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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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- <regstr>0.5</regstr>
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- <SLC>0</SLC>
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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>
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- <vox>1.5</vox>
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- <shootingsurf>Template_T1</shootingsurf>
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- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
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- <reduce_mesh>1</reduce_mesh>
- <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>
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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>
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- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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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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- <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>/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>/var/lib/condor/execute/dir_138838/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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- <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>
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- <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>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- <shootingtpm>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
- <shootingtpms>
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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>
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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>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.475803622633877</SurfaceDefectArea>
- <SurfaceDefectNumber>16</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.067190907895565</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0871506929397583</SurfacePositionRMSE>
- <res_vx_vol>[0.999900817871094 1 1]</res_vx_vol>
- <res_vx_voli>[0.999900817871094 1 1]</res_vx_voli>
- <res_RMS>0.999966940383411</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 14.8280000686646 186.942993164062 369.923004150391]</tissue_mn>
- <tissue_mnr>[0 0.0400840155780315 0.50535649061203 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.92996572524911 34.1149730743854 47.2779274134348 33.2797523391276]</tissue_std>
- <tissue_stdr>[0.00792047474533319 0.0922218188643456 0.127804771065712 0.0899639949202538]</tissue_stdr>
- <contrast>123.703964233398</contrast>
- <contrastr>0.334404617547989</contrastr>
- <res_ECR>0.362214505672455</res_ECR>
- <NCR>0.105543121695518</NCR>
- <ICR>0.276514559984207</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99980163574219 2 2]</res_vx_vol>
- <res_RMS>1.99993388076682</res_RMS>
- <res_ECR>2.7459921836853</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[1.89584374427795 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>3.06726408004761</contrastr>
- <NCR>1.84615445137024</NCR>
- <ICR>1.14562141895294</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11895090565847</SurfaceDefectArea>
- <SurfaceDefectNumber>1.8</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.34381818771362</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.74301385879517</SurfacePositionRMSE>
- <SIQR>2.42803647593467</SIQR>
- <IQR>1.93364064216052</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>20231031-003634</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.475803622633877</SurfaceDefectArea>
- <SurfaceDefectNumber>16</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.067190907895565</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0871506929397583</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.475803622633877</defect_size>
- <vol_abs_CGW>[235.022907223391 676.871565660364 512.178937140252 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.19614801839193</vol_abs_WMH>
- <vol_rel_WMH>0.000839948284949554</vol_rel_WMH>
- <surf_TSA>1937.82293603174</surf_TSA>
- <vol_TIV>1424.07341002401</vol_TIV>
- <vol_rel_CGW>[0.165035668504919 0.475306652659819 0.359657678835263 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.39769658018804 0.617323540212]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.38015174865723 0.766617623489712 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.81856184131891 0.25803152728235 0.314735224401552;2.4294812825469 0.176791455162642 0.44252559193561;3.11205271892778 0.276584448123371 0.242739183662838]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.815088175141774 0.276625101482418 0.559968541093197;4.12671098568484 0.402148242262875 0.440031458906803]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.01379478495348</vol_TIV>
- <vol_rel_CGW>[0.813858988953279 6.38625453771226 4.30922555379423 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08399482849496</vol_rel_WMH>
- <surf_TSA>8.61767487573052</surf_TSA>
- <SQR>5.24999943551969</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11533.192 0.44486965129805]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00138115475419909 0.00117231346666813 0.0965767577290535]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[827.028886946585 433.385909638379 560.224665507597 952.200133709507 1048.60634745813 8479.75891132822]</SPMvols0>
- <SPMvols1>[676.175803301852 406.022639541237 291.677095426163 586.661749043633 928.656433761298 8645.45942026684]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[43.9225006103516 202.936096191406 377.881103515625]</T3th>
- <Tth>
- <T3th>[-4.56544017791748 -4.56543922424316 2.17174029350281 43.9225006103516 202.936096191406 377.881103515625 544.860412597656 991.229919433594]</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>[0.0227566156536341 0.0864093154668808 0.0968927070498466 0 0]</dtc>
- <ll>[0.0904836605052177 0 0.0904836605052177 0;0.210593380418574 0.012146928015591 0.222740308434165 2590.30810546875;0.210593380418574 0.012146928015591 0.222740308434165 2590.30810546875]</ll>
