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- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <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>
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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>
- <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>
- <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>
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- <reduce_mesh>1</reduce_mesh>
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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>
- <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>
- <td>0</td>
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- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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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>
- <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/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>
- <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>
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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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- <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>
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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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- <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_100Parcels_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_200Parcels_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_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_3618456/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <satlas>
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- <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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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.108496579034416</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0627633929252625</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.060245405882597</SurfacePositionRMSE>
- <res_vx_vol>[1.00000000847329 1.00000001267105 1.00000002081384]</res_vx_vol>
- <res_vx_voli>[1.00000006861205 1.00000001332438 1.00000002133704]</res_vx_voli>
- <res_RMS>1.00000001398606</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.35999965667725 63.8370018005371 193.341995239258 300.330993652344]</tissue_mn>
- <tissue_mnr>[0.0311656128615141 0.21255549788475 0.643763065338135 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[10.4127518590032 31.7523224394007 33.2714622349481 20.325556035902]</tissue_std>
- <tissue_stdr>[0.0357862189412117 0.109125383198261 0.11434631049633 0.0698542296886444]</tissue_stdr>
- <contrast>108.057304382324</contrast>
- <contrastr>0.359794050455093</contrastr>
- <res_ECR>0.406126797199249</res_ECR>
- <NCR>0.125643312931061</NCR>
- <ICR>0.268057733774185</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000001694658 2.0000000253421 2.00000004162768]</res_vx_vol>
- <res_RMS>2.00000002797212</res_RMS>
- <res_ECR>2.9700345993042</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>2.68642258644104</contrastr>
- <NCR>2.1347017288208</NCR>
- <ICR>1.12464714050293</ICR>
- <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0271241447586</SurfaceDefectArea>
- <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.25526785850525</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.2049081325531</SurfacePositionRMSE>
- <SIQR>2.62396307711628</SIQR>
- <IQR>2.07495234168736</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>20231031-023124</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.108496579034416</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0627633929252625</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.060245405882597</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>6</EC_abs>
- <defect_size>0.108496579034416</defect_size>
- <vol_abs_CGW>[320.357495829526 620.593369973179 454.739321472308 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.00705108439381</vol_abs_WMH>
- <vol_rel_WMH>0.000721543429605968</vol_rel_WMH>
- <surf_TSA>1733.39792668879</surf_TSA>
- <vol_TIV>1395.69018727501</vol_TIV>
- <vol_rel_CGW>[0.229533386958177 0.444649805258604 0.325816807783219 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.42074437355424 0.605568282739526]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.40253829956055 0.767047428387319 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.87052414650814 0.258809415809142 0.316848933397649;2.45031683667834 0.170806438536015 0.438656865780171;3.10268446018438 0.27928302889866 0.24449420082218]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.836651014142665 0.260385027944209 0.550393137955683;4.13179315005599 0.385291968847037 0.449606862044317]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00044252427904</vol_TIV>
- <vol_rel_CGW>[1.97222318531208 5.83566460593757 3.70145128921012 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0721543429606</vol_rel_WMH>
- <surf_TSA>8.53936653627147</surf_TSA>
- <SQR>4.78775507394765</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.4404537122 0.422971535391111]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00134571653325111 0.00108564621768892 0.0438148528337479]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[709.065163423693 413.054607363462 574.911565255461 557.600206604912 597.988583324979 8522.74831546785]</SPMvols0>
- <SPMvols1>[614.004930077082 390.494122680621 348.754326213145 541.820859877285 511.003025322071 8408.34226835862]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[73.2460021972656 207.603607177734 294.693786621094]</T3th>
- <Tth>
- <T3th>[-3.75826001167297 -3.75825881958008 4.54044771194458 73.2460021972656 207.603607177734 294.693786621094 405.417663574219 734.071899414062]</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>[0.0207982081919909 0.0868588611483574 0.0985758602619171 0 0]</dtc>
- <ll>[0.0887505514901273 0 0.0887505514901273 0;0.207325966275182 0.0137370110702973 0.221062977345479 2929.39013671875;0.207325966275182 0.0137370110702973 0.221062977345479 2929.39013671875]</ll>
- <rmsdtc>[0.0453560166060925 0.124261103570461 0.141374737024307]</rmsdtc>
- <rmsgdt>[0.0321869291365147 0.0642215982079506 0.0806119069457054]</rmsgdt>
