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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>
- <affreg>mni</affreg>
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- <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>
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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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- <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>
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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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- <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>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_110026/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
- </td>
- <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>
- <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>
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- <shooting>
- <shootingtpm>
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- <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>
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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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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.619952183207105</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0712880790233612</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0701483562588692</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>197.074279785156</res_BB>
- <tissue_mn>[15.5319995880127 91.197998046875 262.003997802734 416.274993896484]</tissue_mn>
- <tissue_mnr>[0.0373118743300438 0.21908113360405 0.62940126657486 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[11.5820828775078 43.0268970143625 45.7547110826816 29.5482249557095]</tissue_std>
- <tissue_stdr>[0.0289015248417854 0.107367813587189 0.114174701273441 0.0737336054444313]</tissue_stdr>
- <contrast>148.335784912109</contrast>
- <contrastr>0.356340855360031</contrastr>
- <res_ECR>0.380148112773895</res_ECR>
- <NCR>0.150101631879807</NCR>
- <ICR>0.29944372177124</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.83749032020569</res_ECR>
- <res_BB>10.5</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>2.73822045326233</contrastr>
- <NCR>2.48581171035767</NCR>
- <ICR>1.20248937606812</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.15498804580178</SurfaceDefectArea>
- <SurfaceDefectNumber>1.6</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.42576158046722</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.40296709537506</SurfacePositionRMSE>
- <SIQR>2.58145581632544</SIQR>
- <IQR>2.32606239416106</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>20231031-020547</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.619952183207105</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0712880790233612</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0701483562588692</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.619952183207105</defect_size>
- <vol_abs_CGW>[230.83128627451 791.632368627451 541.10468627451 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.911764705882353</vol_abs_WMH>
- <vol_rel_WMH>0.000583130702938329</vol_rel_WMH>
- <surf_TSA>2206.4680555293</surf_TSA>
- <vol_TIV>1563.56834117647</vol_TIV>
- <vol_rel_CGW>[0.147631082182712 0.506298540191601 0.346070377625687 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.54860801500763 0.630956467250368]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.53102850914001 0.752391465731745 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92165931581231 0.251758902165913 0.295371806293376;2.55452735975206 0.182649449828015 0.431407485619384;3.23445553215192 0.273773592830045 0.273220708087241]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.911090499584894 0.324718437470971 0.498925264550265;4.19431552503825 0.346266842443444 0.501074735449735]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.61150867082455</vol_TIV>
- <vol_rel_CGW>[0.501276619660771 6.94286171321123 4.06520074758777 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05831307029383</vol_rel_WMH>
- <surf_TSA>8.62391436831833</surf_TSA>
- <SQR>5.68737806419642</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.648 0.375765130637161]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00167366047389805 0.00103503814898431 0.269570201635361]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[941.852129411765 483.6056 412.561298039216 663.398368627451 1547.75574117647 6074.48312941176]</SPMvols0>
- <SPMvols1>[826.576823529412 453.982945098039 232.318364705882 556.027015686274 976.730862745098 6326.12409411765]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[108.662399291992 274.773284912109 407.147796630859]</T3th>
- <Tth>
- <T3th>[-7.26520013809204 -7.26519632339478 8.64361667633057 108.662399291992 274.773284912109 407.147796630859 556.390502929688 844.194152832031]</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>[0.0217591319233179 0.0742502436041832 0.0816649347543716 0 0]</dtc>
- <ll>[0.0860644611848646 0 0.0860644611848646 0;0.200054887677727 0.0110539165006823 0.21110880417841 2357.2255859375;0.200054887677727 0.0110539165006823 0.21110880417841 2357.2255859375]</ll>
- <rmsdtc>[0.0470939353108406 0.096656359732151 0.107217110693455]</rmsdtc>
- <rmsgdt>[0.0338191911578178 0.045283954590559 0.0556161291897297]</rmsgdt>
- <rmsdt>0.107217110693455</rmsdt>
- <dt>0.0816649347543716</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>[0.00983204506337643 0.0374568402767181 0.0510144233703613 0.0609165132045746 0.0681688338518143 0.0763484239578247]</dtc>