- <rmsdtc>[0.0515981614589691 0.114521808922291 0.128393828868866]</rmsdtc>
- <rmsgdt>[0.0370199307799339 0.0525343343615532 0.065192736685276]</rmsgdt>
- <rmsdt>0.128393828868866</rmsdt>
- <dt>0.0968927070498466</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>[0.00962618179619312 0.0362815856933594 0.0489742048084736 0.057264406234026 0.0638327673077583 0.0716427564620972]</dtc>
- <ll>[0.0860097322361617 0 0.0860097322361617 0;0.223585592185592 0.0147547466422466 0.238340338827839 7552.5859375;0.20667383706955 0.0168078231183967 0.223481660187947 12096.7919921875;0.186075715937166 0.0191942723954392 0.205269988332605 20696.646484375;0.168726505599499 0.0224506217441534 0.191177127343652 39274.0625;0.168726505599499 0.0224506217441534 0.191177127343652 39274.0625]</ll>
- <rmsdtc>[0.0112806651741266 0.0399669483304024 0.0604567527770996 0.0842315852642059 0.108943715691566 0.115428619086742]</rmsdtc>
- <rmsgdt>[0.00330571504309773 0.0125941270962358 0.0275448597967625 0.0476138852536678 0.0680833756923676 0.0725241377949715]</rmsgdt>
- <rmsdt>0.115428619086742</rmsdt>
- <dt>0.0716427564620972</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027238/ses-1/sub-0027238_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 54s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 6s</item>
- <item>46s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 12s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 88s</item>
- <item>SPM preprocessing 1 (estimate 2): 94s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 50s</item>
- <item>Update probability maps 10s</item>
- <item>104s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 28s</item>
- <item>Fast Optimized Shooting registration 40s</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) 22s</item>
- <item>Estimate local tissue thresholds (GM) 35s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 50s</item>
- <item>133s</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 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 25s</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>78s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 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>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 | 0.0860 0.0000 0.0860 | 32.0000</item>
- <item>2 | 2.50 | 0.0832 0.0012 0.0844 | 29.4886</item>
- <item>3 | 2.50 | 0.0824 0.0018 0.0843 | 26.9772</item>
- <item>4 | 2.50 | 0.0820 0.0020 0.0841 | 24.6107</item>
- <item>5 | 2.50 | 0.0817 0.0022 0.0839 | 22.6548</item>
- <item>6 | 2.50 | 0.0815 0.0023 0.0837 | 20.6989</item>
- <item>7 | 2.50 | 0.0812 0.0024 0.0836 | 18.9688</item>
- <item>8 | 2.50 | 0.0809 0.0025 0.0834 | 17.4455</item>
- <item>9 | 2.50 | 0.0806 0.0025 0.0831 | 15.9223</item>
- <item>10 | 2.50 | 0.0803 0.0026 0.0829 | 14.6627</item>
- <item>11 | 2.50 | 0.0800 0.0027 0.0827 | 13.4764</item>
- <item>12 | 2.50 | 0.0797 0.0028 0.0824 | 12.3015</item>
- <item>13 | 2.50 | 0.0793 0.0029 0.0822 | 11.3776</item>
- <item>14 | 2.50 | 0.0790 0.0029 0.0820 | 10.4537</item>
- <item>15 | 2.25 | 0.0785 0.0030 0.0815 | 9.5920</item>
- <item>16 | 2.25 | 0.0757 0.0044 0.0801 | 8.8725</item>
- <item>17 | 2.25 | 0.0745 0.0049 0.0794 | 8.1530</item>
- <item>29 | 2.00 | 0.0765 0.0022 0.0788 | 3.3283</item>
- <item>30 | 2.00 | 0.0708 0.0046 0.0755 | 3.1221</item>
- <item>31 | 2.00 | 0.0689 0.0056 0.0745 | 2.9160</item>
- <item>43 | 1.75 | 0.0680 0.0032 0.0712 | 1.5785</item>
- <item>44 | 1.75 | 0.0635 0.0056 0.0691 | 1.5194</item>
- <item>45 | 1.75 | 0.0620 0.0064 0.0684 | 1.4626</item>
- <item>57 | 1.50 | 0.0606 0.0046 0.0652 | 1.0900</item>
- <item>58 | 1.50 | 0.0573 0.0068 0.0642 | 1.0730</item>
- <item>59 | 1.50 | 0.0562 0.0075 0.0637 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 209s</item>
- <item>Prepare output 14s</item>
- <item>223s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.060 0.084 0.109 | 0.115429</item>
- <item>Template Matching: 0.086 0.224 0.207 0.186 0.169 | 0.168727</item>
- <item>Write result maps: 45s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 51s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 56s</item>
- <item>134s</item>
- <item>Create initial surface 99s</item>
- <item>Topology correction: 110s</item>
- <item>Surface refinement: 89s</item>
- <item>Reduction of surface collisions with optimization: 74s</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: 37s</item>
- <item>CSF distance: 19s</item>
- <item>PBT2x thickness: 55s</item>
- <item>117s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 115s</item>
- <item>Surface refinement: 91s</item>
- <item>Reduction of surface collisions with optimization: 75s</item>
- <item>Spherical mapping with areal smoothing 99s</item>
- <item>Spherical registration 320s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3977 0.6173 mm</item>
- <item>Surface intensity / position RMSE: 0.0672 / 0.0872</item>
- <item>Euler number / defect number / defect size: 18.0 / 16.0 / 0.48%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/surf/lh.thickness.sub-0027238_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/surf/rh.thickness.sub-0027238_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/sub-0027238_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1969s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 37s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 26s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 16s</item>
- <item>ROI estimation of 'mori' atlas 23s</item>
- <item>ROI estimation of 'anatomy3' atlas 34s</item>
- <item>ROI estimation of 'julichbrain' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 128s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s</item>
- <item>Write results 13s</item>
- <item>477s</item>
- <item>Quality check: 17s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/report/catreport_sub-0027238_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 60 minute(s) and 15 second(s).</item>
- <item>Image Quality Rating (IQR): 85.66% (B)</item>
- <item>GM volume (GMV): 47.53% (676.87 / 1424.07 ml)</item>
- <item>GM thickness (GMT): 2.40 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_138838/ds/IBA_TRT/sub-0027238/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|