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- <opts>
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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>
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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
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- <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>
- <SRP>22</SRP>
- <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>
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- <item>csf</item>
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- <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>
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- <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/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>
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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/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>
- <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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- <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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- <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>
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- <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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- <tr>
- <td>/var/lib/condor/execute/dir_1959710/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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- <satlas>
- <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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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <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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- <shooting>
- <shootingtpm>
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- <restypes>
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- <LASmyostr>0</LASmyostr>
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- </shootingtpms>
- <templates>
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- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.71293641526242</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.068149745464325</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0703558847308159</SurfacePositionRMSE>
- <res_vx_vol>[1.0000479221344 1 1.0000479221344]</res_vx_vol>
- <res_vx_voli>[1.0000479221344 1 1.0000479221344]</res_vx_voli>
- <res_RMS>1.00003194834476</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[13.6359996795654 97.1320037841797 288.678009033203 431.441009521484]</tissue_mn>
- <tissue_mnr>[0.0316057093441486 0.225133910775185 0.669101893901825 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[26.5597019568598 49.3261488620862 45.7664907204719 27.7339264864614]</tissue_std>
- <tissue_stdr>[0.0635696053504944 0.118060208857059 0.109540306031704 0.0663800686597824]</tissue_stdr>
- <contrast>147.422378540039</contrast>
- <contrastr>0.341697663068771</contrastr>
- <res_ECR>0.345875561237335</res_ECR>
- <NCR>0.143814980983734</NCR>
- <ICR>0.256737262010574</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.0000958442688 2 2.0000958442688]</res_vx_vol>
- <res_RMS>2.00006389668952</res_RMS>
- <res_ECR>2.66263031959534</res_ECR>
- <res_BB>1</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>2.95786833763123</contrastr>
- <NCR>2.39556407928467</NCR>
- <ICR>1.09657061100006</ICR>
- <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
- <SurfaceDefectArea>1.17823410381561</SurfaceDefectArea>
- <SurfaceDefectNumber>1.7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.3629949092865</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.40711760520935</SurfacePositionRMSE>
- <SIQR>2.4478288175656</SIQR>
- <IQR>2.25572196202901</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>20231031-010730</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.71293641526242</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.068149745464325</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0703558847308159</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>20</EC_abs>
- <defect_size>0.71293641526242</defect_size>
- <vol_abs_CGW>[234.849334795839 695.008199921576 481.226962668372 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.23564611311777</vol_abs_WMH>
- <vol_rel_WMH>0.000166996458081946</vol_rel_WMH>
- <surf_TSA>1931.93475473277</surf_TSA>
- <vol_TIV>1411.08449738579</vol_TIV>
- <vol_rel_CGW>[0.166431801377541 0.492534785272722 0.341033413349736 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.53665631539577 0.632223393239471]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.54054999351501 0.832832571729828 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92446085273045 0.275280007440097 0.291743294409622;2.56735148498678 0.180100777038448 0.446810270769035;3.23081435137707 0.298496049573853 0.261446434821343]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.814514796998736 0.286272338067126 0.556627680311891;4.3298200830886 0.38578434918585 0.443372319688109]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00292672250766</vol_TIV>
- <vol_rel_CGW>[0.838933214395496 6.69566783894976 3.97473802711452 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01669964580819</vol_rel_WMH>
- <surf_TSA>8.61712796550975</surf_TSA>
- <SQR>5.48597001502725</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9372.54624027228 0.357738350380618]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00156822497956455 0.00100234302226454 0.285741358995438]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[823.906521826439 429.257029064939 335.450505560199 500.014739710281 1426.36280867793 6428.29294918322]</SPMvols0>
- <SPMvols1>[744.430014810185 404.240513900619 218.584501507032 423.129853617205 889.109817798293 6693.07005806086]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[117.970802307129 298.295806884766 418.646606445312]</T3th>
- <Tth>
- <T3th>[-7.05930995941162 -7.0593113899231 7.15690994262695 117.970802307129 298.295806884766 418.646606445312 568.984497070312 1042.16137695312]</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>[0.0213407166302204 0.0751865431666374 0.082704208791256 0 0]</dtc>
- <ll>[0.0829962844512805 0 0.0829962844512805 0;0.189695067480117 0.010050163406427 0.199745230886544 2143.17724609375;0.189695067480117 0.010050163406427 0.199745230886544 2143.17724609375]</ll>
- <rmsdtc>[0.0459310673177242 0.0974987298250198 0.107341170310974]</rmsdtc>
- <rmsgdt>[0.0327177159488201 0.0428113453090191 0.052315279841423]</rmsgdt>
