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- <opts>
- <tpm>
- <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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- <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>
- <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>
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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>
- <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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- <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>
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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>
- <td>
- <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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- <tr>
- <td>/var/lib/condor/execute/dir_2564952/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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- <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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- <optimal>[1 0.3]</optimal>
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- <pbtmethod>pbt2x</pbtmethod>
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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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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>1.06683122621288</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0681464448571205</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0684317797422409</SurfacePositionRMSE>
- <res_vx_vol>[1.00000001125458 1.00000001125458 1]</res_vx_vol>
- <res_vx_voli>[1.00000001174206 1.00000001174206 1]</res_vx_voli>
- <res_RMS>1.00000000750305</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[5.01000022888184 117.069999694824 276.714996337891 394.040008544922]</tissue_mn>
- <tissue_mnr>[0.0127144455909729 0.29710179567337 0.702251017093658 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.63778335684502 43.7064163196542 37.9918901708315 24.6426973354462]</tissue_std>
- <tissue_stdr>[0.00935090705752373 0.112347163259983 0.0976579934358597 0.0633439496159554]</tissue_stdr>
- <contrast>118.835952758789</contrast>
- <contrastr>0.301583468914032</contrastr>
- <res_ECR>0.307428419589996</res_ECR>
- <NCR>0.129830151796341</NCR>
- <ICR>0.341961354017258</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000002250915 2.00000002250915 2]</res_vx_vol>
- <res_RMS>2.0000000150061</res_RMS>
- <res_ECR>2.46647143363953</res_ECR>
- <res_BB>1</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>3.55958127975464</contrastr>
- <NCR>2.19480562210083</NCR>
- <ICR>1.30793988704681</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.26670780655322</SurfaceDefectArea>
- <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.36292886734009</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.36863565444946</SurfacePositionRMSE>
- <SIQR>2.27651312611756</SIQR>
- <IQR>2.11291259736916</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>20231031-013821</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>1.06683122621288</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0681464448571205</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0684317797422409</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>1.06683122621288</defect_size>
- <vol_abs_CGW>[307.828187621231 717.360303121085 461.007348081253 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.669274525521244</vol_abs_WMH>
- <vol_rel_WMH>0.000450327277225472</vol_rel_WMH>
- <surf_TSA>1978.03441647844</surf_TSA>
- <vol_TIV>1486.19583882357</vol_TIV>
- <vol_rel_CGW>[0.207124915559513 0.482682217498958 0.310192866941529 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.59619951403777 0.657556563303236]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.60303640365601 0.806541321692123 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.94214279117183 0.272083471713655 0.286389238864596;2.61152334539185 0.18849569038317 0.422663603349885;3.2960562350814 0.282753643149762 0.290947157785518]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.866920933317469 0.285290956801694 0.569198656865414;4.29788965527977 0.346795634290356 0.430801343134586]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.1749740183086</vol_TIV>
- <vol_rel_CGW>[1.56977219036481 6.51871798669106 3.4208489034039 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04503272772255</vol_rel_WMH>
- <surf_TSA>8.62045638386641</surf_TSA>
- <SQR>5.33461256631072</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.3362596281 0.39539237443834]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00159066019114107 0.00131667265668511 0.0255362447351217]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[808.951795468109 417.506292157709 584.14771175741 501.776152960242 879.89339713411 8940.01794720335]</SPMvols0>
- <SPMvols1>[691.457875061809 388.338538531553 364.538792874598 458.251332330256 733.119915255891 8898.9562403567]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[143.246597290039 291.758911132812 379.490600585938]</T3th>
- <Tth>
- <T3th>[-5.59509992599487 -5.59509944915771 3.07112169265747 143.246597290039 291.758911132812 379.490600585938 497.612609863281 990.775268554688]</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>[0.0222749561071396 0.085423968732357 0.0961376503109932 0 0]</dtc>
- <ll>[0.091252773081889 0 0.091252773081889 0;0.213136029558308 0.013437623737239 0.226573653295547 2865.54638671875;0.213136029558308 0.013437623737239 0.226573653295547 2865.54638671875]</ll>
- <rmsdtc>[0.04680460318923 0.117532059550285 0.133663445711136]</rmsdtc>
- <rmsgdt>[0.0332514904439449 0.0626600831747055 0.0787150338292122]</rmsgdt>
- <rmsdt>0.133663445711136</rmsdt>
- <dt>0.0961376503109932</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>[0.00925623998045921 0.0383933112025261 0.0505471229553223 0.0617285631597042 0.0701447427272797 0.0788804516196251]</dtc>
