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- <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>
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- <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>
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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
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- <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>
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- <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>
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- <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>
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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>
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- <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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- <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>
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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>
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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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- <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>
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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_3468819/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>
- <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>
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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>
- <new_release>0</new_release>
- <lazy>0</lazy>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
- </restypes>
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- <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>
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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>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.873418351725398</SurfaceDefectArea>
- <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0739720240235329</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0835283994674683</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>[13.2639999389648 91.4329986572266 263.881011962891 405.946990966797]</tissue_mn>
- <tissue_mnr>[0.032674215734005 0.225233837962151 0.650038123130798 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[9.36146445355585 43.9596520195457 43.5333724439929 27.2033758131434]</tissue_std>
- <tissue_stdr>[0.0238397512584925 0.111946925520897 0.110861368477345 0.0692756697535515]</tissue_stdr>
- <contrast>146.53742980957</contrast>
- <contrastr>0.360976755619049</contrastr>
- <res_ECR>0.379038870334625</res_ECR>
- <NCR>0.142663717269897</NCR>
- <ICR>0.239982396364212</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 1.99999988079071 1.99999988079071]</res_vx_vol>
- <res_RMS>1.99999992052714</res_RMS>
- <res_ECR>2.83183097839355</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>2.66868209838867</contrastr>
- <NCR>2.37903690338135</NCR>
- <ICR>1.05501580238342</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.21835458793135</SurfaceDefectArea>
- <SurfaceDefectNumber>1.875</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.47944045066833</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.67056798934937</SurfacePositionRMSE>
- <SIQR>2.55321383115617</SIQR>
- <IQR>2.24317656810509</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>20231031-033833</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.873418351725398</SurfaceDefectArea>
- <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0739720240235329</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0835283994674683</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.873418351725398</defect_size>
- <vol_abs_CGW>[234.964258264585 832.526669382529 600.704281331639 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.270113693290132</vol_abs_WMH>
- <vol_rel_WMH>0.000161919715292488</vol_rel_WMH>
- <surf_TSA>2232.91941524761</surf_TSA>
- <vol_TIV>1668.19520897875</vol_TIV>
- <vol_rel_CGW>[0.140849378418025 0.499058302590493 0.360092318991482 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.64931150823881 0.668117922669912]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.68337488174438 0.884350231538081 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.94773292694274 0.306037645224847 0.256443264264054;2.66572969216333 0.195612043068338 0.435879758051051;3.36085160526323 0.296908658841094 0.307676977684895]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.745804193102266 0.313246705108579 0.656942003514938;4.31310655146104 0.305915633034422 0.343057996485062]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.53475517098278</vol_TIV>
- <vol_rel_CGW>[0.5 6.81282871031776 4.31703159108265 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01619197152925</vol_rel_WMH>
- <surf_TSA>8.62394693248559</surf_TSA>
- <SQR>5.5891953252277</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.64688281253 0.347331453714389]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00196656584739685 0.000760204857215285 0.328100293874741]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[986.47385887373 538.244367208815 409.106115936629 518.998883228546 1735.02992650163 5949.94351816238]</SPMvols0>
- <SPMvols1>[874.805370224868 508.890562864924 226.326157333543 506.829704287068 1185.96863117053 6068.88374319928]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[103.76180267334 274.902008056641 398.601196289062]</T3th>
- <Tth>
- <T3th>[-6.44208002090454 -6.44207715988159 8.70573234558105 103.76180267334 274.902008056641 398.601196289062 546.020874023438 1097.037109375]</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>[0.0204364638775587 0.073183000087738 0.080300934612751 0 0]</dtc>
- <ll>[0.0824386822600134 0 0.0824386822600134 0;0.190122258620245 0.00994120182252589 0.200063460442771 2119.94140625;0.190122258620245 0.00994120182252589 0.200063460442771 2119.94140625]</ll>
