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- <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>
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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
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- <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>
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- <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>
- <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>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <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>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/var/lib/condor/execute/dir_2728065/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>
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- <shootingtpm>
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- </darteltpms>
- <shootingtpms>
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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>
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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>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>358</SurfaceEulerNumber>
- <SurfaceDefectArea>11.4012629507689</SurfaceDefectArea>
- <SurfaceDefectNumber>96</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.105204030871391</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.146708428859711</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>[3.49200010299683 10.7659997940063 68.0479965209961 132.891006469727]</tissue_mn>
- <tissue_mnr>[0.0262771733105183 0.0810137540102005 0.512058675289154 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.42450781620294 19.8724668234006 16.1995447559283 13.0922105420847]</tissue_std>
- <tissue_stdr>[0.0187366809695959 0.153575122356415 0.125190645456314 0.101177059113979]</tissue_stdr>
- <contrast>44.2675247192383</contrast>
- <contrastr>0.333111524581909</contrastr>
- <res_ECR>0.391731739044189</res_ECR>
- <NCR>0.202322125434875</NCR>
- <ICR>0.474597066640854</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>2.8965904712677</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[8.62389755249023 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>3.08666038513184</contrastr>
- <NCR>3.23545980453491</NCR>
- <ICR>1.63689756393433</ICR>
- <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
- <SurfaceDefectArea>3.85031573769222</SurfaceDefectArea>
- <SurfaceDefectNumber>5.8</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>2.10408067703247</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.93416857719421</SurfacePositionRMSE>
- <SIQR>2.95838324935653</SIQR>
- <IQR>2.98618128465851</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>20231031-041643</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>358</SurfaceEulerNumber>
- <SurfaceDefectArea>11.4012629507689</SurfaceDefectArea>
- <SurfaceDefectNumber>96</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.105204030871391</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.146708428859711</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>358</EC_abs>
- <defect_size>11.4012629507689</defect_size>
- <vol_abs_CGW>[127.56657254902 757.433070588235 441.741639215686 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.903937254901961</vol_abs_WMH>
- <vol_rel_WMH>0.000681321420329103</vol_rel_WMH>
- <surf_TSA>1914.91380215341</surf_TSA>
- <vol_TIV>1326.74128235294</vol_TIV>
- <vol_rel_CGW>[0.0961503001721508 0.570897341224619 0.33295235860323 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48847382834746 0.778886974473369]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.52617239952087 0.965157266877953 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.60093131298818 0.375952505296554 0.27449534738532;2.50240761828771 0.243604286328504 0.419312067069001;3.351584946582 0.340466687736111 0.306192585545679]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.545022064387922 0.203079483548895 0.649129825965193;4.35469313018542 0.277533571759301 0.350870174034807]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.12679868985352</vol_TIV>
- <vol_rel_CGW>[0.5 8.10304132946514 3.82960414158101 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06813214203291</vol_rel_WMH>
- <surf_TSA>8.61529022858823</surf_TSA>
- <SQR>6.6284466058752</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.439442031178844]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00211839377880096 0.00171874125953764 0.0920008048415184]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[828.045623529412 416.806054901961 212.327007843137 427.718698039216 1044.10291372549 8714.36784313726]</SPMvols0>
- <SPMvols1>[736.83877254902 390.687635294118 110.559078431373 320.062184313725 822.098768627451 8762.34354117647]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[14.2898998260498 77.6836013793945 133.958099365234]</T3th>
- <Tth>
- <T3th>[-14.7496404647827 -14.7496433258057 -0.22987174987793 14.2898998260498 77.6836013793945 133.958099365234 193.792205810547 459.791534423828]</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>[0.0195478107780218 0.0613822601735592 0.066461943089962 0 0]</dtc>
- <ll>[0.0820657791925364 0 0.0820657791925364 0;0.193029726539053 0.00829788645347055 0.201327612992524 1769.50769042969;0.193029726539053 0.00829788645347055 0.201327612992524 1769.50769042969]</ll>
- <rmsdtc>[0.0466322712600231 0.0794675648212433 0.0876191854476929]</rmsdtc>
- <rmsgdt>[0.0339066758751869 0.0386940725147724 0.0477595254778862]</rmsgdt>
- <rmsdt>0.0876191854476929</rmsdt>
- <dt>0.066461943089962</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>[0.00787716452032328 0.0269055441021919 0.0372879058122635 0.0458371676504612 0.0532693788409233 0.0589799545705318]</dtc>