- <ll>[0.0871368664051421 0 0.0871368664051421 0;0.224528311965812 0.0164775564713065 0.241005868437118 8434.44921875;0.208776110270497 0.0186461805316745 0.227422290802172 13419.8798828125;0.187426097033031 0.0209290666571143 0.208355163690145 22567.2265625;0.169480605829698 0.0240278722869255 0.193508478116624 42033.23046875;0.169480605829698 0.0240278722869255 0.193508478116624 42033.23046875]</ll>
- <rmsdtc>[0.0108838435262442 0.0397202856838703 0.0666437894105911 0.0969225913286209 0.125806510448456 0.133434116840363]</rmsdtc>
- <rmsgdt>[0.00350320641882718 0.0147326597943902 0.0336246639490128 0.0575146339833736 0.0782052427530289 0.0856338813900948]</rmsgdt>
- <rmsdt>0.133434116840363</rmsdt>
- <dt>0.0788804516196251</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025844/ses-2/sub-0025844_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 34s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 5s</item>
- <item>32s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 60s</item>
- <item>SPM preprocessing 1 (estimate 2): 49s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 13s</item>
- <item>Update Segmentation 15s</item>
- <item>Update Skull-Stripping 32s</item>
- <item>Update probability maps 7s</item>
- <item>68s</item>
- <item>Global intensity correction: 12s</item>
- <item>SANLM denoising after intensity normalization (medium): 19s</item>
- <item>Fast Optimized Shooting registration 25s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.11) 11s</item>
- <item>Estimate local tissue thresholds (WM) 14s</item>
- <item>Estimate local tissue thresholds (GM) 21s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 35s</item>
- <item>88s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 8s</item>
- <item>Blood vessel detection 7s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.24) 16s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>47s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 27s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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>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 | 0.0871 0.0000 0.0871 | 32.0000</item>
- <item>2 | 2.50 | 0.0847 0.0012 0.0858 | 29.4886</item>
- <item>3 | 2.50 | 0.0840 0.0017 0.0857 | 26.9772</item>
- <item>4 | 2.50 | 0.0836 0.0020 0.0856 | 24.6107</item>
- <item>5 | 2.50 | 0.0833 0.0021 0.0854 | 22.6548</item>
- <item>6 | 2.50 | 0.0831 0.0022 0.0853 | 20.6989</item>
- <item>7 | 2.50 | 0.0828 0.0023 0.0851 | 18.9688</item>
- <item>8 | 2.50 | 0.0825 0.0024 0.0849 | 17.4455</item>
- <item>9 | 2.50 | 0.0823 0.0024 0.0847 | 15.9223</item>
- <item>10 | 2.50 | 0.0820 0.0026 0.0845 | 14.6627</item>
- <item>11 | 2.50 | 0.0817 0.0026 0.0843 | 13.4764</item>
- <item>12 | 2.50 | 0.0814 0.0027 0.0841 | 12.3015</item>
- <item>13 | 2.50 | 0.0810 0.0028 0.0838 | 11.3776</item>
- <item>14 | 2.50 | 0.0807 0.0029 0.0836 | 10.4537</item>
- <item>15 | 2.25 | 0.0808 0.0029 0.0837 | 9.5920</item>
- <item>16 | 2.25 | 0.0776 0.0045 0.0821 | 8.8725</item>
- <item>17 | 2.25 | 0.0763 0.0051 0.0814 | 8.1530</item>
- <item>18 | 2.25 | 0.0755 0.0054 0.0809 | 7.5234</item>
- <item>19 | 2.25 | 0.0748 0.0055 0.0803 | 6.9630</item>
- <item>29 | 2.00 | 0.0770 0.0028 0.0798 | 3.3283</item>
- <item>30 | 2.00 | 0.0714 0.0053 0.0767 | 3.1221</item>
- <item>31 | 2.00 | 0.0696 0.0062 0.0758 | 2.9160</item>
- <item>43 | 1.75 | 0.0689 0.0035 0.0724 | 1.5785</item>
- <item>44 | 1.75 | 0.0640 0.0061 0.0701 | 1.5194</item>
- <item>45 | 1.75 | 0.0625 0.0070 0.0695 | 1.4626</item>
- <item>57 | 1.50 | 0.0610 0.0051 0.0661 | 1.0900</item>
- <item>58 | 1.50 | 0.0576 0.0073 0.0649 | 1.0730</item>
- <item>59 | 1.50 | 0.0565 0.0080 0.0645 | 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): 0.011 0.040 0.067 0.097 0.126 | 0.133434</item>
- <item>Template Matching: 0.087 0.225 0.209 0.187 0.169 | 0.169481</item>
- <item>Write result maps: 27s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 28s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 34s</item>
- <item>80s</item>
- <item>Create initial surface 61s</item>
- <item>Topology correction: 73s</item>
- <item>Surface refinement: 74s</item>
- <item>Reduction of surface collisions with optimization: 54s</item>
- <item>Spherical mapping with areal smoothing 98s</item>
- <item>Spherical registration 251s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 36s</item>
- <item>84s</item>
- <item>Create initial surface 64s</item>
- <item>Topology correction: 80s</item>
- <item>Surface refinement: 87s</item>
- <item>Reduction of surface collisions with optimization: 61s</item>
- <item>Spherical mapping with areal smoothing 77s</item>
- <item>Spherical registration 221s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5962 0.6572 mm</item>
- <item>Surface intensity / position RMSE: 0.0681 / 0.0684</item>
- <item>Euler number / defect number / defect size: 30.0 / 8.5 / 1.07%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/surf/lh.thickness.sub-0025844_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/surf/rh.thickness.sub-0025844_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/sub-0025844_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1445s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 18s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 21s</item>
- <item>ROI estimation of 'julichbrain' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 6s</item>
- <item>293s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/report/catreport_sub-0025844_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 41 minute(s) and 27 second(s).</item>
- <item>Image Quality Rating (IQR): 83.87% (B)</item>
- <item>GM volume (GMV): 48.27% (717.36 / 1486.20 ml)</item>
- <item>GM thickness (GMT): 2.60 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2564952/ds/SWU_4/sub-0025844/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|