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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>
- <affreg>mni</affreg>
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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>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <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>
- <bb>12</bb>
- <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>
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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>
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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>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <td>[false]</td>
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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_1964928/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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- <restypes>
- <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_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.395395377707997</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0659821778535843</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0663935542106628</SurfacePositionRMSE>
- <res_vx_vol>[0.999824509397997 0.99999997624414 0.999999980683053]</res_vx_vol>
- <res_vx_voli>[0.999824449168517 0.999999976146275 0.999999980640433]</res_vx_voli>
- <res_RMS>0.999941492196307</res_RMS>
- <res_BB>0.000956605304963887</res_BB>
- <tissue_mn>[28.2000007629395 109.314002990723 277.234008789062 410.066009521484]</tissue_mn>
- <tissue_mnr>[0.0687694177031517 0.266576588153839 0.676071643829346 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[14.6172053632619 47.0209632626509 42.0865223438742 27.1349544051048]</tissue_std>
- <tissue_stdr>[0.0382783636450768 0.123134724795818 0.110212802886963 0.0710588395595551]</tissue_stdr>
- <contrast>142.641372680664</contrast>
- <contrastr>0.347849786281586</contrastr>
- <res_ECR>0.424023330211639</res_ECR>
- <NCR>0.236098498106003</NCR>
- <ICR>0.299436420202255</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99964901879599 1.99999995248828 1.99999996136611]</res_vx_vol>
- <res_RMS>1.99988298439261</res_RMS>
- <res_ECR>3.06134343147278</res_ECR>
- <res_BB>1.00047826766968</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>2.86558651924133</contrastr>
- <NCR>3.72033452987671</NCR>
- <ICR>1.2024712562561</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.098848844427</SurfaceDefectArea>
- <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31964349746704</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.32787108421326</SurfacePositionRMSE>
- <SIQR>3.32361732995487</SIQR>
- <IQR>3.41452611142746</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>20231030-234446</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.395395377707997</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0659821778535843</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0663935542106628</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.395395377707997</defect_size>
- <vol_abs_CGW>[285.91726424733 543.3260725436 409.682120216727 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.54053336558752</vol_abs_WMH>
- <vol_rel_WMH>0.00124344314411646</vol_rel_WMH>
- <surf_TSA>1587.71581967302</surf_TSA>
- <vol_TIV>1238.92545700766</vol_TIV>
- <vol_rel_CGW>[0.230778423859252 0.438546217183947 0.330675358956802 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.45726438402161 0.67780999766737]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.43760848045349 0.833801225470944 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.76967292741942 0.300909389152174 0.3094601447605;2.48606543616151 0.205199008798467 0.442280208381356;3.24958717067551 0.317833809188386 0.248259646858144]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.785803748460366 0.205869538087668 0.513523131672598;4.28845598458721 0.342292507215552 0.486476868327402]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.59374474113644</vol_TIV>
- <vol_rel_CGW>[1.99458376184001 5.72604556724042 3.78870975137934 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.12434431441165</vol_rel_WMH>
- <surf_TSA>8.24853711955738</surf_TSA>
- <SQR>4.70384955351539</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9828.67443383746 0.465628725050033]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0424580425024033 0.00124629761558026 0.391481071710587]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[641.127045279512 389.215871461869 583.103357251147 596.562001421572 2544.14239707203 5738.27721577628]</SPMvols0>
- <SPMvols1>[513.410208866386 358.56302741282 334.186147814959 619.274569392387 1903.69317784744 6099.59045822214]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[125.263496398926 285.457885742188 392.605285644531]</T3th>
- <Tth>
- <T3th>[-6.93957996368408 -6.93957471847534 17.7131214141846 125.263496398926 285.457885742188 392.605285644531 526.276184082031 1761.791015625]</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>[0.0217573288828135 0.0916552022099495 0.103983528912067 0 0]</dtc>
- <ll>[0.0925238137247086 0 0.0925238137247086 0;0.213459907888937 0.0138685963734859 0.227328504262423 2957.45043945312;0.213459907888937 0.0138685963734859 0.227328504262423 2957.45043945312]</ll>
- <rmsdtc>[0.0471056886017323 0.125626266002655 0.14138300716877]</rmsdtc>
- <rmsgdt>[0.0335149168968201 0.0580307394266129 0.0715402811765671]</rmsgdt>
- <rmsdt>0.14138300716877</rmsdt>
- <dt>0.103983528912067</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>[0.00992542784661055 0.0426901280879974 0.0570157840847969 0.0661369413137436 0.072442352771759 0.0820965319871902]</dtc>
- <ll>[0.0876619190632205 0 0.0876619190632205 0;0.223424465811966 0.0184365995115995 0.241861065323565 9437.234375;0.203532042157141 0.0195808900817271 0.223112932238868 14092.6015625;0.181694704582888 0.0206655808437018 0.20236028542659 22283.1171875;0.164602748844859 0.0230819265751395 0.187684675419998 40378.4375;0.164602748844859 0.0230819265751395 0.187684675419998 40378.4375]</ll>
