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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>
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- <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>
- <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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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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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>
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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_2875243/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>
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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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- <shooting>
- <shootingtpm>
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- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
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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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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.297046460173651</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0659003928303719</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.065777599811554</SurfacePositionRMSE>
- <res_vx_vol>[1 0.9765625 0.9765625]</res_vx_vol>
- <res_vx_voli>[1 0.9765625 0.9765625]</res_vx_voli>
- <res_RMS>0.984437002015619</res_RMS>
- <res_BB>0.0019448040984571</res_BB>
- <tissue_mn>[5.71799993515015 120.544998168945 281.626007080078 404.011993408203]</tissue_mn>
- <tissue_mnr>[0.0141530446708202 0.298369854688644 0.697073400020599 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.73286944282939 51.7310077270824 38.7329373300303 24.2866925505901]</tissue_std>
- <tissue_stdr>[0.00937214586883783 0.129881456494331 0.0972471013665199 0.0609767958521843]</tissue_stdr>
- <contrast>124.142990112305</contrast>
- <contrastr>0.307275503873825</contrastr>
- <res_ECR>0.308786451816559</res_ECR>
- <NCR>0.152906700968742</NCR>
- <ICR>0.334124684333801</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 1.953125 1.953125]</res_vx_vol>
- <res_RMS>1.96887400403124</res_RMS>
- <res_ECR>2.4734001159668</res_ECR>
- <res_BB>1.00097239017487</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>3.47420072555542</contrastr>
- <NCR>2.5260796546936</NCR>
- <ICR>1.28850364685059</ICR>
- <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
- <SurfaceDefectArea>1.07426161504341</SurfaceDefectArea>
- <SurfaceDefectNumber>1.6</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31800782680511</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.31555199623108</SurfacePositionRMSE>
- <SIQR>2.39838377971356</SIQR>
- <IQR>2.35369394055425</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>20231031-041446</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.297046460173651</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0659003928303719</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.065777599811554</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>10</EC_abs>
- <defect_size>0.297046460173651</defect_size>
- <vol_abs_CGW>[271.79339539771 734.05320410635 528.258387247721 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.754049712536382</vol_abs_WMH>
- <vol_rel_WMH>0.000491524191009222</vol_rel_WMH>
- <surf_TSA>2002.49038066886</surf_TSA>
- <vol_TIV>1534.10498675178</vol_TIV>
- <vol_rel_CGW>[0.177167402325696 0.478489549571564 0.34434304810274 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.58202204993254 0.645901355170527]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.57188558578491 0.780365954063821 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92586153277777 0.262702812509306 0.287144300439453;2.58347248916757 0.187057121068553 0.431717460966796;3.26890906234907 0.286030571523745 0.281138238593751]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.899195710804052 0.312157448227495 0.487742641027978;4.26042960195265 0.322270752606303 0.512257358972022]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.41665456337888</vol_TIV>
- <vol_rel_CGW>[1.03174213947012 6.44341863454676 4.03417830644288 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04915241910092</vol_rel_WMH>
- <surf_TSA>8.62153631763386</surf_TSA>
- <SQR>5.28459824821834</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11000 0.360317817884499]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00816775392740965 0.00165608059614897 0.382460355758667]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[873.22208554137 479.175002902162 482.073114432541 2213.41589385388 1711.92894355924 5954.486469194]</SPMvols0>
- <SPMvols1>[742.969453101065 445.344640694413 305.04596934599 2403.72400096819 1540.43606776817 5563.32218319762]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[140.455505371094 296.843200683594 390.635711669922]</T3th>
- <Tth>
- <T3th>[-6.51582002639771 -6.51581764221191 4.60727071762085 140.455505371094 296.843200683594 390.635711669922 515.725830078125 1200.91320800781]</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>[0.0173420291393995 0.0642445310950279 0.0709016248583794 0 0]</dtc>
- <ll>[0.0859797288055847 0 0.0859797288055847 0;0.207484525792739 0.0104265338948079 0.217911059687547 2223.4375;0.207484525792739 0.0104265338948079 0.217911059687547 2223.4375]</ll>
- <rmsdtc>[0.0422291494905949 0.0888815745711327 0.101329252123833]</rmsdtc>
- <rmsgdt>[0.0313720516860485 0.0457349345088005 0.057439960539341]</rmsgdt>
- <rmsdt>0.101329252123833</rmsdt>
- <dt>0.0709016248583794</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>[0.00707719568163157 0.0273567512631416 0.0368971414864063 0.0461752526462078 0.0538829006254673 0.0603138394653797]</dtc>
