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- <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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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
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- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
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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>
- <vdist>2</vdist>
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- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <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>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <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>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_2170477/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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- <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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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.250047689685169</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639966726303101</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0630016028881073</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>174.069747924805</res_BB>
- <tissue_mn>[8.89200019836426 69.4100036621094 209.352005004883 332.996002197266]</tissue_mn>
- <tissue_mnr>[0.0267030242830515 0.208440944552422 0.628692269325256 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.75065758946457 34.2360971747953 37.5383867879358 23.4862839159273]</tissue_std>
- <tissue_stdr>[0.0239141061902046 0.105633057653904 0.115822039544582 0.0724652707576752]</tissue_stdr>
- <contrast>118.891021728516</contrast>
- <contrastr>0.357034385204315</contrastr>
- <res_ECR>0.388373494148254</res_ECR>
- <NCR>0.158942565321922</NCR>
- <ICR>0.241983234882355</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.87945652008057</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>2.72781753540039</contrastr>
- <NCR>2.61272716522217</NCR>
- <ICR>1.05997824668884</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.06251192242129</SurfaceDefectArea>
- <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.2799334526062</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.26003205776215</SurfacePositionRMSE>
- <SIQR>2.64346522209702</SIQR>
- <IQR>2.42949121936496</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>20231031-020315</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.250047689685169</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639966726303101</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0630016028881073</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.250047689685169</defect_size>
- <vol_abs_CGW>[264.443266666667 575.983443137255 419.741290196078 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.24825490196078</vol_abs_WMH>
- <vol_rel_WMH>0.000990546420763568</vol_rel_WMH>
- <surf_TSA>1616.14285038322</surf_TSA>
- <vol_TIV>1260.168</vol_TIV>
- <vol_rel_CGW>[0.209847628781771 0.457068774272363 0.333083596945866 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51793465829984 0.658621361281953]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.48896503448486 0.891872007072658 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.86286860887657 0.326784713412864 0.309409542681983;2.5354869258338 0.197863748713888 0.46042202062111;3.31019604936381 0.334831730239887 0.230168436696907]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.741729125871763 0.190832893074654 0.529873417721519;4.45424762591278 0.345715679735141 0.470126582278481]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.45190301662683</vol_TIV>
- <vol_rel_CGW>[1.61867149392548 6.05870643448928 3.83196115204501 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.09905464207636</vol_rel_WMH>
- <surf_TSA>8.33659713618014</surf_TSA>
- <SQR>4.97029955902096</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.44 0.429672974572612]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00137970829382539 0.0011625955812633 0.0407386720180511]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[680.787576470588 377.466396078431 454.098443137255 642.974592156863 676.379082352941 8472.37144705882]</SPMvols0>
- <SPMvols1>[602.699811764706 356.460325490196 261.906607843137 571.853364705882 626.893776470588 8393.90980392157]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[76.4250030517578 220.846099853516 323.279510498047]</T3th>
- <Tth>
- <T3th>[-4.46574020385742 -4.46573638916016 4.01724576950073 76.4250030517578 220.846099853516 323.279510498047 446.706756591797 761.410217285156]</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>[0.0221315566450357 0.0868420302867889 0.0980298817157745 0 0]</dtc>
- <ll>[0.0866948463955895 0 0.0866948463955895 0;0.193770940993585 0.0134263147397631 0.207197255733348 2863.134765625;0.193770940993585 0.0134263147397631 0.207197255733348 2863.134765625]</ll>
- <rmsdtc>[0.0481413640081882 0.114465348422527 0.133631110191345]</rmsdtc>
- <rmsgdt>[0.0341516025364399 0.0515320152044296 0.0679406151175499]</rmsgdt>
- <rmsdt>0.133631110191345</rmsdt>
- <dt>0.0980298817157745</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>[0.0104231480509043 0.0407029874622822 0.0568946860730648 0.0661931857466698 0.0725058540701866 0.0831259563565254]</dtc>
- <ll>[0.0865601758340623 0 0.0865601758340623 0;0.220732707570208 0.0181063072344322 0.23883901480464 9268.166015625;0.197496251104609 0.0199756402669575 0.217471891371566 14376.7080078125;0.174843421349159 0.0211751073853582 0.196018528734517 22832.525390625;0.157187435869147 0.0236284031689145 0.180815839038062 41334.41796875;0.157187435869147 0.0236284031689145 0.180815839038062 41334.41796875]</ll>
