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- <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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- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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- <fwhm>1</fwhm>
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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>
- <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>
- <item>gm</item>
- <item>wm</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>
- <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/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>
- <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/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>
- </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/julichbrain.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_100Parcels_17Networks_order.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/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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- <tr>
- <td>/var/lib/condor/execute/dir_3242165/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
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- <shooting>
- <shootingtpm>
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- <regstr>0.5</regstr>
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- <restypes>
- <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>
- <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>
- </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>
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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>250</SurfaceEulerNumber>
- <SurfaceDefectArea>8.62682707627733</SurfaceDefectArea>
- <SurfaceDefectNumber>80</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0963138714432716</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.130634352564812</SurfacePositionRMSE>
- <res_vx_vol>[1.33000183105469 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1.12084861758235</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[3.63849997520447 12.4449996948242 78.9860000610352 156.785003662109]</tissue_mn>
- <tissue_mnr>[0.0232069380581379 0.0793762132525444 0.50378543138504 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.25270329997391 22.0184197547285 19.2424049627407 16.2258064732724]</tissue_std>
- <tissue_stdr>[0.021239161491394 0.143773570656776 0.125647038221359 0.105949573218822]</tissue_stdr>
- <contrast>52.0106925964355</contrast>
- <contrastr>0.331732571125031</contrastr>
- <res_ECR>0.414625108242035</res_ECR>
- <NCR>0.188065648078918</NCR>
- <ICR>0.5084547996521</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.01339340209961</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[8.62396430969238 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>3.10734462738037</contrastr>
- <NCR>3.03080177307129</NCR>
- <ICR>1.72087001800537</ICR>
- <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
- <SurfaceDefectArea>3.15670676906933</SurfaceDefectArea>
- <SurfaceDefectNumber>5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.92627739906311</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.61268711090088</SurfacePositionRMSE>
- <SIQR>2.88896043255418</SIQR>
- <IQR>2.80921902836952</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>20231031-024100</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>250</SurfaceEulerNumber>
- <SurfaceDefectArea>8.62682707627733</SurfaceDefectArea>
- <SurfaceDefectNumber>80</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0963138714432716</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.130634352564812</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>250</EC_abs>
- <defect_size>8.62682707627733</defect_size>
- <vol_abs_CGW>[161.865450980392 906.567450980392 532.431239215686 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.53574509803922</vol_abs_WMH>
- <vol_rel_WMH>0.000959322567441982</vol_rel_WMH>
- <surf_TSA>2286.337807156</surf_TSA>
- <vol_TIV>1600.86414117647</vol_TIV>
- <vol_rel_CGW>[0.101111297840326 0.566298805540212 0.332589896619462 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.64207628247605 0.747571461645501]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.68921756744385 0.948116090947454 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.78590352822478 0.354306875340954 0.248483949809279;2.64289352476675 0.231053561120097 0.428124392812951;3.44436714125146 0.320258451336717 0.32339165737777]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.6765637395545 0.236473926268513 0.687457798784605;4.35479012135715 0.248980823566742 0.312542201215395]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.90312297078691</vol_TIV>
- <vol_rel_CGW>[0.5 8.02045268570783 3.82309440767712 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0959322567442</vol_rel_WMH>
- <surf_TSA>8.62398040534017</surf_TSA>
- <SQR>6.56103150516151</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.458873814138728]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00221638288348913 0.00170767679810524 0.207534939050674]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1032.89411372549 477.289160784314 228.667611764706 549.740403921569 990.106639215686 8391.21117647059]</SPMvols0>
- <SPMvols1>[931.272160784314 446.85257254902 123.357298039216 443.466415686275 804.363407843137 8394.03215294118]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[17.132999420166 93.2254028320312 160.663604736328]</T3th>
- <Tth>
- <T3th>[-17.9121704101562 -17.9121704101562 -0.389585494995117 17.132999420166 93.2254028320312 160.663604736328 232.428909301758 541.689697265625]</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>[0.0139994127675891 0.0440333671867847 0.047329343855381 0 0]</dtc>
- <ll>[0.0765226928173613 0 0.0765226928173613 0;0.196453355512127 0.00673587611314057 0.203189231625267 1436.412109375;0.196453355512127 0.00673587611314057 0.203189231625267 1436.412109375]</ll>
- <rmsdtc>[0.0360233671963215 0.0598743595182896 0.0696819722652435]</rmsdtc>
- <rmsgdt>[0.0266460385173559 0.0360752493143082 0.0458800233900547]</rmsgdt>
- <rmsdt>0.0696819722652435</rmsdt>
- <dt>0.047329343855381</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>[0.00490464037284255 0.0155681008473039 0.025724146515131 0.0372798480093479 0.0470796078443527 0.0515623614192009]</dtc>
