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- <fnames>..4141/ds/sub-027/sub-027_ses-t2_T1w</fnames>
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- <parameter>
- <opts>
- <tpm>
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- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
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- <extopts>
- <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>
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- <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_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>20</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>
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- </darteltpm>
- <shootingtpm>
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- </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>
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- <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>
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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>
- <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/lpba40.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/cobra.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/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>
- </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/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>
- </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/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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- </td>
- <td>[false]</td>
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- <tr>
- <td>/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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- <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>
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- <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>
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- <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>
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- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
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- <PH>25</PH>
- <LE>27</LE>
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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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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_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>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>28</SurfaceEulerNumber>
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- <tissue_mn>[0 19404.572265625 43415.01953125 62123.85546875]</tissue_mn>
- <tissue_mnr>[0 0.312352985143661 0.698846161365509 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[5915.32743754859 7167.81719135871 6284.06505703576 3565.27146654461]</tissue_std>
- <tissue_stdr>[0.0952182933688164 0.115379467606544 0.101153813302517 0.0573897324502468]</tissue_stdr>
- <contrast>18708.8359375</contrast>
- <contrastr>0.301153808832169</contrastr>
- <NCR>0.132630482316017</NCR>
- <ICR>0.241589024662971</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000033774353 2.00000003012116 2.00000003192135]</res_vx_vol>
- <res_RMS>2.00000013326202</res_RMS>
- <res_BB>0.5</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>3.56602621078491</contrastr>
- <NCR>2.23500537872314</NCR>
- <ICR>1.05900061130524</ICR>
- <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.28904274500952</SurfaceDefectArea>
- <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.27937459945679</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.40312314033508</SurfacePositionRMSE>
- <IQR>2.13967042106675</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220713-061602</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>28</SurfaceEulerNumber>
- <SurfaceDefectArea>1.15617098003809</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639687329530716</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0701561570167542</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>28</EC_abs>
- <defect_size>1.15617098003809</defect_size>
- <vol_abs_CGW>[337.492291010453 597.592539095512 494.659902828022 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.791513883752126</vol_abs_WMH>
- <vol_rel_WMH>0.000553605035584119</vol_rel_WMH>
- <surf_TSA>1766.31723693298</surf_TSA>
- <vol_TIV>1429.74473293399</vol_TIV>
- <vol_rel_CGW>[0.236050732159638 0.417971491924428 0.345977775915934 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.35565053284965 0.621712086506224]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.32498574256897 0.79033853964816 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.72961339114275 0.27992566972284 0.293918680854062;2.36439981997428 0.183278814872731 0.479656120076105;3.08304325831203 0.304474051415753 0.226425199069833]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.763166251755804 0.233322404813029 0.470588235294118;4.12225899874553 0.340793819520765 0.529411764705882]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.02105003478685</vol_TIV>
- <vol_rel_CGW>[2.08927320689005 5.35652823140137 4.06353764216836 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05536050355841</vol_rel_WMH>
- <surf_TSA>8.56600609223459</surf_TSA>
- <SQR>4.43801286723599</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.459361111111111 10134 2694 5605.34512046917 0.378132478097852]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.353821575641632]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[736.611978656931 441.293598039868 505.751316810438 1299.2508754694 4490.4783135502 3730.09126739439]</SPMvols0>
- <SPMvols1>[639.120782693135 414.213302429128 344.314559041222 77.4011919468323 17.1793524545918 8875.79545313242]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[21425.412109375 46037.765625 60390.6484375]</T3th>
- <Tth>
- <T3th>[0 0 10278.8779296875 21425.412109375 46037.765625 60390.6484375 79873.265625 113497.4375]</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>[0.0221753474324942 0.0887059420347214 0.100336916744709 0 0]</dtc>
- <ll>[0.0903013793407988 0 0.0903013793407988 0;0.19810687336458 0.0147670743559875 0.212873947720568 3149.04907226562;0.19810687336458 0.0147670743559875 0.212873947720568 3149.04907226562]</ll>
- <rmsdtc>[0.0494596585631371 0.118070118129253 0.13642892241478]</rmsdtc>
- <rmsgdt>[0.0355005636811256 0.0542913414537907 0.0706039667129517]</rmsgdt>
- <rmsdt>0.13642892241478</rmsdt>
