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- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <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>
- <BVCstr>0.5</BVCstr>
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- <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>
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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>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <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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- <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>
- <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/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>
- <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>
- <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/Schaefer2018_100Parcels_17Networks_order.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/Schaefer2018_200Parcels_17Networks_order.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/Schaefer2018_400Parcels_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_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_611883/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
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- <td>[false]</td>
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- </atlas>
- <satlas>
- <tr>
- <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>
- </tr>
- <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>
- <NB>0</NB>
- <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>
- </LAB>
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- <lazy>0</lazy>
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- <shooting>
- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
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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>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.453043368428681</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0676583424210548</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0636658668518066</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>202.782424926758</res_BB>
- <tissue_mn>[177.330993652344 622.642028808594 1680.92199707031 2569.75708007812]</tissue_mn>
- <tissue_mnr>[0.0690069124102592 0.242296069860458 0.654117107391357 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[73.2980168782212 280.081439113006 269.968943312147 160.099419565494]</tissue_std>
- <tissue_stdr>[0.030637526884675 0.11707004904747 0.112843170762062 0.0669192746281624]</tissue_stdr>
- <contrast>922.617980957031</contrast>
- <contrastr>0.35902926325798</contrastr>
- <res_ECR>0.400694191455841</res_ECR>
- <NCR>0.141340836882591</NCR>
- <ICR>0.297754645347595</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.94231724739075</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>2.69789433479309</contrastr>
- <NCR>2.36004638671875</NCR>
- <ICR>1.19830024242401</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11326084210717</SurfaceDefectArea>
- <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.35316681861877</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.27331733703613</SurfacePositionRMSE>
- <SIQR>2.62849209398491</SIQR>
- <IQR>2.22892700330196</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>20231031-000413</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.453043368428681</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0676583424210548</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0636658668518066</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.453043368428681</defect_size>
- <vol_abs_CGW>[248.051580392157 793.711050980392 603.250670588235 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.840439215686274</vol_abs_WMH>
- <vol_rel_WMH>0.000510901166990265</vol_rel_WMH>
- <surf_TSA>2156.17488257736</surf_TSA>
- <vol_TIV>1645.01330196078</vol_TIV>
- <vol_rel_CGW>[0.150790014947897 0.482495217536735 0.366714767515367 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.56386788167178 0.615756228054001]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.54010033607483 0.758732943515076 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.98667445752175 0.252831052741883 0.310575331243564;2.57304174883049 0.173696324981939 0.418086552848211;3.23093111357259 0.267838098419704 0.271338115908225]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.936956632758705 0.340006451155559 0.530349580669268;4.21318953398937 0.3584428031406 0.469650419330732]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.30410450657542</vol_TIV>
- <vol_rel_CGW>[0.558010325932067 6.51535951035804 4.43596924416967 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05109011669903</vol_rel_WMH>
- <surf_TSA>8.62379300552089</surf_TSA>
- <SQR>5.35818426541045</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10223.616 0.398920996045328]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00159413914661855 0.00107360957190394 0.283255308866501]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[989.953780392157 533.19222745098 392.001184313726 466.578078431373 1152.10204705882 7283.32322352941]</SPMvols0>
- <SPMvols1>[875.964984313725 502.100458823529 223.36148627451 389.164639215686 886.162380392157 7346.89814117647]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[697.839294433594 1774.99255371094 2557.75219726562]</T3th>
- <Tth>
- <T3th>[-36.0668296813965 -36.0668334960938 70.3243408203125 697.839294433594 1774.99255371094 2557.75219726562 3487.70849609375 11793.60546875]</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>[0.0179909337311983 0.0591892004013062 0.0642453357577324 0 0]</dtc>
- <ll>[0.0802928471193165 0 0.0802928471193165 0;0.1939382747728 0.00833900149415235 0.202277276266952 1778.275390625;0.1939382747728 0.00833900149415235 0.202277276266952 1778.275390625]</ll>
- <rmsdtc>[0.0426183305680752 0.0778422281146049 0.0872678607702255]</rmsdtc>
- <rmsgdt>[0.0311062596738338 0.0396634750068188 0.0496416948735714]</rmsgdt>