- <ll>[0.0869222920934099 0 0.0869222920934099 0;0.224356608669109 0.0173891101953602 0.241745718864469 8901.05078125;0.207086784366524 0.018915435640402 0.226002220006926 13613.666015625;0.18657482179821 0.0210481518693799 0.20762297366759 22695.6328125;0.169181388061758 0.0245667098957443 0.193748097957502 42975.84765625;0.169181388061758 0.0245667098957443 0.193748097957502 42975.84765625]</ll>
- <rmsdtc>[0.0115267941728234 0.0413503684103489 0.0635417476296425 0.0897228941321373 0.114692166447639 0.12076223641634]</rmsdtc>
- <rmsgdt>[0.00339692365378141 0.0134157547727227 0.0294981133192778 0.0506105907261372 0.0710122659802437 0.0760595872998238]</rmsgdt>
- <rmsdt>0.12076223641634</rmsdt>
- <dt>0.0763484239578247</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025322/ses-2/sub-0025322_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 65s</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 6s</item>
- <item>41s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 88s</item>
- <item>SPM preprocessing 1 (estimate 2): 97s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 21s</item>
- <item>Update Skull-Stripping 42s</item>
- <item>Update probability maps 8s</item>
- <item>90s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 32s</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) 22s</item>
- <item>Estimate local tissue thresholds (GM) 36s</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'=0.00) 32s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>87s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</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 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 6s</item>
- <item>Level 1 cleanup (brain masking) 3s</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 | 0.0869 0.0000 0.0869 | 32.0000</item>
- <item>2 | 2.50 | 0.0837 0.0014 0.0851 | 29.4886</item>
- <item>3 | 2.50 | 0.0828 0.0021 0.0849 | 26.9772</item>
- <item>4 | 2.50 | 0.0824 0.0023 0.0847 | 24.6107</item>
- <item>5 | 2.50 | 0.0820 0.0025 0.0845 | 22.6548</item>
- <item>6 | 2.50 | 0.0817 0.0026 0.0843 | 20.6989</item>
- <item>7 | 2.50 | 0.0814 0.0027 0.0841 | 18.9688</item>
- <item>8 | 2.50 | 0.0810 0.0028 0.0838 | 17.4455</item>
- <item>9 | 2.50 | 0.0807 0.0029 0.0836 | 15.9223</item>
- <item>10 | 2.50 | 0.0803 0.0030 0.0833 | 14.6627</item>
- <item>11 | 2.50 | 0.0799 0.0031 0.0830 | 13.4764</item>
- <item>12 | 2.50 | 0.0796 0.0032 0.0827 | 12.3015</item>
- <item>13 | 2.50 | 0.0792 0.0033 0.0824 | 11.3776</item>
- <item>14 | 2.50 | 0.0788 0.0033 0.0821 | 10.4537</item>
- <item>15 | 2.25 | 0.0798 0.0034 0.0833 | 9.5920</item>
- <item>16 | 2.25 | 0.0762 0.0052 0.0814 | 8.8725</item>
- <item>17 | 2.25 | 0.0748 0.0058 0.0806 | 8.1530</item>
- <item>29 | 2.00 | 0.0775 0.0027 0.0801 | 3.3283</item>
- <item>30 | 2.00 | 0.0712 0.0053 0.0765 | 3.1221</item>
- <item>31 | 2.00 | 0.0690 0.0063 0.0753 | 2.9160</item>
- <item>43 | 1.75 | 0.0685 0.0036 0.0721 | 1.5785</item>
- <item>44 | 1.75 | 0.0638 0.0061 0.0699 | 1.5194</item>
- <item>45 | 1.75 | 0.0622 0.0070 0.0692 | 1.4626</item>
- <item>57 | 1.50 | 0.0611 0.0051 0.0663 | 1.0900</item>
- <item>58 | 1.50 | 0.0576 0.0074 0.0651 | 1.0730</item>
- <item>59 | 1.50 | 0.0564 0.0082 0.0646 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 202s</item>
- <item>Prepare output 13s</item>
- <item>216s</item>
- <item>Jacobian determinant (RMS): 0.012 0.041 0.064 0.090 0.115 | 0.120762</item>
- <item>Template Matching: 0.087 0.224 0.207 0.187 0.169 | 0.169181</item>
- <item>Write result maps: 36s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 65s</item>
- <item>141s</item>
- <item>Create initial surface 114s</item>
- <item>Topology correction: 131s</item>
- <item>Surface refinement: 149s</item>
- <item>Reduction of surface collisions with optimization: 100s</item>
- <item>Spherical mapping with areal smoothing 121s</item>
- <item>Spherical registration 338s</item>
- <item>rh:</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 119s</item>
- <item>Topology correction: 164s</item>
- <item>Surface refinement: 111s</item>
- <item>Reduction of surface collisions with optimization: 101s</item>
- <item>Spherical mapping with areal smoothing 132s</item>
- <item>Spherical registration 354s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5486 0.6309 mm</item>
- <item>Surface intensity / position RMSE: 0.0713 / 0.0701</item>
- <item>Euler number / defect number / defect size: 18.0 / 12.0 / 0.62%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/surf/lh.thickness.sub-0025322_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/surf/rh.thickness.sub-0025322_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/sub-0025322_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2340s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 29s</item>
- <item>ROI estimation of 'lpba40' atlas 9s</item>
- <item>ROI estimation of 'hammers' atlas 21s</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 17s</item>
- <item>ROI estimation of 'anatomy3' atlas 26s</item>
- <item>ROI estimation of 'julichbrain' atlas 33s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 79s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 8s</item>
- <item>340s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/report/catreport_sub-0025322_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 63 minute(s) and 12 second(s).</item>
- <item>Image Quality Rating (IQR): 81.74% (B-)</item>
- <item>GM volume (GMV): 50.63% (791.63 / 1563.57 ml)</item>
- <item>GM thickness (GMT): 2.55 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|