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- <file>sub-25_T1w</file>
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- <F>/var/lib/condor/execute/dir_4495/ds/sub-25/sub-25_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_4495/ds/sub-25/mri/msub-25_T1w.nii</Fm>
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- <fnames>.._4495/ds/sub-25/sub-25_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>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_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>
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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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- <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>
- </tr>
- <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>
- </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/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>
- </tr>
- <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>
- <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>
- <td>[false]</td>
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- </atlas>
- <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>
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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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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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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>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
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- <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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- <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>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
- <darteltpms>
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- </darteltpms>
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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>[1.4190000295639 92.4766693115234 200.307968139648 271.814849853516]</tissue_mn>
- <tissue_mnr>[0.00522046582773328 0.340219348669052 0.73692798614502 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.36596852667072 30.2054094273924 23.0728956645438 13.2550190474976]</tissue_std>
- <tissue_stdr>[0.0272414274513721 0.111708112061024 0.085330069065094 0.0490207932889462]</tissue_stdr>
- <contrast>71.8821411132812</contrast>
- <contrastr>0.26445260643959</contrastr>
- <NCR>0.126882135868073</NCR>
- <ICR>0.269344419240952</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000615379376 1.99999995629341 2.00000000333244]</res_vx_vol>
- <res_RMS>2.00000203780865</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[6.59955549240112 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>4.11654424667358</contrastr>
- <NCR>2.15248537063599</NCR>
- <ICR>1.1278383731842</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.08248529378182</SurfaceDefectArea>
- <SurfaceDefectNumber>1.55</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.3540917634964</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.31349778175354</SurfacePositionRMSE>
- <IQR>2.08591639314495</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>20220711-091358</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.329941175127283</SurfaceDefectArea>
- <SurfaceDefectNumber>11</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0677045881748199</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0656748935580254</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.329941175127283</defect_size>
- <vol_abs_CGW>[227.811910551827 799.151855228977 594.469964645463 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.82778293128684</vol_abs_WMH>
- <vol_rel_WMH>0.000510525293604951</vol_rel_WMH>
- <surf_TSA>2225.82403669342</surf_TSA>
- <vol_TIV>1621.43373042627</vol_TIV>
- <vol_rel_CGW>[0.140500290746965 0.492867417417599 0.366632291835436 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.62797622334391 0.624256833728452]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.64621591567993 0.724153758306472 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.96675197209487 0.255046870105248 0.277024176897631;2.63808792201277 0.18409565950605 0.427685766933819;3.28017243003153 0.267907887259949 0.29529005616855]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.97047134248112 0.340136972801563 0.503634293720991;4.20236840051249 0.336764096161912 0.496365706279009]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.08310920540019</vol_TIV>
- <vol_rel_CGW>[0.5 6.70164183580457 4.43448799991804 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0510525293605</vol_rel_WMH>
- <surf_TSA>8.62393960646489</surf_TSA>
- <SQR>5.50515307757271</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.328775182946936 245 3 6774.38670727055 0.272444849236854]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00583653897047043 0.00383113953284919 0.427476167678833]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[948.797404445755 537.023478630981 362.367452697411 759.03237138271 3063.48542042245 5030.58625428049]</SPMvols0>
- <SPMvols1>[844.686857647515 505.199890819667 220.854214700082 1645.77833451234 2727.02843543775 4149.05336988649]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[109.186302185059 205.777801513672 263.690490722656]</T3th>
- <Tth>
- <T3th>[0 40.9495849609375 4.33645915985107 109.186302185059 205.777801513672 263.690490722656 340.942565917969 672.822937011719]</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>[0.0201134588569403 0.0714767649769783 0.0783359855413437 0 0]</dtc>
- <ll>[0.080174861692724 0 0.080174861692724 0;0.190705041782338 0.00975670534021714 0.200461747122555 2080.59790039062;0.190705041782338 0.00975670534021714 0.200461747122555 2080.59790039062]</ll>
- <rmsdtc>[0.0437084846198559 0.0927725955843925 0.10309860855341]</rmsdtc>
- <rmsgdt>[0.0312625728547573 0.0430400259792805 0.052870649844408]</rmsgdt>
- <rmsdt>0.10309860855341</rmsdt>
- <dt>0.0783359855413437</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>[0.00964084360748529 0.0349675118923187 0.0484569482505322 0.0563716739416122 0.0625901520252228 0.0705641582608223]</dtc>
