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- <F>/var/lib/condor/execute/dir_26020/ds/sub-49/sub-49_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_26020/ds/sub-49/mri/msub-49_T1w.nii</Fm>
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- <fnames>..26020/ds/sub-49/sub-49_T1w</fnames>
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- <parameter>
- <opts>
- <tpm>
- <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>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <extopts>
- <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_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>24</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
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- </darteltpm>
- <shootingtpm>
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- </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>
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- </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>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
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- <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>
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- <tr>
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- <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/lpba40.nii</td>
- <td>0</td>
- <td>
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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/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>
- </td>
- <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>
- </td>
- <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>
- <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/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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- <item>wm</item>
- </td>
- <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>
- <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_400Parcels_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_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <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>
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- <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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- <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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- <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>
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- <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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- <CB>3</CB>
- <BG>5</BG>
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- <ON>11</ON>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
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- <PH>25</PH>
- <LE>27</LE>
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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
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- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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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_4_GS.nii</item>
- </templates>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>16</SurfaceEulerNumber>
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- <tissue_mn>[4.13800001144409 139.684432983398 314.13037109375 429.535461425781]</tissue_mn>
- <tissue_mnr>[0.00963366311043501 0.325198829174042 0.731325805187225 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[29.1667405274106 54.2149597452022 38.1197517898896 23.2522594448828]</tissue_std>
- <tissue_stdr>[0.0685635060071945 0.127445429563522 0.0896097272634506 0.0546600818634033]</tissue_stdr>
- <contrast>116.527679443359</contrast>
- <contrastr>0.271287679672241</contrastr>
- <NCR>0.13959701359272</NCR>
- <ICR>0.347234487533569</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999994657329 2 1.99999994657329]</res_vx_vol>
- <res_RMS>1.99999996438219</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62399959564209 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>4.01401805877686</contrastr>
- <NCR>2.33501291275024</NCR>
- <ICR>1.32101809978485</ICR>
- <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
- <SurfaceDefectArea>1.14604762013291</SurfaceDefectArea>
- <SurfaceDefectNumber>1.725</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.40631556510925</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.53678369522095</SurfacePositionRMSE>
- <IQR>2.21040056064086</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220712-164111</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.584190480531624</SurfaceDefectArea>
- <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0703157782554626</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0768391862511635</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>16</EC_abs>
- <defect_size>0.584190480531624</defect_size>
- <vol_abs_CGW>[224.058089967336 609.098061513665 424.457875318708 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.587243105820778</vol_abs_WMH>
- <vol_rel_WMH>0.000466950187662231</vol_rel_WMH>
- <surf_TSA>1626.04027701676</surf_TSA>
- <vol_TIV>1257.61402679971</vol_TIV>
- <vol_rel_CGW>[0.178161252333917 0.484328298296462 0.337510449369621 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.61853669278012 0.68324437099498]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.6208279132843 0.82672744011204 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.93721117167519 0.282758069651434 0.292380829428695;2.63809793110065 0.199720675317705 0.419916312907709;3.36507741536477 0.29883882810772 0.287702857663596]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.859138879946621 0.28707797950588 0.570357300397;4.33728713084785 0.29444170195259 0.429642699603]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.46803947279987</vol_TIV>
- <vol_rel_CGW>[1.04959145714649 6.54828121940486 3.91146640390842 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04669501876622</vol_rel_WMH>
- <surf_TSA>8.3628327555058</surf_TSA>
- <SQR>5.3657305384099</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.0693008163639699 1 12815 4058.59278316274 0.407136168553766]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.01567542552948 0.00788459181785583 0.478175431489944]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[724.820921985884 382.710163827902 401.853672607104 318.287622178292 930.729322728664 2011.21597861754]</SPMvols0>
- <SPMvols1>[623.782033276676 356.594824049341 244.522422205249 295.843623379681 778.798240665197 2061.30162299537]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[174.89990234375 327.692687988281 420.316497802734]</T3th>
- <Tth>
- <T3th>[0 77.9581069946289 14.8519086837769 174.89990234375 327.692687988281 420.316497802734 543.024780273438 1579.54309082031]</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>[0.0215474963188171 0.0785320401191711 0.0870999395847321 0 0]</dtc>
