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- <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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- <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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- <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>
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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>
- <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>
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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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- <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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- <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_3501198/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>
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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>
- </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>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.865763395813641</SurfaceDefectArea>
- <SurfaceDefectNumber>19</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0721960067749023</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0808648318052292</SurfacePositionRMSE>
- <res_vx_vol>[1.00000001125458 0.9765625 0.976562496173639]</res_vx_vol>
- <res_vx_voli>[1.00000001174206 0.9765625 0.976562496173639]</res_vx_voli>
- <res_RMS>0.984437004561201</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[5 127.792999267578 274.673004150391 396.81201171875]</tissue_mn>
- <tissue_mnr>[0.0126004246994853 0.322049230337143 0.692199289798737 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.6386991506592 51.4770593024864 36.8406943895333 23.943633850798]</tissue_std>
- <tissue_stdr>[0.0322570502758026 0.131382033228874 0.0940264537930489 0.0611100047826767]</tissue_stdr>
- <contrast>123.697654724121</contrast>
- <contrastr>0.311728596687317</contrastr>
- <res_ECR>0.294499695301056</res_ECR>
- <NCR>0.141774088144302</NCR>
- <ICR>0.28973314166069</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000002250915 1.953125 1.95312499234728]</res_vx_vol>
- <res_RMS>1.9688740091224</res_RMS>
- <res_ECR>2.40050864219666</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>3.40740442276001</contrastr>
- <NCR>2.36626601219177</NCR>
- <ICR>1.17840564250946</ICR>
- <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
- <SurfaceDefectArea>1.21644084895341</SurfaceDefectArea>
- <SurfaceDefectNumber>1.95</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.44392013549805</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.61729669570923</SurfacePositionRMSE>
- <SIQR>2.29531643832956</SIQR>
- <IQR>2.22669861125549</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>20231031-021602</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.865763395813641</SurfaceDefectArea>
- <SurfaceDefectNumber>19</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0721960067749023</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0808648318052292</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>20</EC_abs>
- <defect_size>0.865763395813641</defect_size>
- <vol_abs_CGW>[209.752043326887 715.880231287417 492.689301100733 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.285122443541268</vol_abs_WMH>
- <vol_rel_WMH>0.0002010280661475</vol_rel_WMH>
- <surf_TSA>2032.7381296033</surf_TSA>
- <vol_TIV>1418.32157571504</vol_TIV>
- <vol_rel_CGW>[0.147887507965986 0.504737602208802 0.347374889825213 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51559752562425 0.612099440776383]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.54070615768433 0.730322318158012 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.88828688026169 0.250561535953016 0.266630226837934;2.53151695243858 0.175152886454486 0.432139928942334;3.15224453490477 0.259498564691953 0.301229844219732]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.854168933415731 0.326476486370864 0.585833032164799;4.0467698375384 0.33646862424435 0.414166967835201]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00799338599079</vol_TIV>
- <vol_rel_CGW>[0.505881967779915 6.91482762587647 4.08862948680339 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02010280661475</vol_rel_WMH>
- <surf_TSA>8.62244659621733</surf_TSA>
- <SQR>5.66519928910451</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11000.0000807002 0.375991410223199]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0014402219094336 0.00116335425991565 0.0321929007768631]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[857.313907075396 442.386099592738 382.351066738496 663.395101464298 915.904781551257 8196.93590855312]</SPMvols0>
- <SPMvols1>[747.570608415481 412.676676070716 223.708375175318 456.904351312389 824.189925564802 8335.00106825292]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[152.863906860352 290.900390625 385.813385009766]</T3th>
- <Tth>
- <T3th>[-5.80777978897095 35.430419921875 3.07406115531921 152.863906860352 290.900390625 385.813385009766 502.288116455078 1018.69744873047]</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>[0.020166764035821 0.0652234181761742 0.0711273103952408 0 0]</dtc>
- <ll>[0.0807493468578838 0 0.0807493468578838 0;0.193034983768898 0.00857683905318719 0.201611822822085 1828.99377441406;0.193034983768898 0.00857683905318719 0.201611822822085 1828.99377441406]</ll>
- <rmsdtc>[0.0412669628858566 0.0855359137058258 0.0945365279912949]</rmsdtc>
- <rmsgdt>[0.0290373265743256 0.0402781255543232 0.0495181791484356]</rmsgdt>
- <rmsdt>0.0945365279912949</rmsdt>
- <dt>0.0711273103952408</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>[0.00891875196248293 0.0312091708183289 0.042485099285841 0.0506113581359386 0.0574483498930931 0.0640224888920784]</dtc>