- <ll>[0.0786028151810116 0 0.0786028151810116 0;0.215974328449328 0.00805779914529915 0.224032127594628 4124.5859375;0.203753615161342 0.0129018363530308 0.216655451514373 9285.6064453125;0.185095530742707 0.0172446125026895 0.202340143245396 18594.3828125;0.168486452562747 0.0213402603348209 0.189826712897568 37331.6484375;0.168486452562747 0.0213402603348209 0.189826712897568 37331.6484375]</ll>
- <rmsdtc>[0.00624487083405256 0.0205645449459553 0.0384684577584267 0.068427212536335 0.0980554968118668 0.104374937713146]</rmsdtc>
- <rmsgdt>[0.00248862197622657 0.00986477918922901 0.0256499126553535 0.0495834685862064 0.0723442956805229 0.0792207270860672]</rmsgdt>
- <rmsdt>0.104374937713146</rmsdt>
- <dt>0.0515623614192009</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025072/ses-1/sub-0025072_ses-1_run-2_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 32s</item>
- <item>Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>24s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 49s</item>
- <item>SPM preprocessing 1 (estimate 2): 42s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 11s</item>
- <item>Update Segmentation 14s</item>
- <item>Update Skull-Stripping 28s</item>
- <item>Update probability maps 6s</item>
- <item>59s</item>
- <item>Global intensity correction: 10s</item>
- <item>SANLM denoising after intensity normalization (medium): 20s</item>
- <item>Fast Optimized Shooting registration 22s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 1s</item>
- <item>Prepare segments (LASmod = 1.00) 10s</item>
- <item>Estimate local tissue thresholds (WM) 13s</item>
- <item>Estimate local tissue thresholds (GM) 19s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 27s</item>
- <item>76s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 6s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 16s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 3s</item>
- <item>42s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 25s</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) 3s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>8s</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 | 0.0786 0.0000 0.0786 | 32.0000</item>
- <item>2 | 2.50 | 0.0772 0.0008 0.0780 | 29.4886</item>
- <item>3 | 2.50 | 0.0768 0.0012 0.0780 | 26.9772</item>
- <item>4 | 2.50 | 0.0767 0.0013 0.0779 | 24.6107</item>
- <item>5 | 2.50 | 0.0765 0.0013 0.0779 | 22.6548</item>
- <item>6 | 2.50 | 0.0764 0.0014 0.0778 | 20.6989</item>
- <item>7 | 2.50 | 0.0763 0.0014 0.0777 | 18.9688</item>
- <item>8 | 2.50 | 0.0762 0.0014 0.0776 | 17.4455</item>
- <item>9 | 2.50 | 0.0760 0.0015 0.0775 | 15.9223</item>
- <item>10 | 2.50 | 0.0759 0.0015 0.0774 | 14.6627</item>
- <item>11 | 2.50 | 0.0757 0.0015 0.0773 | 13.4764</item>
- <item>12 | 2.50 | 0.0756 0.0016 0.0771 | 12.3015</item>
- <item>13 | 2.50 | 0.0754 0.0016 0.0770 | 11.3776</item>
- <item>14 | 2.50 | 0.0753 0.0016 0.0769 | 10.4537</item>
- <item>15 | 2.25 | 0.0742 0.0016 0.0758 | 9.5920</item>
- <item>16 | 2.25 | 0.0720 0.0027 0.0747 | 8.8725</item>
- <item>29 | 2.00 | 0.0751 0.0012 0.0762 | 3.3283</item>
- <item>30 | 2.00 | 0.0695 0.0035 0.0730 | 3.1221</item>
- <item>31 | 2.00 | 0.0679 0.0043 0.0722 | 2.9160</item>
- <item>43 | 1.75 | 0.0678 0.0024 0.0702 | 1.5785</item>
- <item>44 | 1.75 | 0.0631 0.0050 0.0681 | 1.5194</item>
- <item>45 | 1.75 | 0.0617 0.0057 0.0674 | 1.4626</item>
- <item>57 | 1.50 | 0.0608 0.0041 0.0648 | 1.0900</item>
- <item>58 | 1.50 | 0.0573 0.0064 0.0637 | 1.0730</item>
- <item>59 | 1.50 | 0.0562 0.0071 0.0633 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 110s</item>
- <item>Prepare output 7s</item>
- <item>116s</item>
- <item>Jacobian determinant (RMS): 0.006 0.021 0.038 0.068 0.098 | 0.104375</item>
- <item>Template Matching: 0.079 0.216 0.204 0.185 0.168 | 0.168486</item>
- <item>Write result maps: 38s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 18s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 34s</item>
- <item>68s</item>
- <item>Create initial surface 60s</item>
- <item>Topology correction: 91s</item>
- <item>Surface refinement: 91s</item>
- <item>Reduction of surface collisions with optimization: 65s</item>
- <item>Spherical mapping with areal smoothing 83s</item>
- <item>Spherical registration 179s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 18s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 33s</item>
- <item>66s</item>
- <item>Create initial surface 57s</item>
- <item>Topology correction: 82s</item>
- <item>Surface refinement: 73s</item>
- <item>Reduction of surface collisions with optimization: 63s</item>
- <item>Spherical mapping with areal smoothing 67s</item>
- <item>Spherical registration 188s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6422 0.7472 mm</item>
- <item>Surface intensity / position RMSE: 0.0963 / 0.1306</item>
- <item>Euler number / defect number / defect size: 250.0 / 80.0 / 8.63%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/surf/lh.thickness.sub-0025072_ses-1_run-2_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/surf/rh.thickness.sub-0025072_ses-1_run-2_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/sub-0025072_ses-1_run-2_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1309s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 21s</item>
- <item>ROI estimation of 'lpba40' atlas 6s</item>
- <item>ROI estimation of 'hammers' atlas 15s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 8s</item>
- <item>ROI estimation of 'mori' atlas 12s</item>
- <item>ROI estimation of 'anatomy3' atlas 17s</item>
- <item>ROI estimation of 'julichbrain' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 36s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 54s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 5s</item>
- <item>236s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/report/catreport_sub-0025072_ses-1_run-2_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 36 minute(s) and 20 second(s).</item>
- <item>Image Quality Rating (IQR): 76.91% (C+)</item>
- <item>GM volume (GMV): 56.63% (906.57 / 1600.86 ml)</item>
- <item>GM thickness (GMT): 2.64 0.75 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3242165/ds/NYU_2/sub-0025072/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|