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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>
- <LASstr>0.5</LASstr>
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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <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>
- <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>
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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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- <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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- <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>
- <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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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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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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- <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>[false]</td>
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- <td>/var/lib/condor/execute/dir_905704/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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- <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>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <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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- </darteltpms>
- <shootingtpms>
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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_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>184</SurfaceEulerNumber>
- <SurfaceDefectArea>5.05977429591894</SurfaceDefectArea>
- <SurfaceDefectNumber>60</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0795900076627731</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0974380820989609</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>[10.6884994506836 29.4909992218018 214.238998413086 378.246002197266]</tissue_mn>
- <tissue_mnr>[0.0282580628991127 0.0779677778482437 0.566401243209839 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.01322851091127 50.3258830929371 51.6620732846679 34.5939636961921]</tissue_std>
- <tissue_stdr>[0.0190806295722723 0.136919751763344 0.140555083751678 0.0941185131669044]</tissue_stdr>
- <contrast>130.151336669922</contrast>
- <contrastr>0.344091773033142</contrastr>
- <res_ECR>0.442315638065338</res_ECR>
- <NCR>0.143982276320457</NCR>
- <ICR>0.516319036483765</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.15467166900635</res_ECR>
- <res_BB>NaN</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>2.92195653915405</contrastr>
- <NCR>2.39796543121338</NCR>
- <ICR>1.74037456512451</ICR>
- <SurfaceEulerNumber>10.2857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>2.26494357397973</SurfaceDefectArea>
- <SurfaceDefectNumber>4</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.59180021286011</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.94876170158386</SurfacePositionRMSE>
- <SIQR>2.80631568725176</SIQR>
- <IQR>2.32894195283655</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>20231031-031706</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>184</SurfaceEulerNumber>
- <SurfaceDefectArea>5.05977429591894</SurfaceDefectArea>
- <SurfaceDefectNumber>60</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0795900076627731</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0974380820989609</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>184</EC_abs>
- <defect_size>5.05977429591894</defect_size>
- <vol_abs_CGW>[197.316180392157 647.768121568627 503.711749019608 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.21874509803922</vol_abs_WMH>
- <vol_rel_WMH>0.00090357997204496</vol_rel_WMH>
- <surf_TSA>1810.91296097751</surf_TSA>
- <vol_TIV>1348.79605098039</vol_TIV>
- <vol_rel_CGW>[0.146290597639825 0.480256537745486 0.373452864614689 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.52423997309183 0.70371001760463]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55544185638428 0.833606716506535 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.80666347186005 0.292959289505449 0.282305964893631;2.54896990729973 0.205531448212418 0.404852704731786;3.27152335070279 0.296586717380197 0.312841330374583]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.766412662373486 0.241842402029308 0.627909082676809;4.20445571655947 0.282256189184088 0.372090917323191]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.062210242243</vol_TIV>
- <vol_rel_CGW>[0.5 6.47515333594623 4.55698391908565 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0903579972045</vol_rel_WMH>
- <surf_TSA>8.5900812702182</surf_TSA>
- <SQR>5.33397561566328</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.469652292942379]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00198993505910039 0.00162984128110111 0.107453517615795]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[775.459756862745 449.572745098039 361.173568627451 1041.19254901961 950.537019607843 8313.9793372549]</SPMvols0>
- <SPMvols1>[684.431921568627 422.726254901961 194.847364705882 754.931462745098 712.645831372549 8372.09772156863]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[46.8157005310059 235.861694335938 379.789794921875]</T3th>
- <Tth>
- <T3th>[-62.6450614929199 -62.6450576782227 -7.9146785736084 46.8157005310059 235.861694335938 379.789794921875 546.27685546875 1342.58190917969]</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>[0.0238574966788292 0.0858123600482941 0.0950056239962578 0 0]</dtc>
- <ll>[0.0872456282317614 0 0.0872456282317614 0;0.186365848829766 0.0122954504830497 0.198661299312816 2621.98022460938;0.186365848829766 0.0122954504830497 0.198661299312816 2621.98022460938]</ll>
- <rmsdtc>[0.0555434413254261 0.110111601650715 0.122475035488605]</rmsdtc>
- <rmsgdt>[0.0400216691195965 0.0513042621314526 0.0635300725698471]</rmsgdt>