- <ll>[0.0816813021487032 0 0.0816813021487032 0;0.214748290598291 0.0118896319826007 0.226637922580891 6086.00537109375;0.197709465730737 0.0144688572043401 0.212178322935077 10413.41015625;0.179154224884816 0.0170795879019858 0.196233812786801 18416.44140625;0.16266565767458 0.0204271079972138 0.183092765671794 35734.22265625;0.16266565767458 0.0204271079972138 0.183092765671794 35734.22265625]</ll>
- <rmsdtc>[0.0103465290740132 0.0361310429871082 0.0527939088642597 0.0758467465639114 0.100326403975487 0.10742525011301]</rmsdtc>
- <rmsgdt>[0.00315264659002423 0.0119088711217046 0.0263801533728838 0.0468751452863216 0.0657478496432304 0.0714198872447014]</rmsgdt>
- <rmsdt>0.10742525011301</rmsdt>
- <dt>0.0640224888920784</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027162/ses-1/sub-0027162_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 57s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 11s</item>
- <item>Refine background 3s</item>
- <item>Final correction 8s</item>
- <item>Final scaling 5s</item>
- <item>50s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 87s</item>
- <item>SPM preprocessing 1 (estimate 2): 75s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 51s</item>
- <item>Update probability maps 11s</item>
- <item>105s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 31s</item>
- <item>Fast Optimized Shooting registration 45s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.05) 18s</item>
- <item>Estimate local tissue thresholds (WM) 26s</item>
- <item>Estimate local tissue thresholds (GM) 39s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 57s</item>
- <item>153s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 10s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 20s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 6s</item>
- <item>94s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</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 | 0.0817 0.0000 0.0817 | 32.0000</item>
- <item>2 | 2.50 | 0.0793 0.0011 0.0804 | 29.4886</item>
- <item>3 | 2.50 | 0.0786 0.0017 0.0802 | 26.9772</item>
- <item>4 | 2.50 | 0.0782 0.0019 0.0801 | 24.6107</item>
- <item>5 | 2.50 | 0.0780 0.0020 0.0800 | 22.6548</item>
- <item>6 | 2.50 | 0.0777 0.0021 0.0798 | 20.6989</item>
- <item>7 | 2.50 | 0.0775 0.0022 0.0796 | 18.9688</item>
- <item>8 | 2.50 | 0.0772 0.0022 0.0794 | 17.4455</item>
- <item>9 | 2.50 | 0.0770 0.0023 0.0792 | 15.9223</item>
- <item>10 | 2.50 | 0.0767 0.0024 0.0791 | 14.6627</item>
- <item>11 | 2.50 | 0.0764 0.0024 0.0789 | 13.4764</item>
- <item>12 | 2.50 | 0.0761 0.0025 0.0786 | 12.3015</item>
- <item>13 | 2.50 | 0.0758 0.0026 0.0784 | 11.3776</item>
- <item>14 | 2.50 | 0.0756 0.0026 0.0782 | 10.4537</item>
- <item>15 | 2.25 | 0.0743 0.0027 0.0769 | 9.5920</item>
- <item>16 | 2.25 | 0.0716 0.0040 0.0755 | 8.8725</item>
- <item>29 | 2.00 | 0.0731 0.0018 0.0749 | 3.3283</item>
- <item>30 | 2.00 | 0.0677 0.0040 0.0716 | 3.1221</item>
- <item>31 | 2.00 | 0.0659 0.0048 0.0707 | 2.9160</item>
- <item>43 | 1.75 | 0.0652 0.0027 0.0680 | 1.5785</item>
- <item>44 | 1.75 | 0.0611 0.0049 0.0660 | 1.5194</item>
- <item>45 | 1.75 | 0.0597 0.0057 0.0654 | 1.4626</item>
- <item>57 | 1.50 | 0.0584 0.0041 0.0625 | 1.0900</item>
- <item>58 | 1.50 | 0.0553 0.0061 0.0614 | 1.0730</item>
- <item>59 | 1.50 | 0.0542 0.0068 0.0610 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 208s</item>
- <item>Prepare output 15s</item>
- <item>223s</item>
- <item>Jacobian determinant (RMS): 0.010 0.036 0.053 0.076 0.100 | 0.107425</item>
- <item>Template Matching: 0.082 0.215 0.198 0.179 0.163 | 0.162666</item>
- <item>Write result maps: 64s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 41s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 60s</item>
- <item>130s</item>
- <item>Create initial surface 109s</item>
- <item>Topology correction: 118s</item>
- <item>Surface refinement: 100s</item>
- <item>Reduction of surface collisions with optimization: 89s</item>
- <item>Spherical mapping with areal smoothing 108s</item>
- <item>Spherical registration 339s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 58s</item>
- <item>124s</item>
- <item>Create initial surface 104s</item>
- <item>Topology correction: 114s</item>
- <item>Surface refinement: 128s</item>
- <item>Reduction of surface collisions with optimization: 88s</item>
- <item>Spherical mapping with areal smoothing 106s</item>
- <item>Spherical registration 346s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5158 0.6106 mm</item>
- <item>Surface intensity / position RMSE: 0.0722 / 0.0809</item>
- <item>Euler number / defect number / defect size: 20.0 / 19.0 / 0.87%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/surf/lh.thickness.sub-0027162_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/surf/rh.thickness.sub-0027162_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/sub-0027162_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2126s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 15s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 52s</item>
- <item>ROI estimation of 'lpba40' atlas 15s</item>
- <item>ROI estimation of 'hammers' atlas 36s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 21s</item>
- <item>ROI estimation of 'mori' atlas 31s</item>
- <item>ROI estimation of 'anatomy3' atlas 45s</item>
- <item>ROI estimation of 'julichbrain' atlas 62s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 98s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 10s</item>
- <item>527s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/report/catreport_sub-0027162_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 64 minute(s) and 17 second(s).</item>
- <item>Image Quality Rating (IQR): 82.73% (B-)</item>
- <item>GM volume (GMV): 50.47% (715.88 / 1418.32 ml)</item>
- <item>GM thickness (GMT): 2.52 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3501198/ds/SWU_3/sub-0027162/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|