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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>
- <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>
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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>
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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>
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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>
- <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>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <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>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
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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/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_3169435/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</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>
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- <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>
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- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
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- <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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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>388</SurfaceEulerNumber>
- <SurfaceDefectArea>11.9927239174263</SurfaceDefectArea>
- <SurfaceDefectNumber>109</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.109270200133324</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.159267887473106</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>[2.29299998283386 12.293999671936 70.1780014038086 135.740997314453]</tissue_mn>
- <tissue_mnr>[0.0168924648314714 0.0905695408582687 0.516999304294586 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.56067644702799 20.493518248991 16.778231692993 14.4134230628652]</tissue_std>
- <tissue_stdr>[0.0191885717213154 0.15356932580471 0.125728607177734 0.108007788658142]</tissue_stdr>
- <contrast>45.4831924438477</contrast>
- <contrastr>0.335073351860046</contrastr>
- <res_ECR>0.446521997451782</res_ECR>
- <NCR>0.257546722888947</NCR>
- <ICR>0.53215616941452</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.1761326789856</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[8.5226354598999 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>3.05723309516907</contrastr>
- <NCR>4.02823305130005</NCR>
- <ICR>1.77965319156647</ICR>
- <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
- <SurfaceDefectArea>3.99818097935658</SurfaceDefectArea>
- <SurfaceDefectNumber>6.45</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>2.18540382385254</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>3.18535780906677</SurfacePositionRMSE>
- <SIQR>3.57655389106608</SIQR>
- <IQR>3.69813612401047</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>20231031-042008</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>388</SurfaceEulerNumber>
- <SurfaceDefectArea>11.9927239174263</SurfaceDefectArea>
- <SurfaceDefectNumber>109</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.109270200133324</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.159267887473106</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>388</EC_abs>
- <defect_size>11.9927239174263</defect_size>
- <vol_abs_CGW>[123.644541176471 768.235803921569 434.24251372549 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.498345098039216</vol_abs_WMH>
- <vol_rel_WMH>0.000375791047355388</vol_rel_WMH>
- <surf_TSA>1913.39766675833</surf_TSA>
- <vol_TIV>1326.12285882353</vol_TIV>
- <vol_rel_CGW>[0.0932376215022505 0.579309676181217 0.327452702316532 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48977453661837 0.77083186428328]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55366587638855 0.97346413276057 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.58259928174096 0.384426391620522 0.25508544490277;2.51221314547952 0.244354360976921 0.4326458456099;3.33897090501031 0.334862248495975 0.312268709487331]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.50839654463773 0.203668116088399 0.70497803806735;4.24424061814085 0.204673048278843 0.29502196193265]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.12893022247263</vol_TIV>
- <vol_rel_CGW>[0.5 8.25412493141554 3.73083157896071 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03757910473554</vol_rel_WMH>
- <surf_TSA>8.6151061740616</surf_TSA>
- <SQR>6.75140683398187</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.482007767604388]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00192110810894519 0.00151286751497537 0.0999198257923126]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[859.740545098039 415.811988235294 174.750623529412 571.110733333333 932.718317647059 8699.52723921569]</SPMvols0>
- <SPMvols1>[761.734635294118 382.933733333333 93.2390588235294 459.761258823529 735.825490196078 8710.03802352941]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[18.8076992034912 80.2386016845703 136.623794555664]</T3th>
- <Tth>
- <T3th>[-9.11061000823975 -9.1106071472168 1.83338713645935 18.8076992034912 80.2386016845703 136.623794555664 195.531845092773 495.558868408203]</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>[0.0191661715507507 0.0612419433891773 0.0670338869094849 0 0]</dtc>
- <ll>[0.0806729185814951 0 0.0806729185814951 0;0.192367370532197 0.0082397523905192 0.200607122922716 1757.11071777344;0.192367370532197 0.0082397523905192 0.200607122922716 1757.11071777344]</ll>
- <rmsdtc>[0.0431765839457512 0.0833675116300583 0.09372778236866]</rmsdtc>
- <rmsgdt>[0.0310614593327045 0.04154983907938 0.0513229221105576]</rmsgdt>
- <rmsdt>0.09372778236866</rmsdt>
- <dt>0.0670338869094849</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>[0.0078787412494421 0.0267774667590857 0.0395538136363029 0.0513177737593651 0.0603354051709175 0.0685877576470375]</dtc>
