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- <parameter>
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- <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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- <biasfwhm>60</biasfwhm>
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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>
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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>
- <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>
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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_3275175/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>
- <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>
- <new_release>0</new_release>
- <lazy>0</lazy>
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- <shooting>
- <shootingtpm>
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- <restypes>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
- <shootingtpms>
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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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- </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>14</SurfaceEulerNumber>
- <SurfaceDefectArea>1.30879551348694</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639587491750717</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0897578150033951</SurfacePositionRMSE>
- <res_vx_vol>[0.999999989040404 0.999999987321744 0.999999986607191]</res_vx_vol>
- <res_vx_voli>[0.999999987171918 0.99999998872636 0.999999985590012]</res_vx_voli>
- <res_RMS>0.999999987656446</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.48099994659424 85.0910034179688 215.397003173828 305.183990478516]</tissue_mn>
- <tissue_mnr>[0.0310665052384138 0.278818696737289 0.705793917179108 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.83497776224218 30.4445535801499 30.2239595037483 17.7404235120768]</tissue_std>
- <tissue_stdr>[0.0264961048960686 0.102956525981426 0.102210529148579 0.0599940605461597]</tissue_stdr>
- <contrast>92.6657867431641</contrast>
- <contrastr>0.303639084100723</contrastr>
- <res_ECR>0.311420023441315</res_ECR>
- <NCR>0.171553045511246</NCR>
- <ICR>0.530835866928101</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999997808081 1.99999997464349 1.99999997321438]</res_vx_vol>
- <res_RMS>1.99999997531289</res_RMS>
- <res_ECR>2.4868369102478</res_ECR>
- <res_BB>1</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>3.52874708175659</contrastr>
- <NCR>2.79375600814819</NCR>
- <ICR>1.7763786315918</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.32719887837173</SurfaceDefectArea>
- <SurfaceDefectNumber>1.375</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.27917504310608</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.79515624046326</SurfacePositionRMSE>
- <SIQR>2.55393030486012</SIQR>
- <IQR>2.58333658577806</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>20231030-235832</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>1.30879551348694</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0639587491750717</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0897578150033951</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>1.30879551348694</defect_size>
- <vol_abs_CGW>[332.3546813181 592.829537953434 552.268668927267 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.39387445612343</vol_abs_WMH>
- <vol_rel_WMH>0.00094343072950552</vol_rel_WMH>
- <surf_TSA>1908.08904105563</surf_TSA>
- <vol_TIV>1477.4528881988</vol_TIV>
- <vol_rel_CGW>[0.224951119573959 0.401251060313786 0.373797820112255 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.32155351862824 0.635425226496485]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.33922219276428 0.776338311782488 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.67333133395363 0.283827743695056 0.280334922510989;2.33877538912544 0.182522139785036 0.431056692474204;2.9874870347304 0.279126830549265 0.288608385014807]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.693934887679673 0.237448758081784 0.584588537839824;3.99952470663241 0.387716705711128 0.415411462160176]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.1415936264411</vol_TIV>
- <vol_rel_CGW>[1.88992671648634 5.05623312345161 4.56317924052182 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.09434307295055</vol_rel_WMH>
- <surf_TSA>8.61443296370347</surf_TSA>
- <SQR>4.32781031809919</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 12582.9115340465 0.334521876653843]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0267388373613358 0.00157017959281802 0.368019342422485]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[732.645152176739 503.667600210742 549.075316109072 1249.05445385756 2555.38732511707 7805.43609547773]</SPMvols0>
- <SPMvols1>[619.301238894748 470.6122838367 334.037351841532 785.365189362086 1752.52801093852 8621.3076052336]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[106.851600646973 228.337493896484 300.606201171875]</T3th>
- <Tth>
- <T3th>[-5.01001977920532 -5.01002264022827 9.49484062194824 106.851600646973 228.337493896484 300.606201171875 397.483520507812 532.220581054688]</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>[0.0227276384830475 0.0875527411699295 0.0981622636318207 0 0]</dtc>
- <ll>[0.089519963258741 0 0.089519963258741 0;0.204973749753808 0.013482797904318 0.218456547658126 2875.1796875;0.204973749753808 0.013482797904318 0.218456547658126 2875.1796875]</ll>
- <rmsdtc>[0.0468109212815762 0.115758061408997 0.130361571907997]</rmsdtc>
- <rmsgdt>[0.0329488702118397 0.0563958622515202 0.0699308514595032]</rmsgdt>
- <rmsdt>0.130361571907997</rmsdt>
- <dt>0.0981622636318207</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>[0.0107656549662352 0.0452831871807575 0.0574905909597874 0.0668007805943489 0.0734749585390091 0.0839438661932945]</dtc>
- <ll>[0.0883759074802544 0 0.0883759074802544 0;0.224717994505495 0.0183121146214896 0.243030109126984 9373.513671875;0.208020578022876 0.0200811349387845 0.22810171296166 14452.6337890625;0.18508264844121 0.0221081468341244 0.207190795275334 23838.595703125;0.166511400929372 0.0253330490258398 0.191844449955212 44316.4453125;0.166511400929372 0.0253330490258398 0.191844449955212 44316.4453125]</ll>