- <rmsdt>0.107341170310974</rmsdt>
- <dt>0.082704208791256</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>[0.0102613661438227 0.0373881384730339 0.0521625317633152 0.05958142131567 0.0641634464263916 0.0711724981665611]</dtc>
- <ll>[0.083975153186108 0 0.083975153186108 0;0.213985103785104 0.0146185802045177 0.228603683989621 7482.8857421875;0.191641391799775 0.0165109867189063 0.208152378518682 11883.1552734375;0.172543763887961 0.0176050995829438 0.190148863470905 18983.0859375;0.159585840450727 0.0181940815225686 0.177779921973295 31827.87109375;0.159585840450727 0.0181940815225686 0.177779921973295 31827.87109375]</ll>
- <rmsdtc>[0.0120025649666786 0.0429854914546013 0.0626314431428909 0.0840741172432899 0.102867223322392 0.107041172683239]</rmsdtc>
- <rmsgdt>[0.00329719926230609 0.012539790943265 0.0260289255529642 0.0434735082089901 0.0590498559176922 0.0631271600723267]</rmsgdt>
- <rmsdt>0.107041172683239</rmsdt>
- <dt>0.0711724981665611</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025291/ses-3/sub-0025291_ses-3_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 33s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 3s</item>
- <item>Estimate background 3s</item>
- <item>Initial correction 3s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>21s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 5s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 45s</item>
- <item>SPM preprocessing 1 (estimate 2): 41s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 10s</item>
- <item>Update Segmentation 12s</item>
- <item>Update Skull-Stripping 23s</item>
- <item>Update probability maps 5s</item>
- <item>50s</item>
- <item>Global intensity correction: 8s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 21s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 1s</item>
- <item>Prepare segments (LASmod = 1.00) 9s</item>
- <item>Estimate local tissue thresholds (WM) 10s</item>
- <item>Estimate local tissue thresholds (GM) 15s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 22s</item>
- <item>63s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 4s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 8s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 14s</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>39s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s</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>7s</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 | 0.0840 0.0000 0.0840 | 32.0000</item>
- <item>2 | 2.50 | 0.0807 0.0014 0.0821 | 29.4886</item>
- <item>3 | 2.50 | 0.0798 0.0021 0.0819 | 26.9772</item>
- <item>4 | 2.50 | 0.0794 0.0023 0.0817 | 24.6107</item>
- <item>5 | 2.50 | 0.0790 0.0025 0.0815 | 22.6548</item>
- <item>6 | 2.50 | 0.0787 0.0026 0.0813 | 20.6989</item>
- <item>7 | 2.50 | 0.0784 0.0027 0.0810 | 18.9688</item>
- <item>8 | 2.50 | 0.0780 0.0028 0.0808 | 17.4455</item>
- <item>9 | 2.50 | 0.0777 0.0029 0.0806 | 15.9223</item>
- <item>10 | 2.50 | 0.0773 0.0030 0.0803 | 14.6627</item>
- <item>11 | 2.50 | 0.0770 0.0031 0.0801 | 13.4764</item>
- <item>12 | 2.50 | 0.0766 0.0031 0.0798 | 12.3015</item>
- <item>13 | 2.50 | 0.0763 0.0032 0.0795 | 11.3776</item>
- <item>14 | 2.50 | 0.0759 0.0033 0.0792 | 10.4537</item>
- <item>15 | 2.25 | 0.0743 0.0034 0.0777 | 9.5920</item>
- <item>16 | 2.25 | 0.0713 0.0049 0.0762 | 8.8725</item>
- <item>29 | 2.00 | 0.0720 0.0022 0.0742 | 3.3283</item>
- <item>30 | 2.00 | 0.0659 0.0046 0.0705 | 3.1221</item>
- <item>31 | 2.00 | 0.0639 0.0055 0.0694 | 2.9160</item>
- <item>43 | 1.75 | 0.0626 0.0032 0.0658 | 1.5785</item>
- <item>44 | 1.75 | 0.0588 0.0052 0.0640 | 1.5194</item>
- <item>45 | 1.75 | 0.0575 0.0059 0.0634 | 1.4626</item>
- <item>57 | 1.50 | 0.0559 0.0043 0.0602 | 1.0900</item>
- <item>58 | 1.50 | 0.0532 0.0061 0.0593 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 93s</item>
- <item>Prepare output 6s</item>
- <item>100s</item>
- <item>Jacobian determinant (RMS): 0.012 0.043 0.063 0.084 0.103 | 0.107041</item>
- <item>Template Matching: 0.084 0.214 0.192 0.173 0.160 | 0.159586</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: 20s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 30s</item>
- <item>64s</item>
- <item>Create initial surface 54s</item>
- <item>Topology correction: 65s</item>
- <item>Surface refinement: 66s</item>
- <item>Reduction of surface collisions with optimization: 44s</item>
- <item>Spherical mapping with areal smoothing 56s</item>
- <item>Spherical registration 181s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 17s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 28s</item>
- <item>59s</item>
- <item>Create initial surface 53s</item>
- <item>Topology correction: 62s</item>
- <item>Surface refinement: 67s</item>
- <item>Reduction of surface collisions with optimization: 43s</item>
- <item>Spherical mapping with areal smoothing 54s</item>
- <item>Spherical registration 191s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5367 0.6308 mm</item>
- <item>Surface intensity / position RMSE: 0.0681 / 0.0704</item>
- <item>Euler number / defect number / defect size: 20.0 / 14.0 / 0.71%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/surf/lh.thickness.sub-0025291_ses-3_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/surf/rh.thickness.sub-0025291_ses-3_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/sub-0025291_ses-3_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1122s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 5s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 18s</item>
- <item>ROI estimation of 'lpba40' atlas 5s</item>
- <item>ROI estimation of 'hammers' atlas 13s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 4s</item>
- <item>ROI estimation of 'aal3' atlas 7s</item>
- <item>ROI estimation of 'mori' atlas 10s</item>
- <item>ROI estimation of 'anatomy3' atlas 14s</item>
- <item>ROI estimation of 'julichbrain' atlas 19s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 14s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 47s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s</item>
- <item>Write results 5s</item>
- <item>201s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/report/catreport_sub-0025291_ses-3_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 31 minute(s) and 23 second(s).</item>
- <item>Image Quality Rating (IQR): 82.44% (B-)</item>
- <item>GM volume (GMV): 49.25% (695.01 / 1411.08 ml)</item>
- <item>GM thickness (GMT): 2.54 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-3/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|