- <rmsdt>0.0872678607702255</rmsdt>
- <dt>0.0642453357577324</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>[0.00824663415551186 0.0298209358006716 0.0420916192233562 0.0501536317169666 0.0568473339080811 0.0633739307522774]</dtc>
- <ll>[0.0832726398608523 0 0.0832726398608523 0;0.218725976800977 0.0124298668345543 0.231155843635531 6362.5380859375;0.200333518824196 0.0152552815288442 0.215588800353041 10979.4091796875;0.181292556516352 0.0177004307876399 0.198992987303992 19085.87890625;0.164822562255874 0.0210450351144109 0.185867597370285 36815.1953125;0.164822562255874 0.0210450351144109 0.185867597370285 36815.1953125]</ll>
- <rmsdtc>[0.00959504954516888 0.0345139354467392 0.0519350096583366 0.0750135108828545 0.0984790250658989 0.106098912656307]</rmsdtc>
- <rmsgdt>[0.0030506148468703 0.0117710521444678 0.0263377353549004 0.0464245900511742 0.0654311701655388 0.0711227059364319]</rmsgdt>
- <rmsdt>0.106098912656307</rmsdt>
- <dt>0.0633739307522774</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027275/ses-1/sub-0027275_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 56s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>34s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 75s</item>
- <item>SPM preprocessing 1 (estimate 2): 49s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 19s</item>
- <item>Update Skull-Stripping 40s</item>
- <item>Update probability maps 9s</item>
- <item>83s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 30s</item>
- <item>Fast Optimized Shooting registration 31s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 15s</item>
- <item>Estimate local tissue thresholds (WM) 19s</item>
- <item>Estimate local tissue thresholds (GM) 27s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 39s</item>
- <item>111s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>75s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>11s</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 | 0.0833 0.0000 0.0833 | 32.0000</item>
- <item>2 | 2.50 | 0.0807 0.0011 0.0818 | 29.4886</item>
- <item>3 | 2.50 | 0.0799 0.0017 0.0816 | 26.9772</item>
- <item>4 | 2.50 | 0.0795 0.0019 0.0815 | 24.6107</item>
- <item>5 | 2.50 | 0.0792 0.0021 0.0813 | 22.6548</item>
- <item>6 | 2.50 | 0.0790 0.0022 0.0811 | 20.6989</item>
- <item>7 | 2.50 | 0.0787 0.0022 0.0810 | 18.9688</item>
- <item>8 | 2.50 | 0.0785 0.0023 0.0808 | 17.4455</item>
- <item>9 | 2.50 | 0.0782 0.0024 0.0806 | 15.9223</item>
- <item>10 | 2.50 | 0.0779 0.0025 0.0804 | 14.6627</item>
- <item>11 | 2.50 | 0.0776 0.0025 0.0801 | 13.4764</item>
- <item>12 | 2.50 | 0.0773 0.0026 0.0799 | 12.3015</item>
- <item>13 | 2.50 | 0.0770 0.0027 0.0797 | 11.3776</item>
- <item>14 | 2.50 | 0.0767 0.0027 0.0794 | 10.4537</item>
- <item>15 | 2.25 | 0.0757 0.0028 0.0785 | 9.5920</item>
- <item>16 | 2.25 | 0.0729 0.0041 0.0771 | 8.8725</item>
- <item>29 | 2.00 | 0.0743 0.0019 0.0762 | 3.3283</item>
- <item>30 | 2.00 | 0.0687 0.0042 0.0728 | 3.1221</item>
- <item>31 | 2.00 | 0.0668 0.0051 0.0719 | 2.9160</item>
- <item>43 | 1.75 | 0.0659 0.0029 0.0688 | 1.5785</item>
- <item>44 | 1.75 | 0.0618 0.0051 0.0669 | 1.5194</item>
- <item>45 | 1.75 | 0.0604 0.0059 0.0663 | 1.4626</item>
- <item>57 | 1.50 | 0.0591 0.0043 0.0634 | 1.0900</item>
- <item>58 | 1.50 | 0.0560 0.0063 0.0623 | 1.0730</item>
- <item>59 | 1.50 | 0.0549 0.0070 0.0620 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 180s</item>
- <item>Prepare output 10s</item>
- <item>190s</item>
- <item>Jacobian determinant (RMS): 0.010 0.035 0.052 0.075 0.098 | 0.106099</item>
- <item>Template Matching: 0.083 0.219 0.200 0.181 0.165 | 0.164823</item>
- <item>Write result maps: 56s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 51s</item>
- <item>112s</item>
- <item>Create initial surface 100s</item>
- <item>Topology correction: 101s</item>
- <item>Surface refinement: 83s</item>
- <item>Reduction of surface collisions with optimization: 88s</item>
- <item>Spherical mapping with areal smoothing 89s</item>
- <item>Spherical registration 265s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 52s</item>
- <item>113s</item>
- <item>Create initial surface 97s</item>
- <item>Topology correction: 101s</item>
- <item>Surface refinement: 94s</item>
- <item>Reduction of surface collisions with optimization: 84s</item>
- <item>Spherical mapping with areal smoothing 89s</item>
- <item>Spherical registration 292s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5639 0.6153 mm</item>
- <item>Surface intensity / position RMSE: 0.0677 / 0.0637</item>
- <item>Euler number / defect number / defect size: 12.0 / 10.5 / 0.45%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/surf/lh.thickness.sub-0027275_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/surf/rh.thickness.sub-0027275_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/sub-0027275_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1817s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 34s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 28s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 10s</item>
- <item>ROI estimation of 'aal3' atlas 18s</item>
- <item>ROI estimation of 'mori' atlas 25s</item>
- <item>ROI estimation of 'anatomy3' atlas 36s</item>
- <item>ROI estimation of 'julichbrain' atlas 50s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 86s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 110s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s</item>
- <item>Write results 13s</item>
- <item>501s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/report/catreport_sub-0027275_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 54 minute(s) and 47 second(s).</item>
- <item>Image Quality Rating (IQR): 82.71% (B-)</item>
- <item>GM volume (GMV): 48.25% (793.71 / 1645.01 ml)</item>
- <item>GM thickness (GMT): 2.56 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_611883/ds/UWM/sub-0027275/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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