- <ll>[0.0811113537246422 0 0.0811113537246422 0;0.217085668498168 0.0121196314102564 0.229205299908425 6203.736328125;0.197334793292317 0.0157806205164357 0.213115413808753 11357.501953125;0.177274307294449 0.0183425914188396 0.195616898713288 19778.302734375;0.160400338010682 0.0216009147381918 0.182001252748873 37787.625;0.160400338010682 0.0216009147381918 0.182001252748873 37787.625]</ll>
- <rmsdtc>[0.011050689034164 0.0398889370262623 0.0595122948288918 0.0849370136857033 0.111195877194405 0.118831172585487]</rmsdtc>
- <rmsgdt>[0.00323635712265968 0.0128961270675063 0.0290918871760368 0.0509290099143982 0.0714950188994408 0.076927587389946]</rmsgdt>
- <rmsdt>0.118831172585487</rmsdt>
- <dt>0.0705641582608223</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_4495/ds/sub-25/sub-25_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 68s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 9s</item>
- <item>Refine background 4s</item>
- <item>Final correction 8s</item>
- <item>Final scaling 8s</item>
- <item>54s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 13s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 102s</item>
- <item>SPM preprocessing 1 (estimate 2): 107s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 26s</item>
- <item>Update Skull-Stripping 52s</item>
- <item>Update probability maps 10s</item>
- <item>110s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 20s</item>
- <item>Fast Optimized Shooting registration 47s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 21s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 29s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 25s</item>
- <item>110s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 36s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 5s</item>
- <item>95s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 55s</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) 6s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>16s</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 | 0.0811 0.0000 0.0811 | 32.0000</item>
- <item>2 | 2.50 | 0.0790 0.0010 0.0801 | 29.4886</item>
- <item>3 | 2.50 | 0.0784 0.0015 0.0800 | 26.9772</item>
- <item>4 | 2.50 | 0.0781 0.0017 0.0798 | 24.6107</item>
- <item>5 | 2.50 | 0.0779 0.0019 0.0797 | 22.6548</item>
- <item>6 | 2.50 | 0.0776 0.0019 0.0796 | 20.6989</item>
- <item>7 | 2.50 | 0.0774 0.0020 0.0794 | 18.9688</item>
- <item>8 | 2.50 | 0.0772 0.0021 0.0793 | 17.4455</item>
- <item>9 | 2.50 | 0.0769 0.0022 0.0791 | 15.9223</item>
- <item>10 | 2.50 | 0.0766 0.0023 0.0789 | 14.6627</item>
- <item>11 | 2.50 | 0.0764 0.0024 0.0788 | 13.4764</item>
- <item>12 | 2.50 | 0.0761 0.0024 0.0785 | 12.3015</item>
- <item>13 | 2.50 | 0.0758 0.0025 0.0784 | 11.3776</item>
- <item>14 | 2.50 | 0.0756 0.0026 0.0781 | 10.4537</item>
- <item>15 | 2.25 | 0.0752 0.0026 0.0778 | 9.5920</item>
- <item>16 | 2.25 | 0.0724 0.0040 0.0764 | 8.8725</item>
- <item>29 | 2.00 | 0.0738 0.0018 0.0756 | 3.3283</item>
- <item>30 | 2.00 | 0.0678 0.0043 0.0721 | 3.1221</item>
- <item>31 | 2.00 | 0.0658 0.0053 0.0710 | 2.9160</item>
- <item>43 | 1.75 | 0.0649 0.0030 0.0679 | 1.5785</item>
- <item>44 | 1.75 | 0.0606 0.0053 0.0659 | 1.5194</item>
- <item>45 | 1.75 | 0.0591 0.0061 0.0652 | 1.4626</item>
- <item>57 | 1.50 | 0.0578 0.0044 0.0622 | 1.0900</item>
- <item>58 | 1.50 | 0.0546 0.0065 0.0611 | 1.0730</item>
- <item>59 | 1.50 | 0.0535 0.0072 0.0607 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 253s</item>
- <item>Prepare output 13s</item>
- <item>266s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.060 0.085 0.111 | 0.118831</item>
- <item>Template Matching: 0.081 0.217 0.197 0.177 0.160 | 0.160400</item>
- <item>Write result maps: 32s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 51s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 71s</item>
- <item>154s</item>
- <item>Create initial surface 125s</item>
- <item>Topology correction: 143s</item>
- <item>Surface refinement: 124s</item>
- <item>Reduction of surface collisions with optimization: 127s</item>
- <item>Spherical mapping with areal smoothing 128s</item>
- <item>Spherical registration 300s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 51s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 71s</item>
- <item>154s</item>
- <item>Create initial surface 124s</item>
- <item>Topology correction: 143s</item>
- <item>Surface refinement: 136s</item>
- <item>Reduction of surface collisions with optimization: 128s</item>
- <item>Spherical mapping with areal smoothing 126s</item>
- <item>Spherical registration 300s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6280 0.6242 mm</item>
- <item>Surface intensity / position RMSE: 0.0677 / 0.0657</item>
- <item>Euler number / defect number / defect size: 12.0 / 11.0 / 0.33%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4495/ds/sub-25/surf/lh.thickness.sub-25_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4495/ds/sub-25/surf/rh.thickness.sub-25_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4495/ds/sub-25/sub-25_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 2338s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 14s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 52s</item>
- <item>ROI estimation of 'lpba40' atlas 15s</item>
- <item>ROI estimation of 'hammers' atlas 37s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 13s</item>
- <item>ROI estimation of 'aal3' atlas 21s</item>
- <item>ROI estimation of 'mori' atlas 32s</item>
- <item>ROI estimation of 'anatomy3' atlas 46s</item>
- <item>ROI estimation of 'julichbrain' atlas 60s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 98s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 144s</item>
- <item>Write results 145s</item>
- <item>588s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_4495/ds/sub-25/report/catreport_sub-25_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 69 minute(s) and 35 second(s).</item>
- <item>Image Quality Rating (IQR): 84.14% (B)</item>
- <item>GM volume (GMV): 49.29% (799.15 / 1621.43 ml)</item>
- <item>GM thickness (GMT): 2.63 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_4495/ds/sub-25/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_4495/ds/sub-25/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_4495/ds/sub-25/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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