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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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- <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>
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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>
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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>
- </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>
- <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>
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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>
- <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_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_3319016/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
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- <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>
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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>
- <new_release>0</new_release>
- <lazy>0</lazy>
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- <shootingtpm>
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- </shootingtpm>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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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_4_GS.nii</item>
- </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>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.282076238602855</SurfaceDefectArea>
- <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639604926109314</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0622077845036983</SurfacePositionRMSE>
- <res_vx_vol>[1 0.999999940395355 0.999999940395355]</res_vx_vol>
- <res_vx_voli>[1 0.999999940395355 0.999999940395355]</res_vx_voli>
- <res_RMS>0.999999960263571</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[15.1949996948242 88.0059967041016 268.928985595703 416.234985351562]</tissue_mn>
- <tissue_mnr>[0.0365058220922947 0.211433440446854 0.646098971366882 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.5122412943677 43.7536794936418 45.7843320805271 27.4737472737751]</tissue_std>
- <tissue_stdr>[0.031199486926198 0.109100542962551 0.114164009690285 0.0685062557458878]</tissue_stdr>
- <contrast>149.791030883789</contrast>
- <contrastr>0.359871327877045</contrastr>
- <res_ECR>0.377406358718872</res_ECR>
- <NCR>0.139634236693382</NCR>
- <ICR>0.260484278202057</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 1.99999988079071 1.99999988079071]</res_vx_vol>
- <res_RMS>1.99999992052714</res_RMS>
- <res_ECR>2.82350158691406</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>2.68526339530945</contrastr>
- <NCR>2.33554744720459</NCR>
- <ICR>1.10586380958557</ICR>
- <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
- <SurfaceDefectArea>1.07051905965071</SurfaceDefectArea>
- <SurfaceDefectNumber>1.475</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.27920985221863</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.24415564537048</SurfacePositionRMSE>
- <SIQR>2.53897006443673</SIQR>
- <IQR>2.21079297051289</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>20231031-021419</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.282076238602855</SurfaceDefectArea>
- <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639604926109314</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0622077845036983</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>10</EC_abs>
- <defect_size>0.282076238602855</defect_size>
- <vol_abs_CGW>[248.996005611478 776.07649179819 585.329691007571 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.651956785025786</vol_abs_WMH>
- <vol_rel_WMH>0.000404840970606574</vol_rel_WMH>
- <surf_TSA>2197.14879688241</surf_TSA>
- <vol_TIV>1610.40218841724</vol_TIV>
- <vol_rel_CGW>[0.154617279709611 0.481914702662535 0.363468017627854 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.5642813344909 0.631031532683535]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55496168136597 0.7787236976081 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.9634904949659 0.254935420060962 0.301708141562162;2.58572534878369 0.180558215429518 0.427848257381672;3.25156148891756 0.279542686145262 0.270443601056166]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.893436483925434 0.314866105725431 0.532677035076109;4.25006069405181 0.349419281524224 0.467322964923891]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.98500704509564</vol_TIV>
- <vol_rel_CGW>[0.626747121221464 6.5049335966691 4.37765836256921 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04048409706066</vol_rel_WMH>
- <surf_TSA>8.62389888164926</surf_TSA>
- <SQR>5.34698329737336</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.64688281253 0.343738016400033]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00144420401193202 0.000794340157881379 0.302634865045547]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[929.078324539341 523.52909053164 420.776989055156 845.656632523198 2115.30965763934 5243.94242193212]</SPMvols0>
- <SPMvols1>[812.953820735403 493.681258795661 249.622346713283 894.78154431411 1715.93100720977 5204.72137954881]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[103.385299682617 278.425903320312 406.267791748047]</T3th>
- <Tth>
- <T3th>[-7.51212978363037 -7.51212882995605 9.28864192962646 103.385299682617 278.425903320312 406.267791748047 557.709045410156 974.978454589844]</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>[0.0223231017589569 0.0826039090752602 0.0916689708828926 0 0]</dtc>
- <ll>[0.0860538307119723 0 0.0860538307119723 0;0.19459482401359 0.0118796633643692 0.206474487377959 2533.314453125;0.19459482401359 0.0118796633643692 0.206474487377959 2533.314453125]</ll>
- <rmsdtc>[0.0528916381299496 0.107518345117569 0.119917333126068]</rmsdtc>
- <rmsgdt>[0.0385953709483147 0.0492224209010601 0.0605302788317204]</rmsgdt>