- <rmsdtc>[0.0470050796866417 0.0953873842954636 0.104856081306934]</rmsdtc>
- <rmsgdt>[0.0341559238731861 0.0416660346090794 0.0508019775152206]</rmsgdt>
- <rmsdt>0.104856081306934</rmsdt>
- <dt>0.080300934612751</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>[0.00976828392595053 0.0363775044679642 0.0508131757378578 0.0579127818346024 0.0624580010771751 0.0695362016558647]</dtc>
- <ll>[0.0833743309639462 0 0.0833743309639462 0;0.213596581196581 0.0147886189331502 0.228385200129731 7569.92431640625;0.190423630389656 0.016753500445317 0.207177130834973 12057.6953125;0.171320177098172 0.0178317063667609 0.189151883464933 19227.4296875;0.15808742932387 0.0184085949830452 0.176496024306915 32203.130859375;0.15808742932387 0.0184085949830452 0.176496024306915 32203.130859375]</ll>
- <rmsdtc>[0.0114756701514125 0.0421551801264286 0.0622816272079945 0.0846167504787445 0.104717992246151 0.109130725264549]</rmsdtc>
- <rmsgdt>[0.00334605132229626 0.0128810992464423 0.027246018871665 0.0456963218748569 0.0627730935811996 0.0670345351099968]</rmsgdt>
- <rmsdt>0.109130725264549</rmsdt>
- <dt>0.0695362016558647</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025267/ses-3/sub-0025267_ses-3_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 7s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>42s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 105s</item>
- <item>SPM preprocessing 1 (estimate 2): 85s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 18s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 43s</item>
- <item>Update probability maps 8s</item>
- <item>93s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 33s</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) 18s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 35s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 45s</item>
- <item>130s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 31s</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>84s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s</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) 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>14s</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 | 0.0834 0.0000 0.0834 | 32.0000</item>
- <item>2 | 2.50 | 0.0805 0.0013 0.0817 | 29.4886</item>
- <item>3 | 2.50 | 0.0796 0.0019 0.0815 | 26.9772</item>
- <item>4 | 2.50 | 0.0792 0.0022 0.0814 | 24.6107</item>
- <item>5 | 2.50 | 0.0788 0.0024 0.0812 | 22.6548</item>
- <item>6 | 2.50 | 0.0785 0.0025 0.0810 | 20.6989</item>
- <item>7 | 2.50 | 0.0782 0.0026 0.0808 | 18.9688</item>
- <item>8 | 2.50 | 0.0779 0.0027 0.0806 | 17.4455</item>
- <item>9 | 2.50 | 0.0775 0.0028 0.0803 | 15.9223</item>
- <item>10 | 2.50 | 0.0772 0.0029 0.0801 | 14.6627</item>
- <item>11 | 2.50 | 0.0768 0.0030 0.0798 | 13.4764</item>
- <item>12 | 2.50 | 0.0765 0.0030 0.0795 | 12.3015</item>
- <item>13 | 2.50 | 0.0761 0.0032 0.0793 | 11.3776</item>
- <item>14 | 2.50 | 0.0758 0.0032 0.0790 | 10.4537</item>
- <item>15 | 2.25 | 0.0744 0.0033 0.0777 | 9.5920</item>
- <item>16 | 2.25 | 0.0712 0.0049 0.0761 | 8.8725</item>
- <item>29 | 2.00 | 0.0715 0.0022 0.0737 | 3.3283</item>
- <item>30 | 2.00 | 0.0655 0.0046 0.0701 | 3.1221</item>
- <item>31 | 2.00 | 0.0635 0.0056 0.0691 | 2.9160</item>
- <item>43 | 1.75 | 0.0622 0.0032 0.0654 | 1.5785</item>
- <item>44 | 1.75 | 0.0584 0.0052 0.0636 | 1.5194</item>
- <item>45 | 1.75 | 0.0571 0.0059 0.0631 | 1.4626</item>
- <item>57 | 1.50 | 0.0554 0.0044 0.0598 | 1.0900</item>
- <item>58 | 1.50 | 0.0527 0.0061 0.0588 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 163s</item>
- <item>Prepare output 13s</item>
- <item>176s</item>
- <item>Jacobian determinant (RMS): 0.011 0.042 0.062 0.085 0.105 | 0.109131</item>
- <item>Template Matching: 0.083 0.214 0.190 0.171 0.158 | 0.158087</item>
- <item>Write result maps: 33s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 49s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 64s</item>
- <item>141s</item>
- <item>Create initial surface 109s</item>
- <item>Topology correction: 123s</item>
- <item>Surface refinement: 123s</item>
- <item>Reduction of surface collisions with optimization: 102s</item>
- <item>Spherical mapping with areal smoothing 120s</item>
- <item>Spherical registration 318s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 64s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 64s</item>
- <item>157s</item>
- <item>Create initial surface 108s</item>
- <item>Topology correction: 125s</item>
- <item>Surface refinement: 120s</item>
- <item>Reduction of surface collisions with optimization: 98s</item>
- <item>Spherical mapping with areal smoothing 122s</item>
- <item>Spherical registration 331s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6495 0.6675 mm</item>
- <item>Surface intensity / position RMSE: 0.0740 / 0.0835</item>
- <item>Euler number / defect number / defect size: 18.0 / 17.5 / 0.87%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/surf/lh.thickness.sub-0025267_ses-3_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/surf/rh.thickness.sub-0025267_ses-3_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/sub-0025267_ses-3_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 2217s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 28s</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 11s</item>
- <item>ROI estimation of 'mori' atlas 17s</item>
- <item>ROI estimation of 'anatomy3' atlas 24s</item>
- <item>ROI estimation of 'julichbrain' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 77s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 8s</item>
- <item>325s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/report/catreport_sub-0025267_ses-3_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 60 minute(s) and 10 second(s).</item>
- <item>Image Quality Rating (IQR): 82.57% (B-)</item>
- <item>GM volume (GMV): 49.91% (832.53 / 1668.20 ml)</item>
- <item>GM thickness (GMT): 2.65 0.67 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-3/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|