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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>
- <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>
- <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>
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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/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <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>[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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- <tr>
- <td>/var/lib/condor/execute/dir_1912318/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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- <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>
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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>
- </LAB>
- <new_release>0</new_release>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <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>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.797761488532404</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0750022530555725</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0723849311470985</SurfacePositionRMSE>
- <res_vx_vol>[1.20000004768372 0.5 0.5]</res_vx_vol>
- <res_vx_voli>[0.799999952316284 0.800000011920929 0.800000011920929]</res_vx_voli>
- <res_RMS>0.804155895839631</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[23.826000213623 61.4589996337891 230.61799621582 375.016998291016]</tissue_mn>
- <tissue_mnr>[0.0635331198573112 0.163883239030838 0.614953458309174 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[20.5214680252537 39.3131826944907 38.4025649980297 24.2724434208791]</tissue_std>
- <tissue_stdr>[0.0584339201450348 0.111942455172539 0.109349511563778 0.0691146478056908]</tissue_stdr>
- <contrast>131.668258666992</contrast>
- <contrastr>0.351099461317062</contrastr>
- <res_ECR>0.332454085350037</res_ECR>
- <NCR>0.155195817351341</NCR>
- <ICR>0</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.40000009536743 1 1]</res_vx_vol>
- <res_RMS>1.60831179167926</res_RMS>
- <res_ECR>2.59415340423584</res_ECR>
- <res_BB>NaN</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>2.81684136390686</contrastr>
- <NCR>2.55894088745117</NCR>
- <ICR>0.5</ICR>
- <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
- <SurfaceDefectArea>1.1994403721331</SurfaceDefectArea>
- <SurfaceDefectNumber>2</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.50004506111145</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.44769859313965</SurfacePositionRMSE>
- <SIQR>2.45312045816197</SIQR>
- <IQR>2.35362622296633</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>20231030-235536</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.797761488532404</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0750022530555725</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0723849311470985</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>26</EC_abs>
- <defect_size>0.797761488532404</defect_size>
- <vol_abs_CGW>[181.536646134884 699.135294489633 456.104902234464 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.250492478809252</vol_abs_WMH>
- <vol_rel_WMH>0.000187385411519787</vol_rel_WMH>
- <surf_TSA>1870.36659919158</surf_TSA>
- <vol_TIV>1336.77684285898</vol_TIV>
- <vol_rel_CGW>[0.135801758614122 0.523000752312842 0.341197489073036 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.63729648470161 0.638610870326357]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.64921283721924 0.769112404602864 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99977794089614 0.267130538718056 0.285400338396313;2.67311586305447 0.190808764846708 0.444485501468329;3.37047337550197 0.278550680281972 0.270114160135359]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.873633700584385 0.379496236835379 0.62422153024911;4.21914815161841 0.259609307072581 0.37577846975089]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.0946402050573</vol_TIV>
- <vol_rel_CGW>[0.5 7.24282960331972 3.97768478938642 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01873854115198</vol_rel_WMH>
- <surf_TSA>8.60811462973347</surf_TSA>
- <SQR>5.92904028827937</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11796.48046875 0.370990375981427]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00132170494180173 0.00111652188934386 0.00745360879227519]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[827.539879086407 391.021000174116 420.463876535866 601.645419559764 850.799227224597 9248.47179640541]</SPMvols0>
- <SPMvols1>[712.171601175631 371.913981951393 218.891934119649 497.00199127446 726.43475218585 9271.62815223294]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[86.5628967285156 239.393707275391 375.112609863281]</T3th>
- <Tth>
- <T3th>[-158.854293823242 -42.6512908935547 6.37095355987549 86.5628967285156 239.393707275391 375.112609863281 519.387451171875 1003.88525390625]</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>[0.0241384375840425 0.0837458521127701 0.0930439680814743 0 0]</dtc>
- <ll>[0.0860540383145446 0 0.0860540383145446 0;0.190948339785133 0.0114308353804168 0.20237917516555 2437.60278320312;0.190948339785133 0.0114308353804168 0.20237917516555 2437.60278320312]</ll>
- <rmsdtc>[0.0500041767954826 0.10953313857317 0.120588295161724]</rmsdtc>
- <rmsgdt>[0.035318847745657 0.047226320952177 0.0577294044196606]</rmsgdt>
- <rmsdt>0.120588295161724</rmsdt>
- <dt>0.0930439680814743</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>[0.010778971016407 0.0397974960505962 0.0547510236501694 0.0629038289189339 0.0694906711578369 0.0781337469816208]</dtc>
- <ll>[0.0836215760363635 0 0.0836215760363635 0;0.21172148962149 0.0158152854090354 0.227536775030525 8095.44921875;0.189062625918423 0.0177066337059998 0.206769259624423 12743.6767578125;0.169349880526435 0.0190662807888455 0.18841616131528 20558.63671875;0.152895456205809 0.0218070936440501 0.174702549849859 38148.3046875;0.152895456205809 0.0218070936440501 0.174702549849859 38148.3046875]</ll>