- <rmsdtc>[0.0121095469221473 0.0463149026036263 0.0735301226377487 0.0991897508502007 0.12227837741375 0.129587844014168]</rmsdtc>
- <rmsgdt>[0.00347138429060578 0.0139815835282207 0.0303254351019859 0.0506380423903465 0.0695865228772163 0.0760396793484688]</rmsgdt>
- <rmsdt>0.129587844014168</rmsdt>
- <dt>0.0820965319871902</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025378/ses-1/sub-0025378_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 48s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 2s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 5s</item>
- <item>29s</item>
- <item>Correct center-of-mass 8s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 56s</item>
- <item>SPM preprocessing 1 (estimate 2): 41s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 12s</item>
- <item>Update Segmentation 14s</item>
- <item>Update Skull-Stripping 30s</item>
- <item>Update probability maps 6s</item>
- <item>63s</item>
- <item>Global intensity correction: 11s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 27s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.02) 10s</item>
- <item>Estimate local tissue thresholds (WM) 12s</item>
- <item>Estimate local tissue thresholds (GM) 16s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 29s</item>
- <item>75s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 7s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.20) 14s</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>43s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 24s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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>8s</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 | 0.0877 0.0000 0.0877 | 32.0000</item>
- <item>2 | 2.50 | 0.0849 0.0013 0.0861 | 29.4886</item>
- <item>3 | 2.50 | 0.0840 0.0019 0.0859 | 26.9772</item>
- <item>4 | 2.50 | 0.0836 0.0022 0.0858 | 24.6107</item>
- <item>5 | 2.50 | 0.0832 0.0023 0.0856 | 22.6548</item>
- <item>6 | 2.50 | 0.0829 0.0025 0.0854 | 20.6989</item>
- <item>7 | 2.50 | 0.0826 0.0026 0.0852 | 18.9688</item>
- <item>8 | 2.50 | 0.0823 0.0027 0.0850 | 17.4455</item>
- <item>9 | 2.50 | 0.0819 0.0028 0.0847 | 15.9223</item>
- <item>10 | 2.50 | 0.0815 0.0029 0.0845 | 14.6627</item>
- <item>11 | 2.50 | 0.0812 0.0031 0.0842 | 13.4764</item>
- <item>12 | 2.50 | 0.0808 0.0031 0.0839 | 12.3015</item>
- <item>13 | 2.50 | 0.0804 0.0033 0.0836 | 11.3776</item>
- <item>14 | 2.50 | 0.0800 0.0034 0.0833 | 10.4537</item>
- <item>15 | 2.25 | 0.0804 0.0035 0.0839 | 9.5920</item>
- <item>16 | 2.25 | 0.0769 0.0052 0.0821 | 8.8725</item>
- <item>17 | 2.25 | 0.0754 0.0058 0.0813 | 8.1530</item>
- <item>18 | 2.25 | 0.0745 0.0061 0.0806 | 7.5234</item>
- <item>29 | 2.00 | 0.0760 0.0030 0.0790 | 3.3283</item>
- <item>30 | 2.00 | 0.0700 0.0055 0.0755 | 3.1221</item>
- <item>31 | 2.00 | 0.0678 0.0065 0.0744 | 2.9160</item>
- <item>43 | 1.75 | 0.0665 0.0038 0.0703 | 1.5785</item>
- <item>44 | 1.75 | 0.0620 0.0061 0.0681 | 1.5194</item>
- <item>45 | 1.75 | 0.0606 0.0069 0.0675 | 1.4626</item>
- <item>57 | 1.50 | 0.0589 0.0051 0.0640 | 1.0900</item>
- <item>58 | 1.50 | 0.0559 0.0071 0.0629 | 1.0730</item>
- <item>59 | 1.50 | 0.0549 0.0077 0.0626 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 153s</item>
- <item>Prepare output 7s</item>
- <item>160s</item>
- <item>Jacobian determinant (RMS): 0.012 0.046 0.074 0.099 0.122 | 0.129588</item>
- <item>Template Matching: 0.088 0.223 0.204 0.182 0.165 | 0.164603</item>
- <item>Write result maps: 35s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 25s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 28s</item>
- <item>68s</item>
- <item>Create initial surface 52s</item>
- <item>Topology correction: 50s</item>
- <item>Surface refinement: 47s</item>
- <item>Reduction of surface collisions with optimization: 37s</item>
- <item>Spherical mapping with areal smoothing 53s</item>
- <item>Spherical registration 204s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 18s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 26s</item>
- <item>58s</item>
- <item>Create initial surface 49s</item>
- <item>Topology correction: 51s</item>
- <item>Surface refinement: 44s</item>
- <item>Reduction of surface collisions with optimization: 36s</item>
- <item>Spherical mapping with areal smoothing 53s</item>
- <item>Spherical registration 227s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4573 0.6777 mm</item>
- <item>Surface intensity / position RMSE: 0.0660 / 0.0664</item>
- <item>Euler number / defect number / defect size: 14.0 / 8.5 / 0.40%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/surf/lh.thickness.sub-0025378_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/surf/rh.thickness.sub-0025378_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/sub-0025378_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1092s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 22s</item>
- <item>ROI estimation of 'lpba40' atlas 6s</item>
- <item>ROI estimation of 'hammers' atlas 15s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 8s</item>
- <item>ROI estimation of 'mori' atlas 12s</item>
- <item>ROI estimation of 'anatomy3' atlas 18s</item>
- <item>ROI estimation of 'julichbrain' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 10s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 38s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 82s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s</item>
- <item>Write results 11s</item>
- <item>274s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/report/catreport_sub-0025378_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 35 minute(s) and 40 second(s).</item>
- <item>Image Quality Rating (IQR): 70.85% (C-)</item>
- <item>GM volume (GMV): 43.85% (543.33 / 1238.93 ml)</item>
- <item>GM thickness (GMT): 2.46 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1964928/ds/LMU_2/sub-0025378/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|