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- </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>
- <tol>0.0001</tol>
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- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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- <fwhm>1</fwhm>
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- <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_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>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <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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- <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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- <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>
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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>
- <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>
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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>
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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>
- </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/julichbrain.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_100Parcels_17Networks_order.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/Schaefer2018_200Parcels_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_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>
- <td>
- <item>gm</item>
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- </td>
- <td>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_1702845/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
- </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>
- </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>
- </tr>
- <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>
- </tr>
- <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>
- <NB>0</NB>
- <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>
- <new_release>0</new_release>
- <lazy>0</lazy>
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- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- </darteltpms>
- <shootingtpms>
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- <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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- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <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>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.218466262489709</SurfaceDefectArea>
- <SurfaceDefectNumber>11</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.067838229238987</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0640077739953995</SurfacePositionRMSE>
- <res_vx_vol>[0.999999940395355 0.999999940395355 0.99999988079071]</res_vx_vol>
- <res_vx_voli>[1 0.999999940395355 0.99999988079071]</res_vx_voli>
- <res_RMS>0.999999920527141</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[13.8529996871948 95.181999206543 277.605987548828 424.016998291016]</tissue_mn>
- <tissue_mnr>[0.0326708592474461 0.224476844072342 0.654704868793488 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[31.9507071580947 46.7122296096059 45.3638969572102 28.1752398563204]</tissue_std>
- <tissue_stdr>[0.0778973922133446 0.113886713981628 0.110599413514137 0.0686926171183586]</tissue_stdr>
- <contrast>151.355941772461</contrast>
- <contrastr>0.356957256793976</contrastr>
- <res_ECR>0.364077389240265</res_ECR>
- <NCR>0.143611490726471</NCR>
- <ICR>0.288024395704269</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999988079071 1.99999988079071 1.99999976158142]</res_vx_vol>
- <res_RMS>1.99999984105428</res_RMS>
- <res_ECR>2.75549697875977</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>2.72897434234619</contrastr>
- <NCR>2.39264273643494</NCR>
- <ICR>1.17416763305664</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.05461656562243</SurfaceDefectArea>
- <SurfaceDefectNumber>1.55</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.35676455497742</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.28015542030334</SurfacePositionRMSE>
- <SIQR>2.50514681862382</SIQR>
- <IQR>2.25348448771557</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>20231031-003616</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.218466262489709</SurfaceDefectArea>
- <SurfaceDefectNumber>11</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.067838229238987</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0640077739953995</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.218466262489709</defect_size>
- <vol_abs_CGW>[205.907951416078 658.890090024392 444.782108702044 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.243647015256042</vol_abs_WMH>
- <vol_rel_WMH>0.000186049716185395</vol_rel_WMH>
- <surf_TSA>1789.5258950296</surf_TSA>
- <vol_TIV>1309.58015014251</vol_TIV>
- <vol_rel_CGW>[0.157232034552196 0.503130785811535 0.339637179636268 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.61874370290061 0.631684507294361]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.62029361724854 0.766876696719738 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.02157334873318 0.244682142188254 0.311151360810562;2.6452868784618 0.178796723061659 0.398124757423686;3.28442079048159 0.261238067045279 0.290723881765751]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.939859677158058 0.352498109541579 0.547874535699546;4.26074331446578 0.369619485711873 0.452125464300454]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.19231995230976</vol_TIV>
- <vol_rel_CGW>[0.673707517101226 6.88596957276464 3.9496619905939 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01860497161854</vol_rel_WMH>
- <surf_TSA>8.57997805660185</surf_TSA>
- <SQR>5.63931230714102</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.64576562517 0.359421610351598]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00141929078381509 0.00102111813612282 0.258906632661819]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[768.524423361419 399.371959959268 303.307459489882 744.359431604025 1198.97330717546 6458.77513919849]</SPMvols0>
- <SPMvols1>[700.69155705951 377.472387404629 188.988832872825 494.094319492176 828.728942007775 6781.69944223943]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[110.424499511719 290.193115234375 414.871490478516]</T3th>
- <Tth>
- <T3th>[-6.2648401260376 -6.26483774185181 6.0177001953125 110.424499511719 290.193115234375 414.871490478516 567.094970703125 856.997253417969]</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>[0.0217779874801636 0.0758212432265282 0.0838021859526634 0 0]</dtc>
