410812438 0.0123034715652466 0.0268693268299103 0.0471856854856014 0.0657697468996048 0.0713629946112633]</rmsgdt>
- <rmsdt>0.108453288674355</rmsdt>
- <dt>0.0636244043707848</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025625/ses-1/sub-0025625_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 58s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</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): 83s</item>
- <item>SPM preprocessing 1 (estimate 2): 81s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 22s</item>
- <item>Update Segmentation 22s</item>
- <item>Update Skull-Stripping 47s</item>
- <item>Update probability maps 10s</item>
- <item>101s</item>
- <item>Global intensity correction: 18s</item>
- <item>SANLM denoising after intensity normalization (medium): 31s</item>
- <item>Fast Optimized Shooting registration 39s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.12) 17s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 37s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 49s</item>
- <item>138s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 19s</item>
- <item>Blood vessel detection 12s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 28s</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 0.06): 40s</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) 5s</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>13s</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 | 0.0823 0.0000 0.0823 | 32.0000</item>
- <item>2 | 2.50 | 0.0802 0.0010 0.0812 | 29.4886</item>
- <item>3 | 2.50 | 0.0796 0.0015 0.0812 | 26.9772</item>
- <item>4 | 2.50 | 0.0793 0.0017 0.0810 | 24.6107</item>
- <item>5 | 2.50 | 0.0791 0.0018 0.0809 | 22.6548</item>
- <item>6 | 2.50 | 0.0789 0.0019 0.0808 | 20.6989</item>
- <item>7 | 2.50 | 0.0786 0.0020 0.0806 | 18.9688</item>
- <item>8 | 2.50 | 0.0784 0.0021 0.0805 | 17.4455</item>
- <item>9 | 2.50 | 0.0782 0.0021 0.0803 | 15.9223</item>
- <item>10 | 2.50 | 0.0779 0.0022 0.0802 | 14.6627</item>
- <item>11 | 2.50 | 0.0777 0.0023 0.0800 | 13.4764</item>
- <item>12 | 2.50 | 0.0774 0.0024 0.0798 | 12.3015</item>
- <item>13 | 2.50 | 0.0771 0.0025 0.0796 | 11.3776</item>
- <item>14 | 2.50 | 0.0769 0.0025 0.0794 | 10.4537</item>
- <item>15 | 2.25 | 0.0763 0.0026 0.0788 | 9.5920</item>
- <item>16 | 2.25 | 0.0735 0.0039 0.0774 | 8.8725</item>
- <item>29 | 2.00 | 0.0750 0.0018 0.0767 | 3.3283</item>
- <item>30 | 2.00 | 0.0692 0.0041 0.0733 | 3.1221</item>
- <item>31 | 2.00 | 0.0673 0.0050 0.0723 | 2.9160</item>
- <item>43 | 1.75 | 0.0664 0.0029 0.0693 | 1.5785</item>
- <item>44 | 1.75 | 0.0621 0.0051 0.0673 | 1.5194</item>
- <item>45 | 1.75 | 0.0607 0.0059 0.0666 | 1.4626</item>
- <item>57 | 1.50 | 0.0594 0.0043 0.0636 | 1.0900</item>
- <item>58 | 1.50 | 0.0562 0.0064 0.0625 | 1.0730</item>
- <item>59 | 1.50 | 0.0551 0.0070 0.0621 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 205s</item>
- <item>Prepare output 14s</item>
- <item>219s</item>
- <item>Jacobian determinant (RMS): 0.010 0.036 0.054 0.078 0.102 | 0.108453</item>
- <item>Template Matching: 0.082 0.221 0.202 0.182 0.165 | 0.165227</item>
- <item>Write result maps: 45s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 60s</item>
- <item>127s</item>
- <item>Create initial surface 105s</item>
- <item>Topology correction: 124s</item>
- <item>Surface refinement: 132s</item>
- <item>Reduction of surface collisions with optimization: 88s</item>
- <item>Spherical mapping with areal smoothing 111s</item>
- <item>Spherical registration 317s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 40s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 60s</item>
- <item>127s</item>
- <item>Create initial surface 102s</item>
- <item>Topology correction: 128s</item>
- <item>Surface refinement: 137s</item>
- <item>Reduction of surface collisions with optimization: 87s</item>
- <item>Spherical mapping with areal smoothing 109s</item>
- <item>Spherical registration 351s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4779 0.6458 mm</item>
- <item>Surface intensity / position RMSE: 0.0749 / 0.1057</item>
- <item>Euler number / defect number / defect size: 22.0 / 13.0 / 1.65%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/surf/lh.thickness.sub-0025625_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/surf/rh.thickness.sub-0025625_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/sub-0025625_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2170s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 45s</item>
- <item>ROI estimation of 'lpba40' atlas 13s</item>
- <item>ROI estimation of 'hammers' atlas 31s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 20s</item>
- <item>ROI estimation of 'mori' atlas 27s</item>
- <item>ROI estimation of 'anatomy3' atlas 40s</item>
- <item>ROI estimation of 'julichbrain' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 10s</item>
- <item>510s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/report/catreport_sub-0025625_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 63 minute(s) and 16 second(s).</item>
- <item>Image Quality Rating (IQR): 83.02% (B-)</item>
- <item>GM volume (GMV): 49.74% (741.37 / 1490.36 ml)</item>
- <item>GM thickness (GMT): 2.48 0.65 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1682613/ds/JHNU/sub-0025625/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|