- <dt>0.100336916744709</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>[0.0105981724336743 0.0485299117863178 0.0625359565019608 0.0719616413116455 0.0784678682684898 0.0911786556243896]</dtc>
- <ll>[0.0913389077659573 0 0.0913389077659573 0;0.224391025641026 0.0236570379273504 0.248048063568376 12109.4462890625;0.204859330885132 0.0241521983142215 0.229011529199353 17382.626953125;0.180502852596562 0.0248257056487139 0.205328558245276 26768.86328125;0.161912843634189 0.0275459877166015 0.189458831350791 48187.65625;0.161912843634189 0.0275459877166015 0.189458831350791 48187.65625]</ll>
- <rmsdtc>[0.0125844990834594 0.049278449267149 0.0812855064868927 0.111943475902081 0.140458837151527 0.149200066924095]</rmsdtc>
- <rmsgdt>[0.00380253233015537 0.0158249102532864 0.0357839614152908 0.0601197518408298 0.0806257948279381 0.0862311199307442]</rmsgdt>
- <rmsdt>0.149200066924095</rmsdt>
- <dt>0.0911786556243896</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_14141/ds/sub-027/sub-027_ses-t2_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 11s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 7s</item>
- <item>44s</item>
- <item>Correct center-of-mass 10s</item>
- <item>Affine registration 15s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 115s</item>
- <item>SPM preprocessing 1 (estimate 2): 86s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 17s</item>
- <item>Update Segmentation 20s</item>
- <item>Update Skull-Stripping 42s</item>
- <item>Update probability maps 8s</item>
- <item>87s</item>
- <item>Global intensity correction: 17s</item>
- <item>SANLM denoising after intensity normalization (medium): 6s</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 = 1.01) 15s</item>
- <item>Estimate local tissue thresholds (WM) 17s</item>
- <item>Estimate local tissue thresholds (GM) 22s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 15s</item>
- <item>80s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 13s</item>
- <item>Blood vessel detection 9s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 24s</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>69s</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 0.06,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>12s</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 | 0.0913 0.0000 0.0913 | 32.0000</item>
- <item>2 | 2.50 | 0.0873 0.0016 0.0888 | 29.4886</item>
- <item>3 | 2.50 | 0.0860 0.0024 0.0884 | 26.9772</item>
- <item>4 | 2.50 | 0.0854 0.0028 0.0882 | 24.6107</item>
- <item>5 | 2.50 | 0.0849 0.0030 0.0879 | 22.6548</item>
- <item>6 | 2.50 | 0.0845 0.0031 0.0876 | 20.6989</item>
- <item>7 | 2.50 | 0.0840 0.0033 0.0873 | 18.9688</item>
- <item>8 | 2.50 | 0.0836 0.0035 0.0870 | 17.4455</item>
- <item>9 | 2.50 | 0.0831 0.0036 0.0867 | 15.9223</item>
- <item>10 | 2.50 | 0.0826 0.0037 0.0863 | 14.6627</item>
- <item>11 | 2.50 | 0.0821 0.0039 0.0860 | 13.4764</item>
- <item>12 | 2.50 | 0.0816 0.0040 0.0856 | 12.3015</item>
- <item>13 | 2.50 | 0.0811 0.0041 0.0852 | 11.3776</item>
- <item>14 | 2.50 | 0.0806 0.0043 0.0848 | 10.4537</item>
- <item>15 | 2.25 | 0.0829 0.0044 0.0873 | 9.5920</item>
- <item>16 | 2.25 | 0.0788 0.0064 0.0852 | 8.8725</item>
- <item>17 | 2.25 | 0.0770 0.0073 0.0842 | 8.1530</item>
- <item>18 | 2.25 | 0.0757 0.0077 0.0834 | 7.5234</item>
- <item>19 | 2.25 | 0.0748 0.0079 0.0827 | 6.9630</item>
- <item>29 | 2.00 | 0.0770 0.0041 0.0811 | 3.3283</item>
- <item>30 | 2.00 | 0.0707 0.0069 0.0776 | 3.1221</item>
- <item>31 | 2.00 | 0.0683 0.0081 0.0763 | 2.9160</item>
- <item>43 | 1.75 | 0.0670 0.0047 0.0716 | 1.5785</item>
- <item>44 | 1.75 | 0.0619 0.0073 0.0693 | 1.5194</item>
- <item>45 | 1.75 | 0.0602 0.0083 0.0684 | 1.4626</item>
- <item>57 | 1.50 | 0.0587 0.0061 0.0649 | 1.0900</item>
- <item>58 | 1.50 | 0.0552 0.0084 0.0636 | 1.0730</item>
- <item>59 | 1.50 | 0.0540 0.0092 0.0632 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 211s</item>
- <item>Prepare output 10s</item>
- <item>220s</item>
- <item>Jacobian determinant (RMS): 0.013 0.049 0.081 0.112 0.140 | 0.149200</item>
- <item>Template Matching: 0.091 0.224 0.205 0.181 0.162 | 0.161913</item>
- <item>Write result maps: 26s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 67s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 46s</item>
- <item>136s</item>
- <item>Create initial surface 82s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 68s</item>
- <item>Reduction of surface collisions with optimization: 64s</item>
- <item>Spherical mapping with areal smoothing 78s</item>
- <item>Spherical registration 230s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 98s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 46s</item>
- <item>166s</item>
- <item>Create initial surface 80s</item>
- <item>Topology correction: 85s</item>
- <item>Surface refinement: 98s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 79s</item>
- <item>Spherical registration 236s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3556 0.6217 mm</item>
- <item>Surface intensity / position RMSE: 0.0640 / 0.0702</item>
- <item>Euler number / defect number / defect size: 28.0 / 15.5 / 1.16%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_14141/ds/sub-027/surf/lh.thickness.sub-027_ses-t2_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_14141/ds/sub-027/surf/rh.thickness.sub-027_ses-t2_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_14141/ds/sub-027/sub-027_ses-t2_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1634s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 12s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 43s</item>
- <item>ROI estimation of 'lpba40' atlas 12s</item>
- <item>ROI estimation of 'hammers' atlas 30s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 11s</item>
- <item>ROI estimation of 'aal3' atlas 18s</item>
- <item>ROI estimation of 'mori' atlas 26s</item>
- <item>ROI estimation of 'anatomy3' atlas 37s</item>
- <item>ROI estimation of 'julichbrain' atlas 49s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 79s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 119s</item>
- <item>Write results 120s</item>
- <item>480s</item>
- <item>Quality check: 5s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_14141/ds/sub-027/report/catreport_sub-027_ses-t2_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 51 minute(s) and 24 second(s).</item>
- <item>Image Quality Rating (IQR): 83.60% (B)</item>
- <item>GM volume (GMV): 41.80% (597.59 / 1429.74 ml)</item>
- <item>GM thickness (GMT): 2.36 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_14141/ds/sub-027/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|