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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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- <biasfwhm>60</biasfwhm>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <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_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>
- <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>
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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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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/var/lib/condor/execute/dir_2333949/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>148</SurfaceEulerNumber>
- <SurfaceDefectArea>4.55665041058233</SurfaceDefectArea>
- <SurfaceDefectNumber>38</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0827458202838898</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.100434646010399</SurfacePositionRMSE>
- <res_vx_vol>[1.33000183105469 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1.12084861758235</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[0 13.1709995269775 82.6330032348633 153.365005493164]</tissue_mn>
- <tissue_mnr>[0 0.0858800858259201 0.538799583911896 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.36790698036451 19.874458625851 18.4822559008418 13.8628607254167]</tissue_std>
- <tissue_stdr>[0.0219600740820169 0.129589259624481 0.120511561632156 0.0903912931680679]</tissue_stdr>
- <contrast>52.311767578125</contrast>
- <contrastr>0.341093242168427</contrastr>
- <res_ECR>0.463031411170959</res_ECR>
- <NCR>0.181490987539291</NCR>
- <ICR>0.4034244120121</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.26036429405212</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[1.89584374427795 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>2.96693468093872</contrastr>
- <NCR>2.93641948699951</NCR>
- <ICR>1.46037793159485</ICR>
- <SurfaceEulerNumber>8.44897959183674</SurfaceEulerNumber>
- <SurfaceDefectArea>2.13916260264558</SurfaceDefectArea>
- <SurfaceDefectNumber>2.9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.6549164056778</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.00869274139404</SurfacePositionRMSE>
- <SIQR>2.9854784889058</SIQR>
- <IQR>2.72970951266886</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>20231031-025328</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>148</SurfaceEulerNumber>
- <SurfaceDefectArea>4.55665041058233</SurfaceDefectArea>
- <SurfaceDefectNumber>38</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0827458202838898</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.100434646010399</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>148</EC_abs>
- <defect_size>4.55665041058233</defect_size>
- <vol_abs_CGW>[186.820525490196 756.878521568627 596.358980392157 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.575172549019608</vol_abs_WMH>
- <vol_rel_WMH>0.000373474595610921</vol_rel_WMH>
- <surf_TSA>2122.40296213234</surf_TSA>
- <vol_TIV>1540.05802745098</vol_TIV>
- <vol_rel_CGW>[0.121307458654276 0.491461041128023 0.387231500217701 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.46801210912062 0.689836532007496]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.46668934822083 0.787967586239923 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.81597317815135 0.270547325779882 0.325245215520769;2.51859936676905 0.202051314206728 0.399230742251891;3.25123815824778 0.27964240923923 0.27552404222734]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.788063398614938 0.288245610391613 0.609721878352728;4.14957859587231 0.297994247291352 0.390278121647272]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.45332077381802</vol_TIV>
- <vol_rel_CGW>[0.5 6.67638364094868 4.80444504701331 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03734745956109</vol_rel_WMH>
- <surf_TSA>8.62363297803599</surf_TSA>
- <SQR>5.50731661354052</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.437761685996867]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00203393679112196 0.0016417158767581 0.103170618414879]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[922.579670588235 530.552670588235 329.927180392157 612.585294117647 1069.75324705882 8275.57109411765]</SPMvols0>
- <SPMvols1>[797.345047058824 494.719584313725 173.810094117647 468.298662745098 897.918039215686 8309.48530980392]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[19.9298992156982 91.9739990234375 153.560302734375]</T3th>
- <Tth>
- <T3th>[-19.8897094726562 -19.8897113800049 0.0200939178466797 19.9298992156982 91.9739990234375 153.560302734375 220.375503540039 465.460266113281]</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>[0.0190664380788803 0.0618303455412388 0.06673364341259 0 0]</dtc>
- <ll>[0.0790953954824117 0 0.0790953954824117 0;0.191656600384294 0.00824052803799743 0.199897128422292 1757.27612304688;0.191656600384294 0.00824052803799743 0.199897128422292 1757.27612304688]</ll>
- <rmsdtc>[0.0447095669806004 0.078317292034626 0.0866479650139809]</rmsdtc>
- <rmsgdt>[0.0324897803366184 0.0385566726326942 0.0475560985505581]</rmsgdt>
- <rmsdt>0.0866479650139809</rmsdt>
- <dt>0.06673364341259</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>[0.00788121204823256 0.026792261749506 0.0373799167573452 0.0456658117473125 0.0518386512994766 0.0571874640882015]</dtc>
- <ll>[0.0796664118658618 0 0.0796664118658618 0;0.211953937728938 0.0106586290445665 0.222612566773504 5455.8857421875;0.195084457394069 0.0142072928889438 0.209291750283013 10225.1591796875;0.176427408274536 0.0172163899015044 0.19364379817604 18563.951171875;0.160219967753792 0.0204768920280812 0.180696859781874 35821.3125;0.160219967753792 0.0204768920280812 0.180696859781874 35821.3125]</ll>
