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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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- <WMHC>2</WMHC>
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- <SLC>0</SLC>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
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- <shootingsurf>Template_T1</shootingsurf>
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- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
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- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
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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>
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- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <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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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_1726310/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
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- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <SurfaceEulerNumber>58</SurfaceEulerNumber>
- <SurfaceDefectArea>1.63554799666132</SurfaceDefectArea>
- <SurfaceDefectNumber>25</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0709229335188866</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0804997608065605</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>190.453735351562</res_BB>
- <tissue_mn>[10.4680004119873 43.5919990539551 176.975006103516 325.102996826172]</tissue_mn>
- <tissue_mnr>[0.0321990288794041 0.134086728096008 0.54436594247818 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.71422554757053 40.2382245793204 40.3960361166346 28.5517645846844]</tissue_std>
- <tissue_stdr>[0.0245180130004883 0.127888575196266 0.128390148282051 0.09074567258358]</tissue_stdr>
- <contrast>110.266716003418</contrast>
- <contrastr>0.339174717664719</contrastr>
- <res_ECR>0.370310723781586</res_ECR>
- <NCR>0.127728015184402</NCR>
- <ICR>0.335601985454559</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.78729963302612</res_ECR>
- <res_BB>10.5</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>2.99571251869202</contrastr>
- <NCR>2.16462850570679</NCR>
- <ICR>1.29216766357422</ICR>
- <SurfaceEulerNumber>3.85714285714286</SurfaceEulerNumber>
- <SurfaceDefectArea>1.40888699916533</SurfaceDefectArea>
- <SurfaceDefectNumber>2.25</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.41845870018005</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.60999512672424</SurfacePositionRMSE>
- <SIQR>2.4863245768124</SIQR>
- <IQR>2.09353354646429</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>20231031-034014</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>58</SurfaceEulerNumber>
- <SurfaceDefectArea>1.63554799666132</SurfaceDefectArea>
- <SurfaceDefectNumber>25</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0709229335188866</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0804997608065605</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>58</EC_abs>
- <defect_size>1.63554799666132</defect_size>
- <vol_abs_CGW>[247.293576470588 745.812470588235 533.90391372549 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.591678431372549</vol_abs_WMH>
- <vol_rel_WMH>0.000387475161634602</vol_rel_WMH>
- <surf_TSA>2081.87998474367</surf_TSA>
- <vol_TIV>1527.00996078431</vol_TIV>
- <vol_rel_CGW>[0.161946275938876 0.488413625150923 0.349640098910201 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.52851159863863 0.635248216774676]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.522385597229 0.772665972673369 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.88197065880538 0.259922894515551 0.280988787558113;2.52875494243965 0.18284732482909 0.436310238635958;3.20729364159042 0.280932178645115 0.282700973805928]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.862876041823191 0.296078998280134 0.51860754985755;4.20222289971863 0.360905897065275 0.48139245014245]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.37480712799901</vol_TIV>
- <vol_rel_CGW>[0.758374208672337 6.62165275055537 4.12931212123206 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03874751616346</vol_rel_WMH>
- <surf_TSA>8.62328557921786</surf_TSA>
- <SQR>5.43028690984088</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.336 0.474972181237437]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0403921194374561 0.0396734140813351 0.0871886610984802]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[906.450035294118 462.833188235294 439.548666666667 477.558266666667 1753.70370588235 8166.9608627451]</SPMvols0>
- <SPMvols1>[790.76717254902 435.161749019608 243.129415686275 422.543674509804 1266.18730196078 8376.81212941176]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[50.9199981689453 196.663497924805 326.870697021484]</T3th>
- <Tth>
- <T3th>[-2.95332002639771 -2.9533224105835 14.4725971221924 50.9199981689453 196.663497924805 326.870697021484 464.846038818359 1195.72216796875]</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>[0.0212893653661013 0.0747870281338692 0.0822555050253868 0 0]</dtc>
- <ll>[0.0831378816174907 0 0.0831378816174907 0;0.1954674325785 0.0104739977961399 0.20594143037464 2233.55908203125;0.1954674325785 0.0104739977961399 0.20594143037464 2233.55908203125]</ll>
- <rmsdtc>[0.045581042766571 0.0978822633624077 0.109116069972515]</rmsdtc>
- <rmsgdt>[0.0323588512837887 0.0490300618112087 0.0615623816847801]</rmsgdt>
- <rmsdt>0.109116069972515</rmsdt>
- <dt>0.0822555050253868</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>[0.00955194979906082 0.0338859297335148 0.0474343560636044 0.0557197965681553 0.0620581172406673 0.0688490718603134]</dtc>