- <ll>[0.0868169504679008 0 0.0868169504679008 0;0.224202045177045 0.0151994829822955 0.239401528159341 7780.2353515625;0.209150370217531 0.0168064201049343 0.225956790322466 12095.7822265625;0.188797112996535 0.0192550086793963 0.208052121675931 20762.13671875;0.171283933259897 0.0225551335979645 0.193839066857861 39456.890625;0.171283933259897 0.0225551335979645 0.193839066857861 39456.890625]</ll>
- <rmsdtc>[0.00874926429241896 0.0313846953213215 0.0509631074965 0.0757290422916412 0.102354928851128 0.110386095941067]</rmsdtc>
- <rmsgdt>[0.00309483474120498 0.0119242472574115 0.0273690838366747 0.0485930033028126 0.0689068362116814 0.0752563923597336]</rmsgdt>
- <rmsdt>0.110386095941067</rmsdt>
- <dt>0.0603138394653797</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027222/ses-2/sub-0027222_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 51s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 2s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 4s</item>
- <item>31s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 53s</item>
- <item>SPM preprocessing 1 (estimate 2): 43s</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>62s</item>
- <item>Global intensity correction: 11s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 22s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.11) 10s</item>
- <item>Estimate local tissue thresholds (WM) 13s</item>
- <item>Estimate local tissue thresholds (GM) 18s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 31s</item>
- <item>79s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 8s</item>
- <item>Blood vessel detection 7s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 15s</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>45s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 25s</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 | 0.0868 0.0000 0.0868 | 32.0000</item>
- <item>2 | 2.50 | 0.0840 0.0012 0.0852 | 29.4886</item>
- <item>3 | 2.50 | 0.0832 0.0018 0.0851 | 26.9772</item>
- <item>4 | 2.50 | 0.0829 0.0020 0.0849 | 24.6107</item>
- <item>5 | 2.50 | 0.0826 0.0022 0.0847 | 22.6548</item>
- <item>6 | 2.50 | 0.0823 0.0023 0.0846 | 20.6989</item>
- <item>7 | 2.50 | 0.0820 0.0023 0.0844 | 18.9688</item>
- <item>8 | 2.50 | 0.0818 0.0024 0.0842 | 17.4455</item>
- <item>9 | 2.50 | 0.0815 0.0025 0.0840 | 15.9223</item>
- <item>10 | 2.50 | 0.0812 0.0026 0.0838 | 14.6627</item>
- <item>11 | 2.50 | 0.0809 0.0026 0.0836 | 13.4764</item>
- <item>12 | 2.50 | 0.0806 0.0027 0.0833 | 12.3015</item>
- <item>13 | 2.50 | 0.0803 0.0028 0.0831 | 11.3776</item>
- <item>14 | 2.50 | 0.0800 0.0028 0.0829 | 10.4537</item>
- <item>15 | 2.25 | 0.0797 0.0029 0.0826 | 9.5920</item>
- <item>16 | 2.25 | 0.0767 0.0043 0.0810 | 8.8725</item>
- <item>17 | 2.25 | 0.0755 0.0048 0.0803 | 8.1530</item>
- <item>18 | 2.25 | 0.0747 0.0051 0.0798 | 7.5234</item>
- <item>29 | 2.00 | 0.0768 0.0024 0.0792 | 3.3283</item>
- <item>30 | 2.00 | 0.0715 0.0047 0.0762 | 3.1221</item>
- <item>31 | 2.00 | 0.0697 0.0056 0.0753 | 2.9160</item>
- <item>43 | 1.75 | 0.0689 0.0032 0.0721 | 1.5785</item>
- <item>44 | 1.75 | 0.0644 0.0056 0.0700 | 1.5194</item>
- <item>45 | 1.75 | 0.0629 0.0064 0.0694 | 1.4626</item>
- <item>57 | 1.50 | 0.0615 0.0047 0.0661 | 1.0900</item>
- <item>58 | 1.50 | 0.0582 0.0068 0.0650 | 1.0730</item>
- <item>59 | 1.50 | 0.0571 0.0075 0.0646 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 110s</item>
- <item>Prepare output 7s</item>
- <item>117s</item>
- <item>Jacobian determinant (RMS): 0.009 0.031 0.051 0.076 0.102 | 0.110386</item>
- <item>Template Matching: 0.087 0.224 0.209 0.189 0.171 | 0.171284</item>
- <item>Write result maps: 23s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 20s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 30s</item>
- <item>65s</item>
- <item>Create initial surface 52s</item>
- <item>Topology correction: 64s</item>
- <item>Surface refinement: 52s</item>
- <item>Reduction of surface collisions with optimization: 46s</item>
- <item>Spherical mapping with areal smoothing 56s</item>
- <item>Spherical registration 181s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 29s</item>
- <item>73s</item>
- <item>Create initial surface 51s</item>
- <item>Topology correction: 64s</item>
- <item>Surface refinement: 68s</item>
- <item>Reduction of surface collisions with optimization: 45s</item>
- <item>Spherical mapping with areal smoothing 56s</item>
- <item>Spherical registration 187s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5820 0.6458 mm</item>
- <item>Surface intensity / position RMSE: 0.0659 / 0.0658</item>
- <item>Euler number / defect number / defect size: 10.0 / 12.0 / 0.30%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/surf/lh.thickness.sub-0027222_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/surf/rh.thickness.sub-0027222_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/sub-0027222_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1125s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 23s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 16s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 9s</item>
- <item>ROI estimation of 'mori' atlas 14s</item>
- <item>ROI estimation of 'anatomy3' atlas 20s</item>
- <item>ROI estimation of 'julichbrain' atlas 26s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 41s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 60s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 6s</item>
- <item>263s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/report/catreport_sub-0027222_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 34 minute(s) and 23 second(s).</item>
- <item>Image Quality Rating (IQR): 81.46% (B-)</item>
- <item>GM volume (GMV): 47.85% (734.05 / 1534.10 ml)</item>
- <item>GM thickness (GMT): 2.58 0.65 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2875243/ds/SWU_1/sub-0027222/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|