- <ll>[0.0803786316189348 0 0.0803786316189348 0;0.206531547619048 0.0121139947725885 0.218645542391636 6200.85107421875;0.190414989780634 0.0143270225842073 0.204742012364842 10311.330078125;0.173041246781888 0.0167751765092667 0.189816423291155 18088.203125;0.15831197662793 0.0199240693380638 0.178236045965994 34854.23046875;0.15831197662793 0.0199240693380638 0.178236045965994 34854.23046875]</ll>
- <rmsdtc>[0.00946600269526243 0.0319938734173775 0.0482568815350533 0.0723560601472855 0.0972479954361916 0.103601709008217]</rmsdtc>
- <rmsgdt>[0.00299030961468816 0.0112265963107347 0.0260035488754511 0.0473046861588955 0.0678124204277992 0.0743279382586479]</rmsgdt>
- <rmsdt>0.103601709008217</rmsdt>
- <dt>0.0589799545705318</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025005/ses-1/sub-0025005_ses-1_run-2_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 27s</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>23s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 10s</item>
- <item>Use initial fine affine registration. 39s</item>
- <item>SPM preprocessing 1 (estimate 2): 46s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 11s</item>
- <item>Update Segmentation 13s</item>
- <item>Update Skull-Stripping 27s</item>
- <item>Update probability maps 6s</item>
- <item>57s</item>
- <item>Global intensity correction: 10s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</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) 9s</item>
- <item>Estimate local tissue thresholds (WM) 12s</item>
- <item>Estimate local tissue thresholds (GM) 17s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 26s</item>
- <item>71s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 4s</item>
- <item>Blood vessel detection 5s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s</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>36s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.98 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>7s</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 | 0.0804 0.0000 0.0804 | 32.0000</item>
- <item>2 | 2.50 | 0.0771 0.0013 0.0784 | 29.4886</item>
- <item>3 | 2.50 | 0.0762 0.0019 0.0781 | 26.9772</item>
- <item>4 | 2.50 | 0.0757 0.0022 0.0779 | 24.6107</item>
- <item>5 | 2.50 | 0.0754 0.0023 0.0777 | 22.6548</item>
- <item>6 | 2.50 | 0.0751 0.0023 0.0775 | 20.6989</item>
- <item>7 | 2.50 | 0.0749 0.0024 0.0773 | 18.9688</item>
- <item>8 | 2.50 | 0.0746 0.0025 0.0771 | 17.4455</item>
- <item>9 | 2.50 | 0.0743 0.0025 0.0768 | 15.9223</item>
- <item>10 | 2.50 | 0.0740 0.0026 0.0766 | 14.6627</item>
- <item>11 | 2.50 | 0.0737 0.0026 0.0764 | 13.4764</item>
- <item>12 | 2.50 | 0.0735 0.0026 0.0761 | 12.3015</item>
- <item>13 | 2.50 | 0.0732 0.0027 0.0759 | 11.3776</item>
- <item>14 | 2.50 | 0.0729 0.0027 0.0756 | 10.4537</item>
- <item>15 | 2.25 | 0.0715 0.0028 0.0743 | 9.5920</item>
- <item>16 | 2.25 | 0.0688 0.0040 0.0729 | 8.8725</item>
- <item>29 | 2.00 | 0.0706 0.0018 0.0724 | 3.3283</item>
- <item>30 | 2.00 | 0.0652 0.0040 0.0692 | 3.1221</item>
- <item>31 | 2.00 | 0.0635 0.0048 0.0682 | 2.9160</item>
- <item>43 | 1.75 | 0.0630 0.0027 0.0658 | 1.5785</item>
- <item>44 | 1.75 | 0.0589 0.0049 0.0638 | 1.5194</item>
- <item>45 | 1.75 | 0.0577 0.0056 0.0633 | 1.4626</item>
- <item>57 | 1.50 | 0.0566 0.0041 0.0607 | 1.0900</item>
- <item>58 | 1.50 | 0.0537 0.0060 0.0597 | 1.0730</item>
- <item>59 | 1.50 | 0.0528 0.0066 0.0594 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 107s</item>
- <item>Prepare output 7s</item>
- <item>114s</item>
- <item>Jacobian determinant (RMS): 0.009 0.032 0.048 0.072 0.097 | 0.103602</item>
- <item>Template Matching: 0.080 0.207 0.190 0.173 0.158 | 0.158312</item>
- <item>Write result maps: 36s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 29s</item>
- <item>59s</item>
- <item>Create initial surface 53s</item>
- <item>Topology correction: 85s</item>
- <item>Surface refinement: 79s</item>
- <item>Reduction of surface collisions with optimization: 93s</item>
- <item>Spherical mapping with areal smoothing 59s</item>
- <item>Spherical registration 176s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 29s</item>
- <item>58s</item>
- <item>Create initial surface 53s</item>
- <item>Topology correction: 74s</item>
- <item>Surface refinement: 69s</item>
- <item>Reduction of surface collisions with optimization: 87s</item>
- <item>Spherical mapping with areal smoothing 56s</item>
- <item>Spherical registration 187s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4889 0.7783 mm</item>
- <item>Surface intensity / position RMSE: 0.1052 / 0.1467</item>
- <item>Euler number / defect number / defect size: 358.0 / 96.0 / 11.40%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/surf/lh.thickness.sub-0025005_ses-1_run-2_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/surf/rh.thickness.sub-0025005_ses-1_run-2_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/sub-0025005_ses-1_run-2_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1256s</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 5s</item>
- <item>ROI estimation of 'aal3' atlas 9s</item>
- <item>ROI estimation of 'mori' atlas 12s</item>
- <item>ROI estimation of 'anatomy3' atlas 18s</item>
- <item>ROI estimation of 'julichbrain' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 57s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 6s</item>
- <item>245s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/report/catreport_sub-0025005_ses-1_run-2_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 35 minute(s) and 3 second(s).</item>
- <item>Image Quality Rating (IQR): 75.14% (C)</item>
- <item>GM volume (GMV): 57.09% (757.43 / 1326.74 ml)</item>
- <item>GM thickness (GMT): 2.49 0.78 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2728065/ds/NYU_2/sub-0025005/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|