- <rmsdtc>[0.0124563202261925 0.0452682822942734 0.0661589577794075 0.0906739383935928 0.113728299736977 0.120575457811356]</rmsdtc>
- <rmsgdt>[0.00349350576288998 0.0134037174284458 0.029165705665946 0.0489602461457253 0.0674894973635674 0.0730488523840904]</rmsgdt>
- <rmsdt>0.120575457811356</rmsdt>
- <dt>0.0781337469816208</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026019/ses-1/sub-0026019_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 173s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 9s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>46s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 81s</item>
- <item>SPM preprocessing 1 (estimate 2): 36s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 22s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 54s</item>
- <item>Update probability maps 12s</item>
- <item>111s</item>
- <item>Global intensity correction: 21s</item>
- <item>SANLM denoising after intensity normalization (medium): 37s</item>
- <item>Fast Optimized Shooting registration 32s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 18s</item>
- <item>Estimate local tissue thresholds (WM) 24s</item>
- <item>Estimate local tissue thresholds (GM) 34s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 52s</item>
- <item>141s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 11s</item>
- <item>Blood vessel detection 12s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 24s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 6s</item>
- <item>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</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 0.05]</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 | 0.0836 0.0000 0.0836 | 32.0000</item>
- <item>2 | 2.50 | 0.0799 0.0014 0.0813 | 29.4886</item>
- <item>3 | 2.50 | 0.0788 0.0022 0.0810 | 26.9772</item>
- <item>4 | 2.50 | 0.0783 0.0025 0.0808 | 24.6107</item>
- <item>5 | 2.50 | 0.0779 0.0027 0.0805 | 22.6548</item>
- <item>6 | 2.50 | 0.0775 0.0028 0.0803 | 20.6989</item>
- <item>7 | 2.50 | 0.0772 0.0029 0.0800 | 18.9688</item>
- <item>8 | 2.50 | 0.0768 0.0030 0.0798 | 17.4455</item>
- <item>9 | 2.50 | 0.0764 0.0031 0.0795 | 15.9223</item>
- <item>10 | 2.50 | 0.0760 0.0032 0.0792 | 14.6627</item>
- <item>11 | 2.50 | 0.0756 0.0033 0.0789 | 13.4764</item>
- <item>12 | 2.50 | 0.0753 0.0033 0.0786 | 12.3015</item>
- <item>13 | 2.50 | 0.0749 0.0034 0.0783 | 11.3776</item>
- <item>14 | 2.50 | 0.0745 0.0035 0.0780 | 10.4537</item>
- <item>15 | 2.25 | 0.0740 0.0036 0.0776 | 9.5920</item>
- <item>16 | 2.25 | 0.0706 0.0053 0.0758 | 8.8725</item>
- <item>29 | 2.00 | 0.0716 0.0024 0.0740 | 3.3283</item>
- <item>30 | 2.00 | 0.0652 0.0049 0.0701 | 3.1221</item>
- <item>31 | 2.00 | 0.0630 0.0059 0.0689 | 2.9160</item>
- <item>43 | 1.75 | 0.0620 0.0034 0.0654 | 1.5785</item>
- <item>44 | 1.75 | 0.0578 0.0056 0.0635 | 1.5194</item>
- <item>45 | 1.75 | 0.0564 0.0064 0.0628 | 1.4626</item>
- <item>57 | 1.50 | 0.0551 0.0047 0.0597 | 1.0900</item>
- <item>58 | 1.50 | 0.0520 0.0066 0.0586 | 1.0730</item>
- <item>59 | 1.50 | 0.0510 0.0073 0.0582 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 107s</item>
- <item>Prepare output 10s</item>
- <item>117s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.066 0.091 0.114 | 0.120575</item>
- <item>Template Matching: 0.084 0.212 0.189 0.169 0.153 | 0.152895</item>
- <item>Write result maps: 140s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 18s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 27s</item>
- <item>59s</item>
- <item>Create initial surface 49s</item>
- <item>Topology correction: 60s</item>
- <item>Surface refinement: 42s</item>
- <item>Reduction of surface collisions with optimization: 41s</item>
- <item>Spherical mapping with areal smoothing 52s</item>
- <item>Spherical registration 186s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 17s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 28s</item>
- <item>58s</item>
- <item>Create initial surface 51s</item>
- <item>Topology correction: 64s</item>
- <item>Surface refinement: 54s</item>
- <item>Reduction of surface collisions with optimization: 46s</item>
- <item>Spherical mapping with areal smoothing 56s</item>
- <item>Spherical registration 194s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6372 0.6384 mm</item>
- <item>Surface intensity / position RMSE: 0.0750 / 0.0724</item>
- <item>Euler number / defect number / defect size: 26.0 / 20.0 / 0.80%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/surf/lh.thickness.sub-0026019_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/surf/rh.thickness.sub-0026019_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/sub-0026019_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1115s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 12s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 44s</item>
- <item>ROI estimation of 'lpba40' atlas 13s</item>
- <item>ROI estimation of 'hammers' atlas 31s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 11s</item>
- <item>ROI estimation of 'aal3' atlas 16s</item>
- <item>ROI estimation of 'mori' atlas 24s</item>
- <item>ROI estimation of 'anatomy3' atlas 34s</item>
- <item>ROI estimation of 'julichbrain' atlas 46s</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 71s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 106s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 10s</item>
- <item>471s</item>
- <item>Quality check: 35s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/report/catreport_sub-0026019_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 45 minute(s) and 55 second(s).</item>
- <item>Image Quality Rating (IQR): 81.46% (B-)</item>
- <item>GM volume (GMV): 52.30% (699.14 / 1336.78 ml)</item>
- <item>GM thickness (GMT): 2.64 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1912318/ds/Utah_1/sub-0026019/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|