- <rmsdtc>[0.0122386198490858 0.0452057085931301 0.0711359530687332 0.100547827780247 0.127140983939171 0.136573955416679]</rmsdtc>
- <rmsgdt>[0.00357852107845247 0.0142777189612389 0.0316704325377941 0.0545802339911461 0.0748210698366165 0.0816681608557701]</rmsgdt>
- <rmsdt>0.136573955416679</rmsdt>
- <dt>0.0831259563565254</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026154/ses-1/sub-0026154_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 64s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>40s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 14s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 86s</item>
- <item>SPM preprocessing 1 (estimate 2): 70s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 21s</item>
- <item>Update Skull-Stripping 46s</item>
- <item>Update probability maps 10s</item>
- <item>95s</item>
- <item>Global intensity correction: 18s</item>
- <item>SANLM denoising after intensity normalization (medium): 29s</item>
- <item>Fast Optimized Shooting registration 43s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 16s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 33s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 49s</item>
- <item>130s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 13s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.13) 27s</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>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 34s</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) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>13s</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 | 0.0866 0.0000 0.0866 | 32.0000</item>
- <item>2 | 2.50 | 0.0832 0.0014 0.0846 | 29.4886</item>
- <item>3 | 2.50 | 0.0823 0.0021 0.0844 | 26.9772</item>
- <item>4 | 2.50 | 0.0818 0.0024 0.0842 | 24.6107</item>
- <item>5 | 2.50 | 0.0814 0.0026 0.0840 | 22.6548</item>
- <item>6 | 2.50 | 0.0811 0.0027 0.0837 | 20.6989</item>
- <item>7 | 2.50 | 0.0807 0.0028 0.0835 | 18.9688</item>
- <item>8 | 2.50 | 0.0804 0.0029 0.0833 | 17.4455</item>
- <item>9 | 2.50 | 0.0800 0.0030 0.0830 | 15.9223</item>
- <item>10 | 2.50 | 0.0796 0.0032 0.0828 | 14.6627</item>
- <item>11 | 2.50 | 0.0792 0.0033 0.0825 | 13.4764</item>
- <item>12 | 2.50 | 0.0788 0.0033 0.0822 | 12.3015</item>
- <item>13 | 2.50 | 0.0784 0.0035 0.0819 | 11.3776</item>
- <item>14 | 2.50 | 0.0780 0.0036 0.0816 | 10.4537</item>
- <item>15 | 2.25 | 0.0786 0.0037 0.0822 | 9.5920</item>
- <item>16 | 2.25 | 0.0751 0.0054 0.0805 | 8.8725</item>
- <item>17 | 2.25 | 0.0736 0.0060 0.0796 | 8.1530</item>
- <item>29 | 2.00 | 0.0749 0.0028 0.0777 | 3.3283</item>
- <item>30 | 2.00 | 0.0682 0.0055 0.0738 | 3.1221</item>
- <item>31 | 2.00 | 0.0658 0.0067 0.0725 | 2.9160</item>
- <item>43 | 1.75 | 0.0643 0.0039 0.0681 | 1.5785</item>
- <item>44 | 1.75 | 0.0598 0.0062 0.0660 | 1.5194</item>
- <item>45 | 1.75 | 0.0583 0.0071 0.0653 | 1.4626</item>
- <item>57 | 1.50 | 0.0565 0.0052 0.0618 | 1.0900</item>
- <item>58 | 1.50 | 0.0534 0.0072 0.0606 | 1.0730</item>
- <item>59 | 1.50 | 0.0524 0.0079 0.0603 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 203s</item>
- <item>Prepare output 13s</item>
- <item>216s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.071 0.101 0.127 | 0.136574</item>
- <item>Template Matching: 0.087 0.221 0.197 0.175 0.157 | 0.157187</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: 43s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 49s</item>
- <item>115s</item>
- <item>Create initial surface 85s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 90s</item>
- <item>Reduction of surface collisions with optimization: 58s</item>
- <item>Spherical mapping with areal smoothing 86s</item>
- <item>Spherical registration 348s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 47s</item>
- <item>107s</item>
- <item>Create initial surface 82s</item>
- <item>Topology correction: 80s</item>
- <item>Surface refinement: 68s</item>
- <item>Reduction of surface collisions with optimization: 53s</item>
- <item>Spherical mapping with areal smoothing 87s</item>
- <item>Spherical registration 348s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5182 0.6586 mm</item>
- <item>Surface intensity / position RMSE: 0.0640 / 0.0630</item>
- <item>Euler number / defect number / defect size: 14.0 / 8.5 / 0.25%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/surf/lh.thickness.sub-0026154_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/surf/rh.thickness.sub-0026154_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/sub-0026154_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1785s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 35s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 15s</item>
- <item>ROI estimation of 'mori' atlas 22s</item>
- <item>ROI estimation of 'anatomy3' atlas 32s</item>
- <item>ROI estimation of 'julichbrain' atlas 45s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 18s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 72s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 103s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 10s</item>
- <item>439s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/report/catreport_sub-0026154_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 54 minute(s) and 52 second(s).</item>
- <item>Image Quality Rating (IQR): 80.71% (B-)</item>
- <item>GM volume (GMV): 45.71% (575.98 / 1260.17 ml)</item>
- <item>GM thickness (GMT): 2.52 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2170477/ds/UM/sub-0026154/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|