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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <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>
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- <SLC>0</SLC>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
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- <shootingsurf>Template_T1</shootingsurf>
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- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
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- <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>
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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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- <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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- <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>
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- <item>gm</item>
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- <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>/var/lib/condor/execute/dir_3501056/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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- <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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- <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>
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- <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>
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- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- </darteltpms>
- <shootingtpms>
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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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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.332122730051169</SurfaceDefectArea>
- <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0637088268995285</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0648773312568665</SurfacePositionRMSE>
- <res_vx_vol>[0.999900817871094 1 1]</res_vx_vol>
- <res_vx_voli>[0.999900817871094 1 1]</res_vx_voli>
- <res_RMS>0.999966940383411</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[3.38800001144409 17.1019992828369 184.220001220703 369.861999511719]</tissue_mn>
- <tissue_mnr>[0.00916017312556505 0.0462388657033443 0.498077660799026 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.1861596507632 31.6762491041314 47.2047346133843 35.6182288797268]</tissue_std>
- <tissue_stdr>[0.00869409460574389 0.0864351913332939 0.128807872533798 0.0971916913986206]</tissue_stdr>
- <contrast>122.801887512207</contrast>
- <contrastr>0.332020819187164</contrastr>
- <res_ECR>0.375044345855713</res_ECR>
- <NCR>0.12227088958025</NCR>
- <ICR>0.338597923517227</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99980163574219 2 2]</res_vx_vol>
- <res_RMS>1.99993388076682</res_RMS>
- <res_ECR>2.81145071983337</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[8.62378978729248 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>3.10302090644836</contrastr>
- <NCR>2.0862889289856</NCR>
- <ICR>1.29959797859192</ICR>
- <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
- <SurfaceDefectArea>1.08303068251279</SurfaceDefectArea>
- <SurfaceDefectNumber>1.475</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.27417659759521</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.29754662513733</SurfacePositionRMSE>
- <SIQR>2.49592317374513</SIQR>
- <IQR>2.0462912759602</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>20231031-004312</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.332122730051169</SurfaceDefectArea>
- <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0637088268995285</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0648773312568665</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>16</EC_abs>
- <defect_size>0.332122730051169</defect_size>
- <vol_abs_CGW>[246.050076161912 654.008904040976 437.469335967838 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.532825579355277</vol_abs_WMH>
- <vol_rel_WMH>0.000398365831147956</vol_rel_WMH>
- <surf_TSA>1748.3295821665</surf_TSA>
- <vol_TIV>1337.52831617073</vol_TIV>
- <vol_rel_CGW>[0.183958779180347 0.488968267911792 0.327072952907861 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51559666388855 0.677180851814638]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.46535110473633 0.896725623912196 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.8649906071964 0.30066360744021 0.341767776523702;2.53532658856383 0.201282179967832 0.416767776523702;3.32139449119409 0.329848899774146 0.241464446952596]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.786077077402551 0.240137595786034 0.463683835746499;4.44909190677863 0.347017344958329 0.536316164253501]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.09241739074324</vol_TIV>
- <vol_rel_CGW>[1.15371370654359 6.6316140070365 3.72401136687968 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0398365831148</vol_rel_WMH>
- <surf_TSA>8.55256646722007</surf_TSA>
- <SQR>5.42977980183326</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11533.192 0.541852807285415]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00130959961097687 0.00111443095374852 0.0745906308293343]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[827.478132581105 361.188141665231 457.241739410131 789.370492944994 841.318214658101 8803.7707209791]</SPMvols0>
- <SPMvols1>[716.106693458707 338.916774335375 241.603062367997 537.367395510266 776.972201187313 8922.44606698516]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[36.842098236084 203.571792602539 384.957702636719]</T3th>
- <Tth>
- <T3th>[-5.02947998046875 -5.02947854995728 1.82152152061462 36.842098236084 203.571792602539 384.957702636719 559.015502929688 1032.17956542969]</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>[0.0226351916790009 0.0823599770665169 0.0927328243851662 0 0]</dtc>
- <ll>[0.0862034144712572 0 0.0862034144712572 0;0.197869052406119 0.011315018332162 0.209184070738281 2412.90502929688;0.197869052406119 0.011315018332162 0.209184070738281 2412.90502929688]</ll>
- <rmsdtc>[0.050532940775156 0.1132742613554 0.127253592014313]</rmsdtc>
- <rmsgdt>[0.0357858948409557 0.0511281117796898 0.0634878724813461]</rmsgdt>
- <rmsdt>0.127253592014313</rmsdt>