- <rmsdtc>[0.00916614662855864 0.0311613995581865 0.0464301221072674 0.0687243118882179 0.091744638979435 0.0984918028116226]</rmsdtc>
- <rmsgdt>[0.00291744829155505 0.0110931778326631 0.024965213611722 0.0444301068782806 0.0635593608021736 0.0694701448082924]</rmsgdt>
- <rmsdt>0.0984918028116226</rmsdt>
- <dt>0.0571874640882015</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025034/ses-1/sub-0025034_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 31s</item>
- <item>Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 3s</item>
- <item>26s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 59s</item>
- <item>SPM preprocessing 1 (estimate 2): 55s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 13s</item>
- <item>Update Segmentation 15s</item>
- <item>Update Skull-Stripping 30s</item>
- <item>Update probability maps 7s</item>
- <item>64s</item>
- <item>Global intensity correction: 11s</item>
- <item>SANLM denoising after intensity normalization (medium): 20s</item>
- <item>Fast Optimized Shooting registration 24s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.01) 10s</item>
- <item>Estimate local tissue thresholds (WM) 14s</item>
- <item>Estimate local tissue thresholds (GM) 18s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 29s</item>
- <item>78s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 7s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 16s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 3s</item>
- <item>44s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s</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) 3s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>8s</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 | 0.0797 0.0000 0.0797 | 32.0000</item>
- <item>2 | 2.50 | 0.0777 0.0010 0.0786 | 29.4886</item>
- <item>3 | 2.50 | 0.0771 0.0014 0.0785 | 26.9772</item>
- <item>4 | 2.50 | 0.0768 0.0016 0.0784 | 24.6107</item>
- <item>5 | 2.50 | 0.0766 0.0017 0.0783 | 22.6548</item>
- <item>6 | 2.50 | 0.0764 0.0018 0.0782 | 20.6989</item>
- <item>7 | 2.50 | 0.0762 0.0019 0.0780 | 18.9688</item>
- <item>8 | 2.50 | 0.0760 0.0019 0.0779 | 17.4455</item>
- <item>9 | 2.50 | 0.0757 0.0020 0.0777 | 15.9223</item>
- <item>10 | 2.50 | 0.0755 0.0021 0.0776 | 14.6627</item>
- <item>11 | 2.50 | 0.0753 0.0021 0.0774 | 13.4764</item>
- <item>12 | 2.50 | 0.0750 0.0022 0.0772 | 12.3015</item>
- <item>13 | 2.50 | 0.0748 0.0023 0.0770 | 11.3776</item>
- <item>14 | 2.50 | 0.0746 0.0023 0.0768 | 10.4537</item>
- <item>15 | 2.25 | 0.0732 0.0023 0.0755 | 9.5920</item>
- <item>16 | 2.25 | 0.0707 0.0036 0.0742 | 8.8725</item>
- <item>29 | 2.00 | 0.0724 0.0016 0.0740 | 3.3283</item>
- <item>30 | 2.00 | 0.0669 0.0038 0.0707 | 3.1221</item>
- <item>31 | 2.00 | 0.0650 0.0047 0.0698 | 2.9160</item>
- <item>43 | 1.75 | 0.0644 0.0027 0.0671 | 1.5785</item>
- <item>44 | 1.75 | 0.0602 0.0050 0.0651 | 1.5194</item>
- <item>45 | 1.75 | 0.0588 0.0057 0.0645 | 1.4626</item>
- <item>57 | 1.50 | 0.0575 0.0041 0.0616 | 1.0900</item>
- <item>58 | 1.50 | 0.0544 0.0062 0.0606 | 1.0730</item>
- <item>59 | 1.50 | 0.0534 0.0068 0.0602 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 113s</item>
- <item>Prepare output 7s</item>
- <item>120s</item>
- <item>Jacobian determinant (RMS): 0.009 0.031 0.046 0.069 0.092 | 0.098492</item>
- <item>Template Matching: 0.080 0.212 0.195 0.176 0.160 | 0.160220</item>
- <item>Write result maps: 40s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 18s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 32s</item>
- <item>66s</item>
- <item>Create initial surface 62s</item>
- <item>Topology correction: 86s</item>
- <item>Surface refinement: 78s</item>
- <item>Reduction of surface collisions with optimization: 55s</item>
- <item>Spherical mapping with areal smoothing 63s</item>
- <item>Spherical registration 185s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 20s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 31s</item>
- <item>66s</item>
- <item>Create initial surface 58s</item>
- <item>Topology correction: 80s</item>
- <item>Surface refinement: 69s</item>
- <item>Reduction of surface collisions with optimization: 52s</item>
- <item>Spherical mapping with areal smoothing 61s</item>
- <item>Spherical registration 183s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4682 0.6896 mm</item>
- <item>Surface intensity / position RMSE: 0.0827 / 0.1004</item>
- <item>Euler number / defect number / defect size: 148.0 / 38.0 / 4.56%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/surf/lh.thickness.sub-0025034_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/surf/rh.thickness.sub-0025034_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/sub-0025034_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1237s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 23s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 16s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 5s</item>
- <item>ROI estimation of 'aal3' atlas 9s</item>
- <item>ROI estimation of 'mori' atlas 13s</item>
- <item>ROI estimation of 'anatomy3' atlas 18s</item>
- <item>ROI estimation of 'julichbrain' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 36s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 55s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 5s</item>
- <item>244s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/report/catreport_sub-0025034_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 35 minute(s) and 59 second(s).</item>
- <item>Image Quality Rating (IQR): 77.70% (C+)</item>
- <item>GM volume (GMV): 49.15% (756.88 / 1540.06 ml)</item>
- <item>GM thickness (GMT): 2.47 0.69 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2333949/ds/NYU_2/sub-0025034/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|