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- <F>/var/lib/condor/execute/dir_456/ds/sub-13/sub-13_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_456/ds/sub-13/mri/msub-13_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_456/ds/sub-13/mri/p0sub-13_T1w.nii</Fp0>
- <fnames>..r_456/ds/sub-13/sub-13_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>
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- </opts>
- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
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- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
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- <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_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_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>
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- <td>0</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/lpba40.nii</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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- <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>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
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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>
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- <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>
- <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/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>
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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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- <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>
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- <td>1</td>
- <td>0</td>
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- <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>
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- <MB>13</MB>
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- <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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- <regstr>0.5</regstr>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- </shootingtpms>
- <templates>
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- <tissue_mnr>[0.00566171109676361 0.335168212652206 0.728112757205963 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[48.5977937578943 34.6119857356506 23.6785896391747 14.4268001890793]</tissue_std>
- <tissue_stdr>[0.175468191504478 0.124970749020576 0.0854944065213203 0.0520897023379803]</tissue_stdr>
- <contrast>76.1620483398438</contrast>
- <contrastr>0.273435324430466</contrastr>
- <NCR>0.108647391200066</NCR>
- <ICR>0.222386687994003</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99998914803181 2.00000003588702 2.00000005799687]</res_vx_vol>
- <res_RMS>1.9999964139785</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[7.28589296340942 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>3.98180341720581</contrastr>
- <NCR>1.89071762561798</NCR>
- <ICR>1.01137566566467</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.06999045726267</SurfaceDefectArea>
- <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.41485548019409</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.40667581558228</SurfacePositionRMSE>
- <IQR>1.95068752684488</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>20220711-084717</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.279961829050682</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0707427710294724</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.070333793759346</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.279961829050682</defect_size>
- <vol_abs_CGW>[191.893386337897 639.413609293615 435.122779653766 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.520005053742746</vol_abs_WMH>
- <vol_rel_WMH>0.000410607097125151</vol_rel_WMH>
- <surf_TSA>1790.43505138732</surf_TSA>
- <vol_TIV>1266.42977528528</vol_TIV>
- <vol_rel_CGW>[0.151523116467055 0.504894643012937 0.343582240520008 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.5391300827278 0.58837485552795]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55095410346985 0.710858695311869 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.97324785780202 0.232296283698176 0.297677643456831;2.56720567498618 0.16466218208549 0.42448393983703;3.15200602163631 0.2490211291642 0.277838416706139]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.944402456441178 0.345965524534977 0.529801324503311;4.10522084112157 0.374647779316994 0.470198675496689]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.41342984924795</vol_TIV>
- <vol_rel_CGW>[0.571176660687047 6.91764804261741 4.02051437715531 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04106070971252</vol_rel_WMH>
- <surf_TSA>8.58045756499907</surf_TSA>
- <SQR>5.66616768491241</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.409927070914925 1301 86 5955.30496598974 0.32261601482258]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00394910993054509 0 0.352892160415649]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[767.979966700889 380.995454315562 256.631325347221 877.695272287196 2616.30600883208 5740.7871858448]</SPMvols0>
- <SPMvols1>[696.333194163474 358.502096542341 169.75355608006 1945.81770348326 2369.92529124398 4552.20745962544]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[110.760902404785 209.709197998047 270.675994873047]</T3th>
- <Tth>
- <T3th>[0 44.5410003662109 3.46153569221497 110.760902404785 209.709197998047 270.675994873047 350.633544921875 624.126892089844]</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>[0.0231825783848763 0.0841117948293686 0.0929349437355995 0 0]</dtc>
- <ll>[0.0815046843932886 0 0.0815046843932886 0;0.179599116257831 0.0110734822798748 0.190672598537706 2361.39794921875;0.179599116257831 0.0110734822798748 0.190672598537706 2361.39794921875]</ll>
- <rmsdtc>[0.0501103810966015 0.107636749744415 0.117948174476624]</rmsdtc>
