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- <opts>
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- <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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- <biasreg>0.001</biasreg>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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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>
- <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>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
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- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <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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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</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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- <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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- <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_612547/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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- </atlas>
- <satlas>
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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>
- </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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- <shooting>
- <shootingtpm>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- <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_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>22</SurfaceEulerNumber>
- <SurfaceDefectArea>0.602553716793214</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.068365789949894</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0679745823144913</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>194.87190246582</res_BB>
- <tissue_mn>[174.808502197266 575.234985351562 1682.16296386719 2556.63598632812]</tissue_mn>
- <tissue_mnr>[0.0683744177222252 0.224996820092201 0.657959520816803 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[78.2624662461362 326.709725959457 268.649340187454 165.382112049125]</tissue_std>
- <tissue_stdr>[0.0328581593930721 0.137167677283287 0.112791270017624 0.0694349706172943]</tissue_stdr>
- <contrast>920.14501953125</contrast>
- <contrastr>0.359904587268829</contrastr>
- <res_ECR>0.394062638282776</res_ECR>
- <NCR>0.139183789491653</NCR>
- <ICR>0.324656665325165</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.90848278999329</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>2.68476438522339</contrastr>
- <NCR>2.3290810585022</NCR>
- <ICR>1.26502156257629</ICR>
- <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
- <SurfaceDefectArea>1.1506384291983</SurfaceDefectArea>
- <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.36731576919556</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.35949158668518</SurfacePositionRMSE>
- <SIQR>2.5988484898752</SIQR>
- <IQR>2.20605530491868</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>20231031-011117</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>22</SurfaceEulerNumber>
- <SurfaceDefectArea>0.602553716793214</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.068365789949894</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0679745823144913</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>22</EC_abs>
- <defect_size>0.602553716793214</defect_size>
- <vol_abs_CGW>[305.869976470588 748.318007843137 523.12108627451 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.590788235294118</vol_abs_WMH>
- <vol_rel_WMH>0.000374554515858957</vol_rel_WMH>
- <surf_TSA>2088.72282788888</surf_TSA>
- <vol_TIV>1577.30907058824</vol_TIV>
- <vol_rel_CGW>[0.19391885976825 0.474426998358706 0.331654141873044 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48647993029945 0.604243073122378]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.46506977081299 0.721787084264548 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95745104203294 0.242861834220645 0.325559394291394;2.51987618855902 0.168862831995866 0.424870218129345;3.16875135832053 0.258845395912993 0.249570387579261]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.925734498462149 0.316409519626975 0.579638485855556;4.0909620668729 0.333902104949864 0.420361514144444]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.71340436190705</vol_TIV>
- <vol_rel_CGW>[1.33259446422862 6.37045614868366 3.80628846754749 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0374554515859</vol_rel_WMH>
- <surf_TSA>8.62336054187836</surf_TSA>
- <SQR>5.2200436930168</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10223.616 0.411847898169752]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00159514823462814 0.00131735857576132 0.17020471394062]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[926.73888627451 453.940568627451 583.480643137255 623.98988627451 1418.07330980392 6930.32858823529]</SPMvols0>
- <SPMvols1>[777.302231372549 421.112250980392 348.498239215686 646.774898039216 1138.26716862745 6891.69165098039]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[686.630615234375 1788.19982910156 2562.78491210938]</T3th>
- <Tth>
- <T3th>[-32.2472686767578 -32.2472648620605 58.4648323059082 686.630615234375 1788.19982910156 2562.78491210938 3500.86206054688 12228.3916015625]</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>[0.0219029821455479 0.0815907120704651 0.0911220833659172 0 0]</dtc>
- <ll>[0.0903705537390738 0 0.0903705537390738 0;0.208906121042167 0.0128937488844415 0.221799869926608 2749.56616210938;0.208906121042167 0.0128937488844415 0.221799869926608 2749.56616210938]</ll>
- <rmsdtc>[0.0530131459236145 0.113406971096992 0.129229366779327]</rmsdtc>
- <rmsgdt>[0.0384366549551487 0.0629492551088333 0.0804759114980698]</rmsgdt>
- <rmsdt>0.129229366779327</rmsdt>