- <ll>[0.0817979844475294 0 0.0817979844475294 0;0.216472237484737 0.0113769173534799 0.227849154838217 5823.5595703125;0.200628906076319 0.0146631867807887 0.215292092857108 10553.271484375;0.18195437932173 0.0178880211521304 0.19984240047386 19288.15234375;0.166586982444367 0.0214993615675338 0.1880863440119 37609.97265625;0.166586982444367 0.0214993615675338 0.1880863440119 37609.97265625]</ll>
- <rmsdtc>[0.00956041179597378 0.0337486676871777 0.0551752895116806 0.0883138999342918 0.120202079415321 0.12772099673748]</rmsdtc>
- <rmsgdt>[0.00313823274336755 0.0126176597550511 0.0295087471604347 0.0538245178759098 0.076592780649662 0.0835340544581413]</rmsgdt>
- <rmsdt>0.12772099673748</rmsdt>
- <dt>0.0685877576470375</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025003/ses-1/sub-0025003_ses-1_run-2_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 33s</item>
- <item>Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>29s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 11s</item>
- <item>Use initial fine affine registration. 53s</item>
- <item>SPM preprocessing 1 (estimate 2): 50s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 13s</item>
- <item>Update Segmentation 15s</item>
- <item>Update Skull-Stripping 33s</item>
- <item>Update probability maps 7s</item>
- <item>69s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 20s</item>
- <item>Fast Optimized Shooting registration 26s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 11s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 22s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 33s</item>
- <item>88s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 8s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 20s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 3s</item>
- <item>51s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 26s</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>9s</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 | 0.0818 0.0000 0.0818 | 32.0000</item>
- <item>2 | 2.50 | 0.0792 0.0011 0.0803 | 29.4886</item>
- <item>3 | 2.50 | 0.0784 0.0017 0.0801 | 26.9772</item>
- <item>4 | 2.50 | 0.0781 0.0019 0.0800 | 24.6107</item>
- <item>5 | 2.50 | 0.0778 0.0020 0.0798 | 22.6548</item>
- <item>6 | 2.50 | 0.0776 0.0020 0.0796 | 20.6989</item>
- <item>7 | 2.50 | 0.0774 0.0021 0.0795 | 18.9688</item>
- <item>8 | 2.50 | 0.0771 0.0022 0.0793 | 17.4455</item>
- <item>9 | 2.50 | 0.0769 0.0022 0.0791 | 15.9223</item>
- <item>10 | 2.50 | 0.0766 0.0023 0.0789 | 14.6627</item>
- <item>11 | 2.50 | 0.0764 0.0023 0.0787 | 13.4764</item>
- <item>12 | 2.50 | 0.0761 0.0024 0.0785 | 12.3015</item>
- <item>13 | 2.50 | 0.0759 0.0024 0.0783 | 11.3776</item>
- <item>14 | 2.50 | 0.0756 0.0025 0.0781 | 10.4537</item>
- <item>15 | 2.25 | 0.0748 0.0025 0.0774 | 9.5920</item>
- <item>16 | 2.25 | 0.0722 0.0038 0.0759 | 8.8725</item>
- <item>29 | 2.00 | 0.0743 0.0017 0.0760 | 3.3283</item>
- <item>30 | 2.00 | 0.0687 0.0040 0.0727 | 3.1221</item>
- <item>31 | 2.00 | 0.0669 0.0049 0.0718 | 2.9160</item>
- <item>43 | 1.75 | 0.0665 0.0028 0.0693 | 1.5785</item>
- <item>44 | 1.75 | 0.0620 0.0052 0.0673 | 1.5194</item>
- <item>45 | 1.75 | 0.0607 0.0060 0.0666 | 1.4626</item>
- <item>57 | 1.50 | 0.0598 0.0043 0.0642 | 1.0900</item>
- <item>58 | 1.50 | 0.0566 0.0065 0.0631 | 1.0730</item>
- <item>59 | 1.50 | 0.0555 0.0072 0.0627 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 132s</item>
- <item>Prepare output 8s</item>
- <item>140s</item>
- <item>Jacobian determinant (RMS): 0.010 0.034 0.055 0.088 0.120 | 0.127721</item>
- <item>Template Matching: 0.082 0.216 0.201 0.182 0.167 | 0.166587</item>
- <item>Write result maps: 45s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 21s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 38s</item>
- <item>76s</item>
- <item>Create initial surface 70s</item>
- <item>Topology correction: 98s</item>
- <item>Surface refinement: 79s</item>
- <item>Reduction of surface collisions with optimization: 121s</item>
- <item>Spherical mapping with areal smoothing 70s</item>
- <item>Spherical registration 242s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 19s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 38s</item>
- <item>75s</item>
- <item>Create initial surface 71s</item>
- <item>Topology correction: 95s</item>
- <item>Surface refinement: 105s</item>
- <item>Reduction of surface collisions with optimization: 123s</item>
- <item>Spherical mapping with areal smoothing 70s</item>
- <item>Spherical registration 243s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4898 0.7708 mm</item>
- <item>Surface intensity / position RMSE: 0.1093 / 0.1593</item>
- <item>Euler number / defect number / defect size: 388.0 / 109.0 / 11.99%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/surf/lh.thickness.sub-0025003_ses-1_run-2_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/surf/rh.thickness.sub-0025003_ses-1_run-2_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/sub-0025003_ses-1_run-2_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1622s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 24s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 17s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 14s</item>
- <item>ROI estimation of 'anatomy3' atlas 20s</item>
- <item>ROI estimation of 'julichbrain' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 65s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 6s</item>
- <item>279s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/report/catreport_sub-0025003_ses-1_run-2_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 44 minute(s) and 6 second(s).</item>
- <item>Image Quality Rating (IQR): 68.02% (D+)</item>
- <item>GM volume (GMV): 57.93% (768.24 / 1326.12 ml)</item>
- <item>GM thickness (GMT): 2.49 0.77 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3169435/ds/NYU_2/sub-0025003/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|