- <ll>[0.0826040212117425 0 0.0826040212117425 0;0.219873458485958 0.0121922828907204 0.232065741376679 6240.9248046875;0.19988737682573 0.0158413245940737 0.215728701419804 11401.19140625;0.179359356335878 0.0184968294467908 0.197856185782669 19944.61328125;0.162328104304849 0.021585596574848 0.183913700879697 37760.828125;0.162328104304849 0.021585596574848 0.183913700879697 37760.828125]</ll>
- <rmsdtc>[0.0108345663174987 0.0381595864892006 0.0570966452360153 0.0821012929081917 0.106067813932896 0.113143093883991]</rmsdtc>
- <rmsgdt>[0.00310044409707189 0.0124621819704771 0.028701351955533 0.0504604652523994 0.0695295631885529 0.0758793279528618]</rmsgdt>
- <rmsdt>0.113143093883991</rmsdt>
- <dt>0.0688490718603134</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027105/ses-3/sub-0027105_ses-3_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 166s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 4s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 6s</item>
- <item>48s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 91s</item>
- <item>SPM preprocessing 1 (estimate 2): 71s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 50s</item>
- <item>Update probability maps 10s</item>
- <item>103s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 33s</item>
- <item>Fast Optimized Shooting registration 41s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.15) 18s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 35s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 52s</item>
- <item>140s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 16s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 31s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>83s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 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) 4s</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 | 0.0826 0.0000 0.0826 | 32.0000</item>
- <item>2 | 2.50 | 0.0802 0.0011 0.0813 | 29.4886</item>
- <item>3 | 2.50 | 0.0796 0.0016 0.0812 | 26.9772</item>
- <item>4 | 2.50 | 0.0792 0.0018 0.0810 | 24.6107</item>
- <item>5 | 2.50 | 0.0790 0.0019 0.0809 | 22.6548</item>
- <item>6 | 2.50 | 0.0787 0.0020 0.0807 | 20.6989</item>
- <item>7 | 2.50 | 0.0785 0.0021 0.0806 | 18.9688</item>
- <item>8 | 2.50 | 0.0782 0.0022 0.0804 | 17.4455</item>
- <item>9 | 2.50 | 0.0780 0.0023 0.0802 | 15.9223</item>
- <item>10 | 2.50 | 0.0777 0.0024 0.0800 | 14.6627</item>
- <item>11 | 2.50 | 0.0774 0.0024 0.0798 | 13.4764</item>
- <item>12 | 2.50 | 0.0771 0.0025 0.0796 | 12.3015</item>
- <item>13 | 2.50 | 0.0768 0.0026 0.0794 | 11.3776</item>
- <item>14 | 2.50 | 0.0766 0.0026 0.0792 | 10.4537</item>
- <item>15 | 2.25 | 0.0760 0.0027 0.0787 | 9.5920</item>
- <item>16 | 2.25 | 0.0733 0.0041 0.0774 | 8.8725</item>
- <item>29 | 2.00 | 0.0749 0.0018 0.0767 | 3.3283</item>
- <item>30 | 2.00 | 0.0688 0.0043 0.0730 | 3.1221</item>
- <item>31 | 2.00 | 0.0666 0.0053 0.0719 | 2.9160</item>
- <item>43 | 1.75 | 0.0657 0.0030 0.0688 | 1.5785</item>
- <item>44 | 1.75 | 0.0613 0.0054 0.0667 | 1.5194</item>
- <item>45 | 1.75 | 0.0598 0.0062 0.0660 | 1.4626</item>
- <item>57 | 1.50 | 0.0584 0.0045 0.0629 | 1.0900</item>
- <item>58 | 1.50 | 0.0552 0.0065 0.0617 | 1.0730</item>
- <item>59 | 1.50 | 0.0541 0.0072 0.0613 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 194s</item>
- <item>Prepare output 13s</item>
- <item>207s</item>
- <item>Jacobian determinant (RMS): 0.011 0.038 0.057 0.082 0.106 | 0.113143</item>
- <item>Template Matching: 0.083 0.220 0.200 0.179 0.162 | 0.162328</item>
- <item>Write result maps: 40s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 40s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 58s</item>
- <item>125s</item>
- <item>Create initial surface 103s</item>
- <item>Topology correction: 116s</item>
- <item>Surface refinement: 130s</item>
- <item>Reduction of surface collisions with optimization: 85s</item>
- <item>Spherical mapping with areal smoothing 109s</item>
- <item>Spherical registration 330s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 36s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 59s</item>
- <item>123s</item>
- <item>Create initial surface 103s</item>
- <item>Topology correction: 123s</item>
- <item>Surface refinement: 94s</item>
- <item>Reduction of surface collisions with optimization: 85s</item>
- <item>Spherical mapping with areal smoothing 114s</item>
- <item>Spherical registration 344s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5287 0.6351 mm</item>
- <item>Surface intensity / position RMSE: 0.0709 / 0.0805</item>
- <item>Euler number / defect number / defect size: 58.0 / 25.0 / 1.64%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/surf/lh.thickness.sub-0027105_ses-3_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/surf/rh.thickness.sub-0027105_ses-3_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/sub-0027105_ses-3_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2102s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 11s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 40s</item>
- <item>ROI estimation of 'lpba40' atlas 12s</item>
- <item>ROI estimation of 'hammers' atlas 28s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 10s</item>
- <item>ROI estimation of 'aal3' atlas 16s</item>
- <item>ROI estimation of 'mori' atlas 24s</item>
- <item>ROI estimation of 'anatomy3' atlas 35s</item>
- <item>ROI estimation of 'julichbrain' atlas 44s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 96s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>441s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/report/catreport_sub-0027105_ses-3_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 62 minute(s) and 54 second(s).</item>
- <item>Image Quality Rating (IQR): 84.06% (B)</item>
- <item>GM volume (GMV): 48.84% (745.81 / 1527.01 ml)</item>
- <item>GM thickness (GMT): 2.53 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1726310/ds/NYU_1/sub-0027105/ses-3/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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