- <rmsgdt>[0.0357599817216396 0.0455325990915298 0.055339265614748]</rmsgdt>
- <rmsdt>0.117948174476624</rmsdt>
- <dt>0.0929349437355995</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>[0.0115332687273622 0.0439163446426392 0.0623226054012775 0.0697228461503983 0.0738978758454323 0.0828021839261055]</dtc>
- <ll>[0.0823953542376396 0 0.0823953542376396 0;0.207908485958486 0.0165832951770452 0.224491781135531 8488.57421875;0.182832225772253 0.0182340799275439 0.201066305699797 13123.2861328125;0.163324629592533 0.0184857258882731 0.181810355480806 19932.640625;0.150797930720672 0.0187758077557817 0.169573738476454 32845.515625;0.150797930720672 0.0187758077557817 0.169573738476454 32845.515625]</ll>
- <rmsdtc>[0.0133326184004545 0.0493148379027843 0.0725559368729591 0.0966320112347603 0.117222361266613 0.120685078203678]</rmsdtc>
- <rmsgdt>[0.00354258785955608 0.013907827436924 0.0289645753800869 0.0476471558213234 0.0675701126456261 0.0679083690047264]</rmsgdt>
- <rmsdt>0.120685078203678</rmsdt>
- <dt>0.0828021839261055</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_456/ds/sub-13/sub-13_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 23s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 6s</item>
- <item>36s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 67s</item>
- <item>SPM preprocessing 1 (estimate 2): 57s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 36s</item>
- <item>Update probability maps 7s</item>
- <item>74s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 9s</item>
- <item>Fast Optimized Shooting registration 30s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.01) 13s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 20s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 20s</item>
- <item>76s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 12s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 22s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>59s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 30s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>10s</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 | 0.0824 0.0000 0.0824 | 32.0000</item>
- <item>2 | 2.50 | 0.0790 0.0014 0.0804 | 29.4886</item>
- <item>3 | 2.50 | 0.0780 0.0022 0.0801 | 26.9772</item>
- <item>4 | 2.50 | 0.0775 0.0024 0.0799 | 24.6107</item>
- <item>5 | 2.50 | 0.0771 0.0026 0.0797 | 22.6548</item>
- <item>6 | 2.50 | 0.0767 0.0028 0.0795 | 20.6989</item>
- <item>7 | 2.50 | 0.0764 0.0029 0.0793 | 18.9688</item>
- <item>8 | 2.50 | 0.0760 0.0030 0.0790 | 17.4455</item>
- <item>9 | 2.50 | 0.0756 0.0031 0.0787 | 15.9223</item>
- <item>10 | 2.50 | 0.0752 0.0033 0.0785 | 14.6627</item>
- <item>11 | 2.50 | 0.0748 0.0034 0.0782 | 13.4764</item>
- <item>12 | 2.50 | 0.0744 0.0035 0.0778 | 12.3015</item>
- <item>13 | 2.50 | 0.0739 0.0036 0.0775 | 11.3776</item>
- <item>14 | 2.50 | 0.0735 0.0037 0.0772 | 10.4537</item>
- <item>15 | 2.25 | 0.0728 0.0038 0.0766 | 9.5920</item>
- <item>16 | 2.25 | 0.0693 0.0055 0.0748 | 8.8725</item>
- <item>29 | 2.00 | 0.0696 0.0025 0.0721 | 3.3283</item>
- <item>30 | 2.00 | 0.0632 0.0051 0.0683 | 3.1221</item>
- <item>31 | 2.00 | 0.0609 0.0061 0.0670 | 2.9160</item>
- <item>43 | 1.75 | 0.0595 0.0035 0.0631 | 1.5785</item>
- <item>44 | 1.75 | 0.0557 0.0055 0.0612 | 1.5194</item>
- <item>45 | 1.75 | 0.0544 0.0062 0.0606 | 1.4626</item>
- <item>57 | 1.50 | 0.0529 0.0046 0.0575 | 1.0900</item>
- <item>58 | 1.50 | 0.0503 0.0063 0.0565 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 134s</item>
- <item>Prepare output 9s</item>
- <item>143s</item>
- <item>Jacobian determinant (RMS): 0.013 0.049 0.073 0.097 0.117 | 0.120685</item>
- <item>Template Matching: 0.082 0.208 0.183 0.163 0.151 | 0.150798</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: 25s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 37s</item>
- <item>79s</item>
- <item>Create initial surface 77s</item>
- <item>Topology correction: 85s</item>
- <item>Surface refinement: 70s</item>
- <item>Reduction of surface collisions with optimization: 59s</item>
- <item>Spherical mapping with areal smoothing 79s</item>
- <item>Spherical registration 300s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 39s</item>
- <item>83s</item>
- <item>Create initial surface 75s</item>
- <item>Topology correction: 71s</item>
- <item>Surface refinement: 93s</item>
- <item>Reduction of surface collisions with optimization: 60s</item>
- <item>Spherical mapping with areal smoothing 71s</item>
- <item>Spherical registration 288s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5391 0.5884 mm</item>
- <item>Surface intensity / position RMSE: 0.0707 / 0.0703</item>
- <item>Euler number / defect number / defect size: 18.0 / 15.0 / 0.28%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_456/ds/sub-13/surf/lh.thickness.sub-13_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_456/ds/sub-13/surf/rh.thickness.sub-13_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_456/ds/sub-13/sub-13_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1570s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 25s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 17s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 21s</item>
- <item>ROI estimation of 'julichbrain' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 44s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 66s</item>
- <item>Write results 67s</item>
- <item>276s</item>
- <item>Quality check: 4s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_456/ds/sub-13/report/catreport_sub-13_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 43 minute(s) and 14 second(s).</item>
- <item>Image Quality Rating (IQR): 85.49% (B)</item>
- <item>GM volume (GMV): 50.49% (639.41 / 1266.43 ml)</item>
- <item>GM thickness (GMT): 2.54 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_456/ds/sub-13/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_456/ds/sub-13/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_456/ds/sub-13/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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