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- <filedata>
- <path>/var/lib/condor/execute/dir_7213/ds/sub-sc036</path>
- <file>sub-sc036_T1w</file>
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- <F>/var/lib/condor/execute/dir_7213/ds/sub-sc036/sub-sc036_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_7213/ds/sub-sc036/mri/msub-sc036_T1w.nii</Fm>
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- <fnames>..13/ds/sub-sc036/sub-sc036_T1w</fnames>
- </filedata>
- <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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- <fwhm>1</fwhm>
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- </opts>
- <extopts>
- <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_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>32</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>
- <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>
- <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/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>
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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>
- <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_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>
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- <item>gm</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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- <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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- <CT>1</CT>
- <CB>3</CB>
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- <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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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
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- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <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>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
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- <tissue_mn>[0 162203.09375 349571.4375 495552.625]</tissue_mn>
- <tissue_mnr>[0 0.327317595481873 0.705417394638062 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[70381.8199005452 64199.5119333336 46900.5695818301 30097.3834654181]</tissue_std>
- <tissue_stdr>[0.14202693104744 0.129551351070404 0.0946429669857025 0.0607349909842014]</tissue_stdr>
- <contrast>145981.1875</contrast>
- <contrastr>0.294582605361938</contrastr>
- <NCR>0.104286216199398</NCR>
- <ICR>0.27102991938591</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999995148426 2.00000000690767 2.00000001969131]</res_vx_vol>
- <res_RMS>1.99999999269442</res_RMS>
- <res_BB>0.5</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>3.66459441184998</contrastr>
- <NCR>1.82811117172241</NCR>
- <ICR>1.13201868534088</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.07747779508673</SurfaceDefectArea>
- <SurfaceDefectNumber>1.55</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.24630308151245</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.20948731899261</SurfacePositionRMSE>
- <IQR>1.9273049211154</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>20220711-172144</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.309911180346902</SurfaceDefectArea>
- <SurfaceDefectNumber>11</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0623151548206806</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0604743659496307</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.309911180346902</defect_size>
- <vol_abs_CGW>[317.682033457681 810.359343138653 589.374607842369 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.38798812446791</vol_abs_WMH>
- <vol_rel_WMH>0.000808184002620389</vol_rel_WMH>
- <surf_TSA>2198.00501935951</surf_TSA>
- <vol_TIV>1717.4159844387</vol_TIV>
- <vol_rel_CGW>[0.184976753643939 0.471848026617442 0.343175219738619 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.70217960672224 0.640050444202705]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.71876907348633 0.74896850094403 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99006382692477 0.265848549319282 0.24654142674254;2.6798600762144 0.190385233861275 0.430769317534529;3.35502511963182 0.266073441897984 0.322689255722931]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.937982048344551 0.332933081644951 0.54982004167456;4.24999809270153 0.315084714592366 0.45017995832544]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>3.05927074905212</vol_TIV>
- <vol_rel_CGW>[1.17199629389258 6.32413840907762 4.01320437748957 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08081840026204</vol_rel_WMH>
- <surf_TSA>8.6239004092456</surf_TSA>
- <SQR>5.18847064316289</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.559684085845947 2883 968 4617.04694940466 0.356386512828842]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.381329894065857]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[981.911113754543 527.679722572421 494.421184051533 665.233135118652 2412.15136426052 6075.6512599776]</SPMvols0>
- <SPMvols1>[859.099025521462 494.099380155659 319.672076436038 798.481391145891 1893.0853194317 6121.35292691671]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[190359.796875 373286.1875 485401.40625]</T3th>
- <Tth>
- <T3th>[0 0 4364.8662109375 190359.796875 373286.1875 485401.40625 632922.25 1102557.25]</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>[0.0227934289723635 0.0852574110031128 0.0950071662664413 0 0]</dtc>
- <ll>[0.0888497549898866 0 0.0888497549898866 0;0.196973070233953 0.0125883601579059 0.209561430391859 2684.44262695312;0.196973070233953 0.0125883601579059 0.209561430391859 2684.44262695312]</ll>
- <rmsdtc>[0.0490117818117142 0.111241571605206 0.123824842274189]</rmsdtc>
- <rmsgdt>[0.0347417667508125 0.0505611188709736 0.0621194876730442]</rmsgdt>
- <rmsdt>0.123824842274189</rmsdt>
- <dt>0.0950071662664413</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>[0.0109382513910532 0.0451695770025253 0.060969490557909 0.0695168599486351 0.0755893364548683 0.0853046625852585]</dtc>