- <dt>0.0927328243851662</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>[0.0105868158861995 0.0434730388224125 0.0564926713705063 0.0655105635523796 0.0723265334963799 0.0822658091783524]</dtc>
- <ll>[0.0876630510081554 0 0.0876630510081554 0;0.222595848595849 0.0176194692460317 0.24021531784188 9018.9658203125;0.206151644685652 0.0183563089949521 0.224507953680604 13211.255859375;0.184796977246928 0.0199691721743215 0.20476614942125 21532.19921875;0.167368235570522 0.0228477953706313 0.190216030941154 39968.859375;0.167368235570522 0.0228477953706313 0.190216030941154 39968.859375]</ll>
- <rmsdtc>[0.0126628689467907 0.0465129725635052 0.0720408484339714 0.0987525135278702 0.124862693250179 0.131459951400757]</rmsdtc>
- <rmsgdt>[0.00332402787171304 0.0131580801680684 0.0294557064771652 0.0511501617729664 0.0710834711790085 0.0756715312600136]</rmsgdt>
- <rmsdt>0.131459951400757</rmsdt>
- <dt>0.0822658091783524</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027248/ses-2/sub-0027248_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 49s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>42s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 88s</item>
- <item>SPM preprocessing 1 (estimate 2): 61s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 22s</item>
- <item>Update Skull-Stripping 53s</item>
- <item>Update probability maps 12s</item>
- <item>107s</item>
- <item>Global intensity correction: 21s</item>
- <item>SANLM denoising after intensity normalization (medium): 30s</item>
- <item>Fast Optimized Shooting registration 43s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 17s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 37s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 53s</item>
- <item>141s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 10s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 16s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 26s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>78s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 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>14s</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 | 0.0877 0.0000 0.0877 | 32.0000</item>
- <item>2 | 2.50 | 0.0845 0.0013 0.0858 | 29.4886</item>
- <item>3 | 2.50 | 0.0836 0.0020 0.0856 | 26.9772</item>
- <item>4 | 2.50 | 0.0832 0.0023 0.0854 | 24.6107</item>
- <item>5 | 2.50 | 0.0828 0.0024 0.0852 | 22.6548</item>
- <item>6 | 2.50 | 0.0825 0.0025 0.0850 | 20.6989</item>
- <item>7 | 2.50 | 0.0821 0.0026 0.0848 | 18.9688</item>
- <item>8 | 2.50 | 0.0818 0.0028 0.0846 | 17.4455</item>
- <item>9 | 2.50 | 0.0815 0.0029 0.0843 | 15.9223</item>
- <item>10 | 2.50 | 0.0811 0.0030 0.0841 | 14.6627</item>
- <item>11 | 2.50 | 0.0807 0.0031 0.0838 | 13.4764</item>
- <item>12 | 2.50 | 0.0804 0.0031 0.0835 | 12.3015</item>
- <item>13 | 2.50 | 0.0800 0.0033 0.0832 | 11.3776</item>
- <item>14 | 2.50 | 0.0796 0.0033 0.0829 | 10.4537</item>
- <item>15 | 2.25 | 0.0796 0.0034 0.0830 | 9.5920</item>
- <item>16 | 2.25 | 0.0764 0.0050 0.0814 | 8.8725</item>
- <item>17 | 2.25 | 0.0751 0.0056 0.0807 | 8.1530</item>
- <item>18 | 2.25 | 0.0742 0.0059 0.0801 | 7.5234</item>
- <item>29 | 2.00 | 0.0762 0.0028 0.0790 | 3.3283</item>
- <item>30 | 2.00 | 0.0707 0.0052 0.0759 | 3.1221</item>
- <item>31 | 2.00 | 0.0687 0.0061 0.0748 | 2.9160</item>
- <item>43 | 1.75 | 0.0676 0.0035 0.0711 | 1.5785</item>
- <item>44 | 1.75 | 0.0632 0.0058 0.0690 | 1.5194</item>
- <item>45 | 1.75 | 0.0616 0.0067 0.0683 | 1.4626</item>
- <item>57 | 1.50 | 0.0601 0.0049 0.0650 | 1.0900</item>
- <item>58 | 1.50 | 0.0568 0.0070 0.0638 | 1.0730</item>
- <item>59 | 1.50 | 0.0558 0.0076 0.0634 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 213s</item>
- <item>Prepare output 14s</item>
- <item>227s</item>
- <item>Jacobian determinant (RMS): 0.013 0.047 0.072 0.099 0.125 | 0.131460</item>
- <item>Template Matching: 0.088 0.223 0.206 0.185 0.167 | 0.167368</item>
- <item>Write result maps: 59s</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: 19s</item>
- <item>PBT2x thickness: 56s</item>
- <item>117s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 86s</item>
- <item>Surface refinement: 75s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 91s</item>
- <item>Spherical registration 330s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 31s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 53s</item>
- <item>108s</item>
- <item>Create initial surface 94s</item>
- <item>Topology correction: 85s</item>
- <item>Surface refinement: 78s</item>
- <item>Reduction of surface collisions with optimization: 63s</item>
- <item>Spherical mapping with areal smoothing 90s</item>
- <item>Spherical registration 350s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5157 0.6770 mm</item>
- <item>Surface intensity / position RMSE: 0.0637 / 0.0649</item>
- <item>Euler number / defect number / defect size: 16.0 / 9.5 / 0.33%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/surf/lh.thickness.sub-0027248_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/surf/rh.thickness.sub-0027248_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/sub-0027248_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1842s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 14s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 39s</item>
- <item>ROI estimation of 'lpba40' atlas 14s</item>
- <item>ROI estimation of 'hammers' atlas 32s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 20s</item>
- <item>ROI estimation of 'mori' atlas 30s</item>
- <item>ROI estimation of 'anatomy3' atlas 37s</item>
- <item>ROI estimation of 'julichbrain' atlas 55s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 93s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 147s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 14s</item>
- <item>Write results 16s</item>
- <item>576s</item>
- <item>Quality check: 16s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/report/catreport_sub-0027248_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 59 minute(s) and 22 second(s).</item>
- <item>Image Quality Rating (IQR): 84.54% (B)</item>
- <item>GM volume (GMV): 48.90% (654.01 / 1337.53 ml)</item>
- <item>GM thickness (GMT): 2.52 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3501056/ds/IBA_TRT/sub-0027248/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|