- <rmsdt>0.119917333126068</rmsdt>
- <dt>0.0916689708828926</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>[0.0105078779160976 0.0395319238305092 0.0560659915208817 0.0645103603601456 0.0706975236535072 0.0795804485678673]</dtc>
- <ll>[0.0858569338192547 0 0.0858569338192547 0;0.221634416971917 0.0164022340506716 0.238036651022589 8395.8935546875;0.198044321895425 0.0188010289836421 0.216845350879067 13531.326171875;0.177306215987246 0.0202223133837056 0.197528529370952 21805.154296875;0.160762061030564 0.0230468198456801 0.183808880876244 40317.0234375;0.160762061030564 0.0230468198456801 0.183808880876244 40317.0234375]</ll>
- <rmsdtc>[0.0119669772684574 0.0444348491728306 0.0664635449647903 0.0920643657445908 0.114823326468468 0.122757650911808]</rmsdtc>
- <rmsgdt>[0.00356124714016914 0.0143721792846918 0.0302159562706947 0.050851222127676 0.0694256275892258 0.0754028111696243]</rmsgdt>
- <rmsdt>0.122757650911808</rmsdt>
- <dt>0.0795804485678673</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025255/ses-2/sub-0025255_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 66s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 7s</item>
- <item>44s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 102s</item>
- <item>SPM preprocessing 1 (estimate 2): 98s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 46s</item>
- <item>Update probability maps 9s</item>
- <item>96s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 34s</item>
- <item>Fast Optimized Shooting registration 40s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 18s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 35s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 46s</item>
- <item>132s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 19s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 33s</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>90s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 41s</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) 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>15s</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 | 0.0859 0.0000 0.0859 | 32.0000</item>
- <item>2 | 2.50 | 0.0824 0.0015 0.0838 | 29.4886</item>
- <item>3 | 2.50 | 0.0813 0.0022 0.0836 | 26.9772</item>
- <item>4 | 2.50 | 0.0808 0.0025 0.0833 | 24.6107</item>
- <item>5 | 2.50 | 0.0805 0.0027 0.0831 | 22.6548</item>
- <item>6 | 2.50 | 0.0801 0.0028 0.0829 | 20.6989</item>
- <item>7 | 2.50 | 0.0798 0.0029 0.0827 | 18.9688</item>
- <item>8 | 2.50 | 0.0794 0.0030 0.0824 | 17.4455</item>
- <item>9 | 2.50 | 0.0790 0.0031 0.0821 | 15.9223</item>
- <item>10 | 2.50 | 0.0786 0.0032 0.0819 | 14.6627</item>
- <item>11 | 2.50 | 0.0782 0.0033 0.0816 | 13.4764</item>
- <item>12 | 2.50 | 0.0778 0.0034 0.0812 | 12.3015</item>
- <item>13 | 2.50 | 0.0774 0.0035 0.0809 | 11.3776</item>
- <item>14 | 2.50 | 0.0770 0.0036 0.0806 | 10.4537</item>
- <item>15 | 2.25 | 0.0774 0.0037 0.0811 | 9.5920</item>
- <item>16 | 2.25 | 0.0739 0.0055 0.0793 | 8.8725</item>
- <item>29 | 2.00 | 0.0751 0.0025 0.0775 | 3.3283</item>
- <item>30 | 2.00 | 0.0683 0.0052 0.0735 | 3.1221</item>
- <item>31 | 2.00 | 0.0660 0.0063 0.0723 | 2.9160</item>
- <item>43 | 1.75 | 0.0650 0.0036 0.0686 | 1.5785</item>
- <item>44 | 1.75 | 0.0606 0.0059 0.0665 | 1.5194</item>
- <item>45 | 1.75 | 0.0591 0.0067 0.0658 | 1.4626</item>
- <item>57 | 1.50 | 0.0579 0.0049 0.0628 | 1.0900</item>
- <item>58 | 1.50 | 0.0547 0.0070 0.0617 | 1.0730</item>
- <item>59 | 1.50 | 0.0536 0.0077 0.0613 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 202s</item>
- <item>Prepare output 14s</item>
- <item>216s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.066 0.092 0.115 | 0.122758</item>
- <item>Template Matching: 0.086 0.222 0.198 0.177 0.161 | 0.160762</item>
- <item>Write result maps: 37s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 46s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 66s</item>
- <item>142s</item>
- <item>Create initial surface 121s</item>
- <item>Topology correction: 126s</item>
- <item>Surface refinement: 102s</item>
- <item>Reduction of surface collisions with optimization: 99s</item>
- <item>Spherical mapping with areal smoothing 120s</item>
- <item>Spherical registration 337s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 66s</item>
- <item>144s</item>
- <item>Create initial surface 119s</item>
- <item>Topology correction: 128s</item>
- <item>Surface refinement: 110s</item>
- <item>Reduction of surface collisions with optimization: 99s</item>
- <item>Spherical mapping with areal smoothing 123s</item>
- <item>Spherical registration 363s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5643 0.6309 mm</item>
- <item>Surface intensity / position RMSE: 0.0640 / 0.0622</item>
- <item>Euler number / defect number / defect size: 10.0 / 9.5 / 0.28%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/surf/lh.thickness.sub-0025255_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/surf/rh.thickness.sub-0025255_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/sub-0025255_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 2258s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 34s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 14s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 30s</item>
- <item>ROI estimation of 'julichbrain' atlas 39s</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 60s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 9s</item>
- <item>391s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/report/catreport_sub-0025255_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 63 minute(s) and 19 second(s).</item>
- <item>Image Quality Rating (IQR): 82.89% (B-)</item>
- <item>GM volume (GMV): 48.19% (776.08 / 1610.40 ml)</item>
- <item>GM thickness (GMT): 2.56 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3319016/ds/UPSM_1/sub-0025255/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|