- <ll>[0.0887717415493519 0 0.0887717415493519 0;0.220915369352869 0.0194397206959707 0.24035509004884 9950.70703125;0.199133776774599 0.0200781185955285 0.219211895370127 14450.462890625;0.176953626380913 0.0211280196027765 0.19808164598369 22781.751953125;0.15962221104031 0.0235954423221042 0.183217653362415 41276.7578125;0.15962221104031 0.0235954423221042 0.183217653362415 41276.7578125]</ll>
- <rmsdtc>[0.0125603880733252 0.0478971861302853 0.0726056918501854 0.0984311550855637 0.121265277266502 0.127836748957634]</rmsdtc>
- <rmsgdt>[0.00354343932121992 0.0143775548785925 0.0309279374778271 0.0510538071393967 0.0678979083895683 0.0728709697723389]</rmsgdt>
- <rmsdt>0.127836748957634</rmsdt>
- <dt>0.0853046625852585</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_7213/ds/sub-sc036/sub-sc036_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 30s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>38s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 77s</item>
- <item>SPM preprocessing 1 (estimate 2): 59s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 19s</item>
- <item>Update Skull-Stripping 39s</item>
- <item>Update probability maps 8s</item>
- <item>81s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 13s</item>
- <item>Fast Optimized Shooting registration 29s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.05) 16s</item>
- <item>Estimate local tissue thresholds (WM) 18s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 18s</item>
- <item>85s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 20s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.09) 30s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>82s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 37s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>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 | 0.0888 0.0000 0.0888 | 32.0000</item>
- <item>2 | 2.50 | 0.0844 0.0016 0.0860 | 29.4886</item>
- <item>3 | 2.50 | 0.0831 0.0024 0.0855 | 26.9772</item>
- <item>4 | 2.50 | 0.0825 0.0027 0.0852 | 24.6107</item>
- <item>5 | 2.50 | 0.0820 0.0029 0.0850 | 22.6548</item>
- <item>6 | 2.50 | 0.0816 0.0030 0.0847 | 20.6989</item>
- <item>7 | 2.50 | 0.0812 0.0032 0.0844 | 18.9688</item>
- <item>8 | 2.50 | 0.0808 0.0033 0.0841 | 17.4455</item>
- <item>9 | 2.50 | 0.0804 0.0034 0.0838 | 15.9223</item>
- <item>10 | 2.50 | 0.0800 0.0035 0.0835 | 14.6627</item>
- <item>11 | 2.50 | 0.0795 0.0036 0.0831 | 13.4764</item>
- <item>12 | 2.50 | 0.0791 0.0037 0.0828 | 12.3015</item>
- <item>13 | 2.50 | 0.0786 0.0038 0.0824 | 11.3776</item>
- <item>14 | 2.50 | 0.0782 0.0039 0.0821 | 10.4537</item>
- <item>15 | 2.25 | 0.0787 0.0040 0.0827 | 9.5920</item>
- <item>16 | 2.25 | 0.0751 0.0058 0.0810 | 8.8725</item>
- <item>17 | 2.25 | 0.0736 0.0065 0.0801 | 8.1530</item>
- <item>29 | 2.00 | 0.0752 0.0030 0.0781 | 3.3283</item>
- <item>30 | 2.00 | 0.0687 0.0056 0.0744 | 3.1221</item>
- <item>31 | 2.00 | 0.0664 0.0067 0.0731 | 2.9160</item>
- <item>43 | 1.75 | 0.0650 0.0039 0.0690 | 1.5785</item>
- <item>44 | 1.75 | 0.0606 0.0062 0.0668 | 1.5194</item>
- <item>45 | 1.75 | 0.0590 0.0070 0.0660 | 1.4626</item>
- <item>57 | 1.50 | 0.0574 0.0052 0.0626 | 1.0900</item>
- <item>58 | 1.50 | 0.0542 0.0072 0.0615 | 1.0730</item>
- <item>59 | 1.50 | 0.0532 0.0079 0.0611 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 161s</item>
- <item>Prepare output 10s</item>
- <item>171s</item>
- <item>Jacobian determinant (RMS): 0.013 0.048 0.073 0.098 0.121 | 0.127837</item>
- <item>Template Matching: 0.089 0.221 0.199 0.177 0.160 | 0.159622</item>
- <item>Write result maps: 21s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 44s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 51s</item>
- <item>119s</item>
- <item>Create initial surface 100s</item>
- <item>Topology correction: 104s</item>
- <item>Surface refinement: 97s</item>
- <item>Reduction of surface collisions with optimization: 83s</item>
- <item>Spherical mapping with areal smoothing 93s</item>
- <item>Spherical registration 291s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 39s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 52s</item>
- <item>116s</item>
- <item>Create initial surface 97s</item>
- <item>Topology correction: 104s</item>
- <item>Surface refinement: 97s</item>
- <item>Reduction of surface collisions with optimization: 83s</item>
- <item>Spherical mapping with areal smoothing 100s</item>
- <item>Spherical registration 301s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.7022 0.6400 mm</item>
- <item>Surface intensity / position RMSE: 0.0623 / 0.0605</item>
- <item>Euler number / defect number / defect size: 12.0 / 11.0 / 0.31%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_7213/ds/sub-sc036/surf/lh.thickness.sub-sc036_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_7213/ds/sub-sc036/surf/rh.thickness.sub-sc036_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_7213/ds/sub-sc036/sub-sc036_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 1886s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 16s</item>
- <item>ROI estimation of 'anatomy3' atlas 23s</item>
- <item>ROI estimation of 'julichbrain' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 72s</item>
- <item>Write results 73s</item>
- <item>306s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_7213/ds/sub-sc036/report/catreport_sub-sc036_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 50 minute(s) and 58 second(s).</item>
- <item>Image Quality Rating (IQR): 85.73% (B)</item>
- <item>GM volume (GMV): 47.18% (810.36 / 1717.42 ml)</item>
- <item>GM thickness (GMT): 2.70 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_7213/ds/sub-sc036/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_7213/ds/sub-sc036/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_7213/ds/sub-sc036/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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