- <ll>[0.0850865248443127 0 0.0850865248443127 0;0.198418735169849 0.0106714679127266 0.209090203082576 2275.66918945312;0.198418735169849 0.0106714679127266 0.209090203082576 2275.66918945312]</ll>
- <rmsdtc>[0.0455549880862236 0.103956609964371 0.115117885172367]</rmsdtc>
- <rmsgdt>[0.0322767049074173 0.0449113920331001 0.0551339164376259]</rmsgdt>
- <rmsdt>0.115117885172367</rmsdt>
- <dt>0.0870999395847321</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>[0.0100594656541944 0.0372918285429478 0.0519953407347202 0.0600385628640652 0.0659471303224564 0.0737332552671432]</dtc>
- <ll>[0.0838827864794158 0 0.0838827864794158 0;0.220252426739927 0.0140022378663004 0.234254664606227 7167.3955078125;0.199062046693677 0.0167825322403267 0.215844578934004 12078.58984375;0.178002628279321 0.0186393136425688 0.19664194192189 20098.25;0.161321928735938 0.0212678719646635 0.182589800700602 37205.015625;0.161321928735938 0.0212678719646635 0.182589800700602 37205.015625]</ll>
- <rmsdtc>[0.011797203682363 0.043538685888052 0.0634521618485451 0.0868639796972275 0.110064812004566 0.115183666348457]</rmsdtc>
- <rmsgdt>[0.00317897764034569 0.0123562011867762 0.0271416250616312 0.0473147593438625 0.069518156349659 0.071234367787838]</rmsgdt>
- <rmsdt>0.115183666348457</rmsdt>
- <dt>0.0737332552671432</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_26020/ds/sub-49/sub-49_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 28s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 3s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>26s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 11s</item>
- <item>Use initial fine affine registration. 61s</item>
- <item>SPM preprocessing 1 (estimate 2): 57s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 12s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 29s</item>
- <item>Update probability maps 5s</item>
- <item>64s</item>
- <item>Global intensity correction: 9s</item>
- <item>SANLM denoising after intensity normalization (medium): 12s</item>
- <item>Fast Optimized Shooting registration 40s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 1s</item>
- <item>Prepare segments (LASmod = 1.00) 16s</item>
- <item>Estimate local tissue thresholds (WM) 12s</item>
- <item>Estimate local tissue thresholds (GM) 20s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 14s</item>
- <item>71s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 13s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 29s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 3s</item>
- <item>73s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 41s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>12s</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 | 0.0839 0.0000 0.0839 | 32.0000</item>
- <item>2 | 2.50 | 0.0812 0.0012 0.0824 | 29.4886</item>
- <item>3 | 2.50 | 0.0804 0.0018 0.0822 | 26.9772</item>
- <item>4 | 2.50 | 0.0800 0.0020 0.0821 | 24.6107</item>
- <item>5 | 2.50 | 0.0797 0.0022 0.0819 | 22.6548</item>
- <item>6 | 2.50 | 0.0794 0.0023 0.0817 | 20.6989</item>
- <item>7 | 2.50 | 0.0791 0.0024 0.0815 | 18.9688</item>
- <item>8 | 2.50 | 0.0788 0.0025 0.0814 | 17.4455</item>
- <item>9 | 2.50 | 0.0785 0.0026 0.0811 | 15.9223</item>
- <item>10 | 2.50 | 0.0782 0.0027 0.0809 | 14.6627</item>
- <item>11 | 2.50 | 0.0779 0.0028 0.0807 | 13.4764</item>
- <item>12 | 2.50 | 0.0775 0.0029 0.0804 | 12.3015</item>
- <item>13 | 2.50 | 0.0772 0.0030 0.0802 | 11.3776</item>
- <item>14 | 2.50 | 0.0768 0.0031 0.0799 | 10.4537</item>
- <item>15 | 2.25 | 0.0765 0.0032 0.0797 | 9.5920</item>
- <item>16 | 2.25 | 0.0734 0.0047 0.0781 | 8.8725</item>
- <item>29 | 2.00 | 0.0748 0.0021 0.0769 | 3.3283</item>
- <item>30 | 2.00 | 0.0686 0.0046 0.0732 | 3.1221</item>
- <item>31 | 2.00 | 0.0664 0.0056 0.0719 | 2.9160</item>
- <item>43 | 1.75 | 0.0651 0.0033 0.0684 | 1.5785</item>
- <item>44 | 1.75 | 0.0608 0.0055 0.0663 | 1.5194</item>
- <item>45 | 1.75 | 0.0593 0.0062 0.0655 | 1.4626</item>
- <item>57 | 1.50 | 0.0578 0.0046 0.0624 | 1.0900</item>
- <item>58 | 1.50 | 0.0548 0.0065 0.0613 | 1.0730</item>
- <item>59 | 1.50 | 0.0538 0.0071 0.0609 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 260s</item>
- <item>Prepare output 10s</item>
- <item>269s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.063 0.087 0.110 | 0.115184</item>
- <item>Template Matching: 0.084 0.220 0.199 0.178 0.161 | 0.161322</item>
- <item>Write result maps: 20s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 56s</item>
- <item>129s</item>
- <item>Create initial surface 100s</item>
- <item>Topology correction: 90s</item>
- <item>Surface refinement: 99s</item>
- <item>Reduction of surface collisions with optimization: 73s</item>
- <item>Spherical mapping with areal smoothing 96s</item>
- <item>Spherical registration 290s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 42s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 55s</item>
- <item>122s</item>
- <item>Create initial surface 97s</item>
- <item>Topology correction: 91s</item>
- <item>Surface refinement: 85s</item>
- <item>Reduction of surface collisions with optimization: 75s</item>
- <item>Spherical mapping with areal smoothing 94s</item>
- <item>Spherical registration 299s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6186 0.6832 mm</item>
- <item>Surface intensity / position RMSE: 0.0703 / 0.0768</item>
- <item>Euler number / defect number / defect size: 16.0 / 14.5 / 0.58%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_26020/ds/sub-49/surf/lh.thickness.sub-49_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_26020/ds/sub-49/surf/rh.thickness.sub-49_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_26020/ds/sub-49/sub-49_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1832s</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 6s</item>
- <item>ROI estimation of 'hammers' atlas 16s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 9s</item>
- <item>ROI estimation of 'mori' atlas 14s</item>
- <item>ROI estimation of 'anatomy3' atlas 20s</item>
- <item>ROI estimation of 'julichbrain' atlas 26s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s</item>
- <item>Write results 64s</item>
- <item>256s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_26020/ds/sub-49/report/catreport_sub-49_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 49 minute(s) and 52 second(s).</item>
- <item>Image Quality Rating (IQR): 82.90% (B-)</item>
- <item>GM volume (GMV): 48.43% (609.10 / 1257.61 ml)</item>
- <item>GM thickness (GMT): 2.62 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_26020/ds/sub-49/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_26020/ds/sub-49/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_26020/ds/sub-49/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|