- <rmsdtc>[0.0123715288937092 0.0447991229593754 0.0714621096849442 0.0987313315272331 0.125567004084587 0.134492039680481]</rmsdtc>
- <rmsgdt>[0.00372454919852316 0.0148595869541168 0.0329622365534306 0.0558256655931473 0.0755929872393608 0.0821904912590981]</rmsgdt>
- <rmsdt>0.134492039680481</rmsdt>
- <dt>0.0839438661932945</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027023/ses-1/sub-0027023_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 74s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>38s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 69s</item>
- <item>SPM preprocessing 1 (estimate 2): 44s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 39s</item>
- <item>Update probability maps 9s</item>
- <item>80s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 22s</item>
- <item>Fast Optimized Shooting registration 27s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.17) 12s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 20s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 37s</item>
- <item>91s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 9s</item>
- <item>Blood vessel detection 7s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.19) 18s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>51s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s</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) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>10s</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 | 0.0884 0.0000 0.0884 | 32.0000</item>
- <item>2 | 2.50 | 0.0854 0.0013 0.0867 | 29.4886</item>
- <item>3 | 2.50 | 0.0845 0.0020 0.0865 | 26.9772</item>
- <item>4 | 2.50 | 0.0841 0.0022 0.0863 | 24.6107</item>
- <item>5 | 2.50 | 0.0838 0.0024 0.0862 | 22.6548</item>
- <item>6 | 2.50 | 0.0835 0.0025 0.0860 | 20.6989</item>
- <item>7 | 2.50 | 0.0831 0.0026 0.0858 | 18.9688</item>
- <item>8 | 2.50 | 0.0828 0.0027 0.0855 | 17.4455</item>
- <item>9 | 2.50 | 0.0825 0.0028 0.0853 | 15.9223</item>
- <item>10 | 2.50 | 0.0821 0.0030 0.0851 | 14.6627</item>
- <item>11 | 2.50 | 0.0818 0.0031 0.0848 | 13.4764</item>
- <item>12 | 2.50 | 0.0814 0.0031 0.0845 | 12.3015</item>
- <item>13 | 2.50 | 0.0810 0.0033 0.0843 | 11.3776</item>
- <item>14 | 2.50 | 0.0806 0.0033 0.0840 | 10.4537</item>
- <item>15 | 2.25 | 0.0812 0.0034 0.0846 | 9.5920</item>
- <item>16 | 2.25 | 0.0779 0.0051 0.0830 | 8.8725</item>
- <item>17 | 2.25 | 0.0765 0.0057 0.0822 | 8.1530</item>
- <item>18 | 2.25 | 0.0756 0.0059 0.0816 | 7.5234</item>
- <item>19 | 2.25 | 0.0749 0.0061 0.0810 | 6.9630</item>
- <item>29 | 2.00 | 0.0771 0.0031 0.0802 | 3.3283</item>
- <item>30 | 2.00 | 0.0714 0.0057 0.0771 | 3.1221</item>
- <item>31 | 2.00 | 0.0693 0.0067 0.0760 | 2.9160</item>
- <item>43 | 1.75 | 0.0682 0.0038 0.0720 | 1.5785</item>
- <item>44 | 1.75 | 0.0634 0.0064 0.0698 | 1.5194</item>
- <item>45 | 1.75 | 0.0617 0.0074 0.0691 | 1.4626</item>
- <item>57 | 1.50 | 0.0602 0.0054 0.0656 | 1.0900</item>
- <item>58 | 1.50 | 0.0567 0.0077 0.0644 | 1.0730</item>
- <item>59 | 1.50 | 0.0555 0.0084 0.0639 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 161s</item>
- <item>Prepare output 8s</item>
- <item>169s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.071 0.099 0.126 | 0.134492</item>
- <item>Template Matching: 0.088 0.225 0.208 0.185 0.167 | 0.166511</item>
- <item>Write result maps: 33s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 31s</item>
- <item>77s</item>
- <item>Create initial surface 63s</item>
- <item>Topology correction: 69s</item>
- <item>Surface refinement: 56s</item>
- <item>Reduction of surface collisions with optimization: 46s</item>
- <item>Spherical mapping with areal smoothing 59s</item>
- <item>Spherical registration 198s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 26s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 31s</item>
- <item>72s</item>
- <item>Create initial surface 58s</item>
- <item>Topology correction: 70s</item>
- <item>Surface refinement: 57s</item>
- <item>Reduction of surface collisions with optimization: 47s</item>
- <item>Spherical mapping with areal smoothing 59s</item>
- <item>Spherical registration 212s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3216 0.6350 mm</item>
- <item>Surface intensity / position RMSE: 0.0640 / 0.0898</item>
- <item>Euler number / defect number / defect size: 14.0 / 7.5 / 1.31%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/surf/lh.thickness.sub-0027023_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/surf/rh.thickness.sub-0027023_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/sub-0027023_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1221s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 18s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 69s</item>
- <item>ROI estimation of 'lpba40' atlas 19s</item>
- <item>ROI estimation of 'hammers' atlas 46s</item>
- <item>ROI estimation of 'thalamus' atlas 4s</item>
- <item>ROI estimation of 'ibsr' atlas 17s</item>
- <item>ROI estimation of 'aal3' atlas 30s</item>
- <item>ROI estimation of 'mori' atlas 44s</item>
- <item>ROI estimation of 'anatomy3' atlas 66s</item>
- <item>ROI estimation of 'julichbrain' atlas 82s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 35s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 111s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 158s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s</item>
- <item>Write results 16s</item>
- <item>773s</item>
- <item>Quality check: 11s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/report/catreport_sub-0027023_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 48 minute(s) and 39 second(s).</item>
- <item>Image Quality Rating (IQR): 79.17% (C+)</item>
- <item>GM volume (GMV): 40.13% (592.83 / 1477.45 ml)</item>
- <item>GM thickness (GMT): 2.32 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3275175/ds/MRN/sub-0027023/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|