- <rmsdt>0.122475035488605</rmsdt>
- <dt>0.0950056239962578</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>[0.0109016029164195 0.0413010455667973 0.0588723346590996 0.0679017007350922 0.0739819556474686 0.0837199985980988]</dtc>
- <ll>[0.0873091767228655 0 0.0873091767228655 0;0.214518742368742 0.0181066620879121 0.232625404456654 9268.34765625;0.18931600417945 0.0198125026377739 0.209128506817223 14259.2958984375;0.167871299519045 0.0207241163407749 0.18859541585982 22346.234375;0.151352082026898 0.0229864939709138 0.174338575997812 40211.4921875;0.151352082026898 0.0229864939709138 0.174338575997812 40211.4921875]</ll>
- <rmsdtc>[0.0125670395791531 0.0468586832284927 0.070514053106308 0.0989650413393974 0.124300189316273 0.132131725549698]</rmsdtc>
- <rmsgdt>[0.00369564653374255 0.0146569134667516 0.0315258577466011 0.0537779852747917 0.0732668042182922 0.0793195739388466]</rmsgdt>
- <rmsdt>0.132131725549698</rmsdt>
- <dt>0.0837199985980988</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025094/ses-1/sub-0025094_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 42s</item>
- <item>Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>33s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 66s</item>
- <item>SPM preprocessing 1 (estimate 2): 67s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 37s</item>
- <item>Update probability maps 8s</item>
- <item>77s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 22s</item>
- <item>Fast Optimized Shooting registration 29s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.12) 12s</item>
- <item>Estimate local tissue thresholds (WM) 16s</item>
- <item>Estimate local tissue thresholds (GM) 22s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 36s</item>
- <item>93s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 10s</item>
- <item>Blood vessel detection 7s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 21s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>55s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 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>9s</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 | 0.0873 0.0000 0.0873 | 32.0000</item>
- <item>2 | 2.50 | 0.0823 0.0017 0.0840 | 29.4886</item>
- <item>3 | 2.50 | 0.0807 0.0027 0.0834 | 26.9772</item>
- <item>4 | 2.50 | 0.0800 0.0031 0.0831 | 24.6107</item>
- <item>5 | 2.50 | 0.0795 0.0033 0.0828 | 22.6548</item>
- <item>6 | 2.50 | 0.0790 0.0034 0.0824 | 20.6989</item>
- <item>7 | 2.50 | 0.0786 0.0035 0.0821 | 18.9688</item>
- <item>8 | 2.50 | 0.0781 0.0036 0.0818 | 17.4455</item>
- <item>9 | 2.50 | 0.0777 0.0037 0.0814 | 15.9223</item>
- <item>10 | 2.50 | 0.0772 0.0038 0.0810 | 14.6627</item>
- <item>11 | 2.50 | 0.0768 0.0039 0.0807 | 13.4764</item>
- <item>12 | 2.50 | 0.0763 0.0040 0.0803 | 12.3015</item>
- <item>13 | 2.50 | 0.0758 0.0041 0.0799 | 11.3776</item>
- <item>14 | 2.50 | 0.0754 0.0041 0.0795 | 10.4537</item>
- <item>15 | 2.25 | 0.0751 0.0043 0.0794 | 9.5920</item>
- <item>16 | 2.25 | 0.0715 0.0060 0.0775 | 8.8725</item>
- <item>29 | 2.00 | 0.0726 0.0027 0.0753 | 3.3283</item>
- <item>30 | 2.00 | 0.0655 0.0055 0.0710 | 3.1221</item>
- <item>31 | 2.00 | 0.0631 0.0066 0.0697 | 2.9160</item>
- <item>43 | 1.75 | 0.0618 0.0039 0.0657 | 1.5785</item>
- <item>44 | 1.75 | 0.0574 0.0061 0.0635 | 1.5194</item>
- <item>45 | 1.75 | 0.0560 0.0069 0.0629 | 1.4626</item>
- <item>57 | 1.50 | 0.0544 0.0051 0.0595 | 1.0900</item>
- <item>58 | 1.50 | 0.0514 0.0070 0.0585 | 1.0730</item>
- <item>59 | 1.50 | 0.0505 0.0077 0.0581 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 142s</item>
- <item>Prepare output 9s</item>
- <item>151s</item>
- <item>Jacobian determinant (RMS): 0.013 0.047 0.071 0.099 0.124 | 0.132132</item>
- <item>Template Matching: 0.087 0.215 0.189 0.168 0.151 | 0.151352</item>
- <item>Write result maps: 49s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 23s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 36s</item>
- <item>77s</item>
- <item>Create initial surface 73s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 68s</item>
- <item>Reduction of surface collisions with optimization: 58s</item>
- <item>Spherical mapping with areal smoothing 67s</item>
- <item>Spherical registration 249s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 24s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 35s</item>
- <item>77s</item>
- <item>Create initial surface 70s</item>
- <item>Topology correction: 80s</item>
- <item>Surface refinement: 66s</item>
- <item>Reduction of surface collisions with optimization: 57s</item>
- <item>Spherical mapping with areal smoothing 67s</item>
- <item>Spherical registration 258s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5242 0.7037 mm</item>
- <item>Surface intensity / position RMSE: 0.0796 / 0.0974</item>
- <item>Euler number / defect number / defect size: 184.0 / 60.0 / 5.06%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/surf/lh.thickness.sub-0025094_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/surf/rh.thickness.sub-0025094_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/sub-0025094_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1429s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 24s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 17s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 21s</item>
- <item>ROI estimation of 'julichbrain' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 45s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>289s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/report/catreport_sub-0025094_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 42 minute(s) and 20 second(s).</item>
- <item>Image Quality Rating (IQR): 81.71% (B-)</item>
- <item>GM volume (GMV): 48.03% (647.77 / 1348.80 ml)</item>
- <item>GM thickness (GMT): 2.52 0.70 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_905704/ds/NYU_2/sub-0025094/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|