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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>
- <LASstr>0.5</LASstr>
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- <regstr>0.5</regstr>
- <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>
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- </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>
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- <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>
- <item>gm</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>
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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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- <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_2583505/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <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>
- </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>
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- <VT>15</VT>
- <NV>17</NV>
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- <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>
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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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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <SurfaceEulerNumber>360</SurfaceEulerNumber>
- <SurfaceDefectArea>12.1448449372506</SurfaceDefectArea>
- <SurfaceDefectNumber>103.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.114575922489166</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.18809762597084</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>[0 10.8290004730225 71.4629974365234 138.235992431641]</tissue_mn>
- <tissue_mnr>[0 0.078337050974369 0.5169637799263 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.4429532196305 22.0589540462666 16.886125770261 15.0769075315284]</tissue_std>
- <tissue_stdr>[0.0176723375916481 0.159574612975121 0.122154332697392 0.109066441655159]</tissue_stdr>
- <contrast>46.5476608276367</contrast>
- <contrastr>0.336726069450378</contrastr>
- <res_ECR>0.475939273834229</res_ECR>
- <NCR>0.266716122627258</NCR>
- <ICR>0.387341201305389</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.32622075080872</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.03244233131409</contrastr>
- <NCR>4.15986394882202</NCR>
- <ICR>1.42048907279968</ICR>
- <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
- <SurfaceDefectArea>4.03621123431264</SurfaceDefectArea>
- <SurfaceDefectNumber>6.175</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>2.29151844978333</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>3.7619526386261</SurfacePositionRMSE>
- <SIQR>3.69962121521752</SIQR>
- <IQR>3.81799267462026</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>20231031-031655</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>360</SurfaceEulerNumber>
- <SurfaceDefectArea>12.1448449372506</SurfaceDefectArea>
- <SurfaceDefectNumber>103.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.114575922489166</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.18809762597084</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>360</EC_abs>
- <defect_size>12.1448449372506</defect_size>
- <vol_abs_CGW>[139.08208627451 714.616364705882 393.704364705882 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.885886274509804</vol_abs_WMH>
- <vol_rel_WMH>0.000710184603858235</vol_rel_WMH>
- <surf_TSA>1760.77708807398</surf_TSA>
- <vol_TIV>1247.40281568627</vol_TIV>
- <vol_rel_CGW>[0.111497332317622 0.572883398786243 0.315619268896135 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.42116353462057 0.805248834288162]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.4744565486908 0.983692594310805 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.36265720649448 0.401507810475045 0.230495773711334;2.3769872742737 0.266751140101153 0.431740003324766;3.27855593141459 0.354968443564049 0.337764222963901]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.345965103182977 0.163253104085252 0.548392132375898;4.22355320385242 0.204949676361813 0.451607867624102]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.53508194896869</vol_TIV>
- <vol_rel_CGW>[0.5 8.13871046670695 3.5183058350599 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.07101846038582</vol_rel_WMH>
- <surf_TSA>8.56213104305758</surf_TSA>
- <SQR>6.65657021089949</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.448590497360212]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00213312217965722 0.00177492026705295 0.0621189139783382]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[810.15708627451 376.200156862745 280.605905882353 380.485717647059 897.347337254902 8915.47245882353]</SPMvols0>
- <SPMvols1>[693.723792156863 342.123764705882 149.679309803922 332.98517254902 715.422443137255 8908.11370588235]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[24.0240993499756 81.2350006103516 136.196105957031]</T3th>
- <Tth>
- <T3th>[-11.7347497940063 -11.7347526550293 1.95550322532654 24.0240993499756 81.2350006103516 136.196105957031 192.282104492188 446.6005859375]</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>[0.0184918604791164 0.0626381039619446 0.0687746182084084 0 0]</dtc>
- <ll>[0.0834427887365884 0 0.0834427887365884 0;0.203924355386686 0.00883325208135012 0.212757607468036 1883.67333984375;0.203924355386686 0.00883325208135012 0.212757607468036 1883.67333984375]</ll>
- <rmsdtc>[0.0405542179942131 0.0853462889790535 0.096390500664711]</rmsdtc>
- <rmsgdt>[0.0291700251400471 0.0422065518796444 0.0525716952979565]</rmsgdt>
- <rmsdt>0.096390500664711</rmsdt>
- <dt>0.0687746182084084</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>[0.00738417403772473 0.0276276580989361 0.038733646273613 0.0494023896753788 0.0584205500781536 0.0657526552677155]</dtc>
- <ll>[0.084095012005408 0 0.084095012005408 0;0.223630189255189 0.0131574328449328 0.236787622100122 6734.9609375;0.209285102930061 0.0154512461451595 0.22473634907522 11120.447265625;0.190504865655419 0.0183099056580807 0.2088147713135 19743.05859375;0.176003874718253 0.0217927021625995 0.197796576880853 38123.12890625;0.176003874718253 0.0217927021625995 0.197796576880853 38123.12890625]</ll>