- <rmsdt>0.141374737024307</rmsdt>
- <dt>0.0985758602619171</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>[0.00908852089196444 0.0388640351593494 0.0537159852683544 0.0637491196393967 0.070913590490818 0.0810055285692215]</dtc>
- <ll>[0.0860319678794777 0 0.0860319678794777 0;0.224201587301587 0.0161347107753358 0.240336298076923 8258.955078125;0.204277804871949 0.0187788005827331 0.223056605454682 13515.328125;0.18214458527162 0.0206776661524179 0.202822251424038 22296.1484375;0.164412160524491 0.0234563663501592 0.18786852687465 41033.46484375;0.164412160524491 0.0234563663501592 0.18786852687465 41033.46484375]</ll>
- <rmsdtc>[0.0110954158008099 0.0432451441884041 0.0735190138220787 0.105973303318024 0.135220259428024 0.144506901502609]</rmsdtc>
- <rmsgdt>[0.00350553286261857 0.0154803087934852 0.0359206832945347 0.0612203106284142 0.0826382637023926 0.0911990627646446]</rmsgdt>
- <rmsdt>0.144506901502609</rmsdt>
- <dt>0.0810055285692215</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026007/ses-2/sub-0026007_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 37s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>24s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 5s</item>
- <item>Use initial fine affine registration. 44s</item>
- <item>SPM preprocessing 1 (estimate 2): 36s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 12s</item>
- <item>Update Segmentation 14s</item>
- <item>Update Skull-Stripping 29s</item>
- <item>Update probability maps 6s</item>
- <item>60s</item>
- <item>Global intensity correction: 11s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 23s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 1s</item>
- <item>Prepare segments (LASmod = 1.05) 9s</item>
- <item>Estimate local tissue thresholds (WM) 12s</item>
- <item>Estimate local tissue thresholds (GM) 17s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 26s</item>
- <item>70s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 7s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.26) 12s</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>38s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</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>8s</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 | 0.0860 0.0000 0.0860 | 32.0000</item>
- <item>2 | 2.50 | 0.0840 0.0010 0.0850 | 29.4886</item>
- <item>3 | 2.50 | 0.0833 0.0015 0.0849 | 26.9772</item>
- <item>4 | 2.50 | 0.0830 0.0018 0.0848 | 24.6107</item>
- <item>5 | 2.50 | 0.0827 0.0019 0.0846 | 22.6548</item>
- <item>6 | 2.50 | 0.0825 0.0020 0.0845 | 20.6989</item>
- <item>7 | 2.50 | 0.0822 0.0021 0.0843 | 18.9688</item>
- <item>8 | 2.50 | 0.0820 0.0022 0.0842 | 17.4455</item>
- <item>9 | 2.50 | 0.0817 0.0023 0.0840 | 15.9223</item>
- <item>10 | 2.50 | 0.0814 0.0024 0.0838 | 14.6627</item>
- <item>11 | 2.50 | 0.0811 0.0025 0.0836 | 13.4764</item>
- <item>12 | 2.50 | 0.0808 0.0026 0.0834 | 12.3015</item>
- <item>13 | 2.50 | 0.0805 0.0027 0.0832 | 11.3776</item>
- <item>14 | 2.50 | 0.0802 0.0028 0.0830 | 10.4537</item>
- <item>15 | 2.25 | 0.0800 0.0029 0.0828 | 9.5920</item>
- <item>16 | 2.25 | 0.0768 0.0045 0.0813 | 8.8725</item>
- <item>17 | 2.25 | 0.0756 0.0051 0.0807 | 8.1530</item>
- <item>18 | 2.25 | 0.0747 0.0054 0.0801 | 7.5234</item>
- <item>29 | 2.00 | 0.0760 0.0026 0.0786 | 3.3283</item>
- <item>30 | 2.00 | 0.0701 0.0052 0.0753 | 3.1221</item>
- <item>31 | 2.00 | 0.0681 0.0063 0.0744 | 2.9160</item>
- <item>43 | 1.75 | 0.0667 0.0036 0.0703 | 1.5785</item>
- <item>44 | 1.75 | 0.0622 0.0061 0.0682 | 1.5194</item>
- <item>45 | 1.75 | 0.0607 0.0069 0.0676 | 1.4626</item>
- <item>57 | 1.50 | 0.0591 0.0050 0.0641 | 1.0900</item>
- <item>58 | 1.50 | 0.0558 0.0071 0.0630 | 1.0730</item>
- <item>59 | 1.50 | 0.0548 0.0078 0.0626 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 123s</item>
- <item>Prepare output 7s</item>
- <item>130s</item>
- <item>Jacobian determinant (RMS): 0.011 0.043 0.074 0.106 0.135 | 0.144507</item>
- <item>Template Matching: 0.086 0.224 0.204 0.182 0.164 | 0.164412</item>
- <item>Write result maps: 25s</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: 9s</item>
- <item>PBT2x thickness: 27s</item>
- <item>60s</item>
- <item>Create initial surface 49s</item>
- <item>Topology correction: 51s</item>
- <item>Surface refinement: 53s</item>
- <item>Reduction of surface collisions with optimization: 38s</item>
- <item>Spherical mapping with areal smoothing 53s</item>
- <item>Spherical registration 192s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 23s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 27s</item>
- <item>63s</item>
- <item>Create initial surface 47s</item>
- <item>Topology correction: 50s</item>
- <item>Surface refinement: 44s</item>
- <item>Reduction of surface collisions with optimization: 36s</item>
- <item>Spherical mapping with areal smoothing 50s</item>
- <item>Spherical registration 194s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4207 0.6054 mm</item>
- <item>Surface intensity / position RMSE: 0.0628 / 0.0602</item>
- <item>Euler number / defect number / defect size: 6.0 / 8.5 / 0.11%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/surf/lh.thickness.sub-0026007_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/surf/rh.thickness.sub-0026007_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/sub-0026007_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1040s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</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 17s</item>
- <item>ROI estimation of 'anatomy3' atlas 25s</item>
- <item>ROI estimation of 'julichbrain' atlas 32s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 72s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 6s</item>
- <item>320s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/report/catreport_sub-0026007_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 33 minute(s) and 7 second(s).</item>
- <item>Image Quality Rating (IQR): 84.25% (B)</item>
- <item>GM volume (GMV): 44.46% (620.59 / 1395.69 ml)</item>
- <item>GM thickness (GMT): 2.42 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3618456/ds/UM/sub-0026007/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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