- <dt>0.0911220833659172</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>[0.00978871993720531 0.0409382581710815 0.0549051724374294 0.0651541650295258 0.0726115256547928 0.081645280122757]</dtc>
- <ll>[0.0887427496097054 0 0.0887427496097054 0;0.224555280830281 0.0190981208028083 0.243653401633089 9775.8505859375;0.206779065792984 0.0202420771368443 0.227021142929828 14568.4658203125;0.185788697100546 0.0218383919479501 0.207627089048496 23547.7265625;0.168360155869056 0.0248856537066847 0.19324580957574 43533.79296875;0.168360155869056 0.0248856537066847 0.19324580957574 43533.79296875]</ll>
- <rmsdtc>[0.0114234946668148 0.0434488095343113 0.0725810676813126 0.104065224528313 0.132191732525826 0.140660777688026]</rmsdtc>
- <rmsgdt>[0.0035337321460247 0.0155102591961622 0.0354594700038433 0.0604582764208317 0.0818371772766113 0.0907462239265442]</rmsgdt>
- <rmsdt>0.140660777688026</rmsdt>
- <dt>0.081645280122757</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027265/ses-2/sub-0027265_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 56s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</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 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 70s</item>
- <item>SPM preprocessing 1 (estimate 2): 62s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 37s</item>
- <item>Update probability maps 8s</item>
- <item>78s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 28s</item>
- <item>Fast Optimized Shooting registration 31s</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) 14s</item>
- <item>Estimate local tissue thresholds (WM) 16s</item>
- <item>Estimate local tissue thresholds (GM) 25s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 37s</item>
- <item>102s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 19s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 23s</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>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s</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) 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 | 0.0887 0.0000 0.0887 | 32.0000</item>
- <item>2 | 2.50 | 0.0853 0.0014 0.0867 | 29.4886</item>
- <item>3 | 2.50 | 0.0843 0.0021 0.0864 | 26.9772</item>
- <item>4 | 2.50 | 0.0838 0.0024 0.0862 | 24.6107</item>
- <item>5 | 2.50 | 0.0834 0.0026 0.0860 | 22.6548</item>
- <item>6 | 2.50 | 0.0831 0.0027 0.0858 | 20.6989</item>
- <item>7 | 2.50 | 0.0827 0.0028 0.0855 | 18.9688</item>
- <item>8 | 2.50 | 0.0824 0.0029 0.0853 | 17.4455</item>
- <item>9 | 2.50 | 0.0820 0.0030 0.0850 | 15.9223</item>
- <item>10 | 2.50 | 0.0816 0.0031 0.0848 | 14.6627</item>
- <item>11 | 2.50 | 0.0812 0.0032 0.0845 | 13.4764</item>
- <item>12 | 2.50 | 0.0809 0.0033 0.0842 | 12.3015</item>
- <item>13 | 2.50 | 0.0804 0.0034 0.0839 | 11.3776</item>
- <item>14 | 2.50 | 0.0801 0.0035 0.0835 | 10.4537</item>
- <item>15 | 2.25 | 0.0809 0.0036 0.0845 | 9.5920</item>
- <item>16 | 2.25 | 0.0772 0.0054 0.0827 | 8.8725</item>
- <item>17 | 2.25 | 0.0758 0.0061 0.0819 | 8.1530</item>
- <item>18 | 2.25 | 0.0749 0.0064 0.0812 | 7.5234</item>
- <item>29 | 2.00 | 0.0770 0.0031 0.0800 | 3.3283</item>
- <item>30 | 2.00 | 0.0709 0.0058 0.0767 | 3.1221</item>
- <item>31 | 2.00 | 0.0689 0.0067 0.0757 | 2.9160</item>
- <item>43 | 1.75 | 0.0682 0.0039 0.0721 | 1.5785</item>
- <item>44 | 1.75 | 0.0635 0.0064 0.0699 | 1.5194</item>
- <item>45 | 1.75 | 0.0619 0.0073 0.0692 | 1.4626</item>
- <item>57 | 1.50 | 0.0607 0.0053 0.0660 | 1.0900</item>
- <item>58 | 1.50 | 0.0572 0.0076 0.0648 | 1.0730</item>
- <item>59 | 1.50 | 0.0561 0.0083 0.0644 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 170s</item>
- <item>Prepare output 10s</item>
- <item>180s</item>
- <item>Jacobian determinant (RMS): 0.011 0.043 0.073 0.104 0.132 | 0.140661</item>
- <item>Template Matching: 0.089 0.225 0.207 0.186 0.168 | 0.168360</item>
- <item>Write result maps: 31s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 35s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 48s</item>
- <item>106s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 99s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 77s</item>
- <item>Spherical mapping with areal smoothing 84s</item>
- <item>Spherical registration 283s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 33s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 47s</item>
- <item>103s</item>
- <item>Create initial surface 92s</item>
- <item>Topology correction: 101s</item>
- <item>Surface refinement: 89s</item>
- <item>Reduction of surface collisions with optimization: 78s</item>
- <item>Spherical mapping with areal smoothing 87s</item>
- <item>Spherical registration 296s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4866 0.6039 mm</item>
- <item>Surface intensity / position RMSE: 0.0684 / 0.0680</item>
- <item>Euler number / defect number / defect size: 22.0 / 10.5 / 0.60%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/surf/lh.thickness.sub-0027265_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/surf/rh.thickness.sub-0027265_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/sub-0027265_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1771s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 16s</item>
- <item>ROI estimation of 'anatomy3' atlas 24s</item>
- <item>ROI estimation of 'julichbrain' atlas 32s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 115s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s</item>
- <item>Write results 12s</item>
- <item>382s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/report/catreport_sub-0027265_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 51 minute(s) and 24 second(s).</item>
- <item>Image Quality Rating (IQR): 82.94% (B-)</item>
- <item>GM volume (GMV): 47.44% (748.32 / 1577.31 ml)</item>
- <item>GM thickness (GMT): 2.49 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_612547/ds/UWM/sub-0027265/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|