- <rmsdtc>[0.00906043592840433 0.0328129939734936 0.0541096813976765 0.0839418023824692 0.112757258117199 0.120015971362591]</rmsdtc>
- <rmsgdt>[0.00303561706095934 0.0123198237270117 0.0290347915142775 0.0519265681505203 0.0733769983053207 0.080418698489666]</rmsgdt>
- <rmsdt>0.120015971362591</rmsdt>
- <dt>0.0657526552677155</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025011/ses-1/sub-0025011_ses-1_run-2_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 24s</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 3s</item>
- <item>Initial correction 3s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 2s</item>
- <item>22s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 5s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 10s</item>
- <item>Use initial fine affine registration. 8s</item>
- <item>Use previous fine affine registration. 35s</item>
- <item>SPM preprocessing 1 (estimate 2): 45s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 10s</item>
- <item>Update Segmentation 11s</item>
- <item>Update Skull-Stripping 25s</item>
- <item>Update probability maps 6s</item>
- <item>52s</item>
- <item>Global intensity correction: 9s</item>
- <item>SANLM denoising after intensity normalization (medium): 14s</item>
- <item>Fast Optimized Shooting registration 20s</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) 7s</item>
- <item>Estimate local tissue thresholds (WM) 11s</item>
- <item>Estimate local tissue thresholds (GM) 16s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 24s</item>
- <item>63s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 4s</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) 10s</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>31s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 21s</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) 2s</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>6s</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 | 0.0841 0.0000 0.0841 | 32.0000</item>
- <item>2 | 2.50 | 0.0816 0.0011 0.0827 | 29.4886</item>
- <item>3 | 2.50 | 0.0809 0.0016 0.0825 | 26.9772</item>
- <item>4 | 2.50 | 0.0805 0.0018 0.0824 | 24.6107</item>
- <item>5 | 2.50 | 0.0803 0.0020 0.0822 | 22.6548</item>
- <item>6 | 2.50 | 0.0800 0.0020 0.0821 | 20.6989</item>
- <item>7 | 2.50 | 0.0798 0.0021 0.0819 | 18.9688</item>
- <item>8 | 2.50 | 0.0796 0.0022 0.0818 | 17.4455</item>
- <item>9 | 2.50 | 0.0793 0.0022 0.0816 | 15.9223</item>
- <item>10 | 2.50 | 0.0791 0.0023 0.0814 | 14.6627</item>
- <item>11 | 2.50 | 0.0788 0.0024 0.0812 | 13.4764</item>
- <item>12 | 2.50 | 0.0785 0.0024 0.0810 | 12.3015</item>
- <item>13 | 2.50 | 0.0783 0.0025 0.0808 | 11.3776</item>
- <item>14 | 2.50 | 0.0780 0.0025 0.0805 | 10.4537</item>
- <item>15 | 2.25 | 0.0783 0.0026 0.0809 | 9.5920</item>
- <item>16 | 2.25 | 0.0756 0.0039 0.0795 | 8.8725</item>
- <item>17 | 2.25 | 0.0745 0.0044 0.0789 | 8.1530</item>
- <item>29 | 2.00 | 0.0768 0.0020 0.0788 | 3.3283</item>
- <item>30 | 2.00 | 0.0715 0.0043 0.0758 | 3.1221</item>
- <item>31 | 2.00 | 0.0698 0.0052 0.0749 | 2.9160</item>
- <item>43 | 1.75 | 0.0693 0.0029 0.0722 | 1.5785</item>
- <item>44 | 1.75 | 0.0649 0.0054 0.0702 | 1.5194</item>
- <item>45 | 1.75 | 0.0635 0.0061 0.0696 | 1.4626</item>
- <item>57 | 1.50 | 0.0630 0.0044 0.0674 | 1.0900</item>
- <item>58 | 1.50 | 0.0597 0.0066 0.0663 | 1.0730</item>
- <item>59 | 1.50 | 0.0587 0.0073 0.0659 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 101s</item>
- <item>Prepare output 6s</item>
- <item>107s</item>
- <item>Jacobian determinant (RMS): 0.009 0.033 0.054 0.084 0.113 | 0.120016</item>
- <item>Template Matching: 0.084 0.224 0.209 0.191 0.176 | 0.176004</item>
- <item>Write result maps: 34s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 13s</item>
- <item>CSF distance: 8s</item>
- <item>PBT2x thickness: 24s</item>
- <item>49s</item>
- <item>Create initial surface 44s</item>
- <item>Topology correction: 70s</item>
- <item>Surface refinement: 56s</item>
- <item>Reduction of surface collisions with optimization: 74s</item>
- <item>Spherical mapping with areal smoothing 55s</item>
- <item>Spherical registration 160s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 13s</item>
- <item>CSF distance: 8s</item>
- <item>PBT2x thickness: 24s</item>
- <item>48s</item>
- <item>Create initial surface 43s</item>
- <item>Topology correction: 68s</item>
- <item>Surface refinement: 57s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 47s</item>
- <item>Spherical registration 170s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4221 0.8042 mm</item>
- <item>Surface intensity / position RMSE: 0.1146 / 0.1881</item>
- <item>Euler number / defect number / defect size: 360.0 / 103.5 / 12.14%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/surf/lh.thickness.sub-0025011_ses-1_run-2_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/surf/rh.thickness.sub-0025011_ses-1_run-2_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/sub-0025011_ses-1_run-2_T1w.nii</item>
- <item>Surface ROI estimation: 5s</item>
- <item>Surface and thickness estimation takes: 1066s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 5s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 19s</item>
- <item>ROI estimation of 'lpba40' atlas 6s</item>
- <item>ROI estimation of 'hammers' atlas 14s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 5s</item>
- <item>ROI estimation of 'aal3' atlas 7s</item>
- <item>ROI estimation of 'mori' atlas 11s</item>
- <item>ROI estimation of 'anatomy3' atlas 16s</item>
- <item>ROI estimation of 'julichbrain' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 8s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 14s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 47s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 4s</item>
- <item>Write results 5s</item>
- <item>209s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/report/catreport_sub-0025011_ses-1_run-2_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 30 minute(s) and 31 second(s).</item>
- <item>Image Quality Rating (IQR): 66.82% (D+)</item>
- <item>GM volume (GMV): 57.29% (714.62 / 1247.40 ml)</item>
- <item>GM thickness (GMT): 2.42 0.81 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2583505/ds/NYU_2/sub-0025011/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|