- <ll>[0.0828415961111007 0 0.0828415961111007 0;0.189687410608775 0.0108838808350489 0.200571291443824 2320.9658203125;0.189687410608775 0.0108838808350489 0.200571291443824 2320.9658203125]</ll>
- <rmsdtc>[0.0477765537798405 0.100207805633545 0.111195147037506]</rmsdtc>
- <rmsgdt>[0.0345279052853584 0.0449063144624233 0.0552152171730995]</rmsgdt>
- <rmsdt>0.111195147037506</rmsdt>
- <dt>0.0838021859526634</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>[0.0103989634662867 0.0381548888981342 0.0535423085093498 0.0613015778362751 0.067277692258358 0.0758414268493652]</dtc>
- <ll>[0.0840567734905741 0 0.0840567734905741 0;0.217332188644689 0.015291990995116 0.232624179639805 7827.587890625;0.19365875690554 0.0177128902776388 0.211371647183179 12748.1796875;0.173295617896041 0.0192111251700638 0.192506743066105 20714.818359375;0.156837109920068 0.0218033087625825 0.17864041868265 38141.68359375;0.156837109920068 0.0218033087625825 0.17864041868265 38141.68359375]</ll>
- <rmsdtc>[0.0120599269866943 0.0439575165510178 0.0652944445610046 0.090561680495739 0.113421715795994 0.120810687541962]</rmsdtc>
- <rmsgdt>[0.00336220883764327 0.01338723115623 0.0294469203799963 0.0504280738532543 0.0686924010515213 0.0744805485010147]</rmsgdt>
- <rmsdt>0.120810687541962</rmsdt>
- <dt>0.0758414268493652</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025254/ses-2/sub-0025254_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 54s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>39s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 89s</item>
- <item>SPM preprocessing 1 (estimate 2): 72s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 18s</item>
- <item>Update Segmentation 20s</item>
- <item>Update Skull-Stripping 42s</item>
- <item>Update probability maps 9s</item>
- <item>89s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 28s</item>
- <item>Fast Optimized Shooting registration 38s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 16s</item>
- <item>Estimate local tissue thresholds (WM) 20s</item>
- <item>Estimate local tissue thresholds (GM) 32s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 43s</item>
- <item>120s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s</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>75s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 35s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.98 0.05]</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>13s</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 | 0.0841 0.0000 0.0841 | 32.0000</item>
- <item>2 | 2.50 | 0.0810 0.0013 0.0823 | 29.4886</item>
- <item>3 | 2.50 | 0.0801 0.0020 0.0821 | 26.9772</item>
- <item>4 | 2.50 | 0.0797 0.0022 0.0819 | 24.6107</item>
- <item>5 | 2.50 | 0.0793 0.0024 0.0818 | 22.6548</item>
- <item>6 | 2.50 | 0.0790 0.0025 0.0815 | 20.6989</item>
- <item>7 | 2.50 | 0.0787 0.0026 0.0813 | 18.9688</item>
- <item>8 | 2.50 | 0.0784 0.0028 0.0811 | 17.4455</item>
- <item>9 | 2.50 | 0.0780 0.0028 0.0809 | 15.9223</item>
- <item>10 | 2.50 | 0.0777 0.0030 0.0806 | 14.6627</item>
- <item>11 | 2.50 | 0.0773 0.0031 0.0804 | 13.4764</item>
- <item>12 | 2.50 | 0.0769 0.0031 0.0801 | 12.3015</item>
- <item>13 | 2.50 | 0.0766 0.0033 0.0798 | 11.3776</item>
- <item>14 | 2.50 | 0.0762 0.0033 0.0795 | 10.4537</item>
- <item>15 | 2.25 | 0.0758 0.0034 0.0792 | 9.5920</item>
- <item>16 | 2.25 | 0.0724 0.0051 0.0775 | 8.8725</item>
- <item>29 | 2.00 | 0.0732 0.0023 0.0755 | 3.3283</item>
- <item>30 | 2.00 | 0.0668 0.0049 0.0716 | 3.1221</item>
- <item>31 | 2.00 | 0.0646 0.0059 0.0705 | 2.9160</item>
- <item>43 | 1.75 | 0.0633 0.0034 0.0668 | 1.5785</item>
- <item>44 | 1.75 | 0.0592 0.0056 0.0648 | 1.5194</item>
- <item>45 | 1.75 | 0.0578 0.0064 0.0642 | 1.4626</item>
- <item>57 | 1.50 | 0.0563 0.0047 0.0610 | 1.0900</item>
- <item>58 | 1.50 | 0.0533 0.0066 0.0599 | 1.0730</item>
- <item>59 | 1.50 | 0.0523 0.0073 0.0595 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 206s</item>
- <item>Prepare output 13s</item>
- <item>219s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.065 0.091 0.113 | 0.120811</item>
- <item>Template Matching: 0.084 0.217 0.194 0.173 0.157 | 0.156837</item>
- <item>Write result maps: 38s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 45s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 55s</item>
- <item>125s</item>
- <item>Create initial surface 97s</item>
- <item>Topology correction: 88s</item>
- <item>Surface refinement: 110s</item>
- <item>Reduction of surface collisions with optimization: 71s</item>
- <item>Spherical mapping with areal smoothing 97s</item>
- <item>Spherical registration 344s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 52s</item>
- <item>107s</item>
- <item>Create initial surface 91s</item>
- <item>Topology correction: 88s</item>
- <item>Surface refinement: 80s</item>
- <item>Reduction of surface collisions with optimization: 69s</item>
- <item>Spherical mapping with areal smoothing 95s</item>
- <item>Spherical registration 339s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6188 0.6316 mm</item>
- <item>Surface intensity / position RMSE: 0.0678 / 0.0640</item>
- <item>Euler number / defect number / defect size: 8.0 / 11.0 / 0.22%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/surf/lh.thickness.sub-0025254_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/surf/rh.thickness.sub-0025254_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/sub-0025254_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1905s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 29s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 20s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 12s</item>
- <item>ROI estimation of 'mori' atlas 18s</item>
- <item>ROI estimation of 'anatomy3' atlas 27s</item>
- <item>ROI estimation of 'julichbrain' atlas 37s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 10s</item>
- <item>372s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/report/catreport_sub-0025254_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 55 minute(s) and 32 second(s).</item>
- <item>Image Quality Rating (IQR): 82.47% (B-)</item>
- <item>GM volume (GMV): 50.31% (658.89 / 1309.58 ml)</item>
- <item>GM thickness (GMT): 2.62 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1702845/ds/UPSM_1/sub-0025254/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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