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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>
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- <restype>optimal</restype>
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- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
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- <species>human</species>
- <APP>1070</APP>
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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>
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- <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>
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- <tr>
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- <td>0</td>
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- <item>csf</item>
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- <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>
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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/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>
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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/suit.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/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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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>/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>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
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- <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_110230/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <td>Desikan</td>
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- <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>
- <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>
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- <shootingtpm>
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- </shootingtpms>
- <templates>
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- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.852226311960372</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0795615911483765</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0854471027851105</SurfacePositionRMSE>
- <res_vx_vol>[1 0.999999940395355 0.999999940395355]</res_vx_vol>
- <res_vx_voli>[1 0.999999940395355 0.999999940395355]</res_vx_voli>
- <res_RMS>0.999999960263571</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[13.2770004272461 92.6880035400391 256.609008789062 410.010986328125]</tissue_mn>
- <tissue_mnr>[0.0323820598423481 0.2260622382164 0.625858843326569 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[8.90800505996506 43.8973653295561 45.4763575423337 30.5453993517906]</tissue_std>
- <tissue_stdr>[0.0224533453583717 0.110646851360798 0.114626824855804 0.0769921466708183]</tissue_stdr>
- <contrast>145.964294433594</contrast>
- <contrastr>0.356000930070877</contrastr>
- <res_ECR>0.406142115592957</res_ECR>
- <NCR>0.146510496735573</NCR>
- <ICR>0.342483371496201</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 1.99999988079071 1.99999988079071]</res_vx_vol>
- <res_RMS>1.99999992052714</res_RMS>
- <res_ECR>2.97011280059814</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>2.743319272995</contrastr>
- <NCR>2.43425941467285</NCR>
- <ICR>1.30923461914062</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.21305657799009</SurfaceDefectArea>
- <SurfaceDefectNumber>2</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.59123182296753</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.70894205570221</SurfacePositionRMSE>
- <SIQR>2.66113213396505</SIQR>
- <IQR>2.28549441755036</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>20231031-021126</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.852226311960372</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0795615911483765</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0854471027851105</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.852226311960372</defect_size>
- <vol_abs_CGW>[200.507427078042 932.776449588686 544.91120955132 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.28822729741172</vol_abs_WMH>
- <vol_rel_WMH>0.000767626665094608</vol_rel_WMH>
- <surf_TSA>2476.38294945925</surf_TSA>
- <vol_TIV>1678.19508621805</vol_TIV>
- <vol_rel_CGW>[0.119478020597654 0.555821225582763 0.324700753819583 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.63478316693774 0.65551460751754]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.63212442398071 0.800157142085017 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99786703323863 0.272458737593194 0.315356507806241;2.66977253518856 0.192157721043212 0.419201985266819;3.36699651013043 0.282195124948029 0.26544150692694]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.92646745802432 0.335981036993492 0.546792366061163;4.36513067449024 0.337091146504289 0.453207633938837]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.637843310303</vol_TIV>
- <vol_rel_CGW>[0.5 7.83227775831112 3.68140721658733 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.07676266650946</vol_rel_WMH>
- <surf_TSA>8.62399959123277</surf_TSA>
- <SQR>6.40687139728317</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.64688281253 0.37199165459697]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0294319689273834 0.000826030853204429 0.325557947158813]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1061.18688918293 498.907916996125 340.13286925692 446.148876226669 1569.38573840482 6227.61527721818]</SPMvols0>
- <SPMvols1>[946.386471495657 467.038367854095 187.781099183374 340.463735884145 901.231061192327 6528.86055503243]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[103.413902282715 273.064208984375 400.601806640625]</T3th>
- <Tth>
- <T3th>[-6.29694986343384 -6.29694700241089 9.99400520324707 103.413902282715 273.064208984375 400.601806640625 549.195739746094 1138.90063476562]</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>[0.0192820392549038 0.0657318830490112 0.0721244961023331 0 0]</dtc>
- <ll>[0.0809641117189063 0 0.0809641117189063 0;0.196556814864618 0.00875779904094206 0.20531461390556 1867.58312988281;0.196556814864618 0.00875779904094206 0.20531461390556 1867.58312988281]</ll>
- <rmsdtc>[0.0429157242178917 0.0882228165864944 0.0981432050466537]</rmsdtc>
- <rmsgdt>[0.0306582096964121 0.0418066792190075 0.0514007620513439]</rmsgdt>
- <rmsdt>0.0981432050466537</rmsdt>
- <dt>0.0721244961023331</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>[0.00864454172551632 0.030363904312253 0.042664498090744 0.0523036420345306 0.06058469414711 0.0676298663020134]</dtc>
- <ll>[0.0811354995250359 0 0.0811354995250359 0;0.216386553724054 0.011748039720696 0.22813459344475 6013.52783203125;0.200739323507181 0.0143619038869888 0.215101227394169 10336.4345703125;0.183007627018044 0.0172769450507386 0.200284572068782 18629.24609375;0.166981628350596 0.0211829611076209 0.188164589458217 37056.4765625;0.166981628350596 0.0211829611076209 0.188164589458217 37056.4765625]</ll>
- <rmsdtc>[0.0104554845020175 0.0369796380400658 0.0557188838720322 0.0812398418784142 0.107339821755886 0.113553620874882]</rmsdtc>
- <rmsgdt>[0.00305395270697773 0.0119028529152274 0.0267126373946667 0.0480617471039295 0.0697919279336929 0.0755836665630341]</rmsgdt>
- <rmsdt>0.113553620874882</rmsdt>
- <dt>0.0676298663020134</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025263/ses-1/sub-0025263_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 77s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 7s</item>
- <item>44s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 95s</item>
- <item>SPM preprocessing 1 (estimate 2): 76s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 23s</item>
- <item>Update Skull-Stripping 44s</item>
- <item>Update probability maps 9s</item>
- <item>95s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 40s</item>
- <item>Fast Optimized Shooting registration 39s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 19s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 39s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 48s</item>
- <item>140s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 23s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 36s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 4s</item>
- <item>98s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 43s</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) 6s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>16s</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 | 0.0811 0.0000 0.0811 | 32.0000</item>
- <item>2 | 2.50 | 0.0789 0.0010 0.0799 | 29.4886</item>
- <item>3 | 2.50 | 0.0782 0.0016 0.0798 | 26.9772</item>
- <item>4 | 2.50 | 0.0779 0.0018 0.0797 | 24.6107</item>
- <item>5 | 2.50 | 0.0776 0.0019 0.0795 | 22.6548</item>
- <item>6 | 2.50 | 0.0774 0.0020 0.0794 | 20.6989</item>
- <item>7 | 2.50 | 0.0772 0.0021 0.0793 | 18.9688</item>
- <item>8 | 2.50 | 0.0769 0.0022 0.0791 | 17.4455</item>
- <item>9 | 2.50 | 0.0767 0.0022 0.0789 | 15.9223</item>
- <item>10 | 2.50 | 0.0765 0.0023 0.0788 | 14.6627</item>
- <item>11 | 2.50 | 0.0762 0.0024 0.0786 | 13.4764</item>
- <item>12 | 2.50 | 0.0759 0.0024 0.0784 | 12.3015</item>
- <item>13 | 2.50 | 0.0757 0.0025 0.0782 | 11.3776</item>
- <item>14 | 2.50 | 0.0754 0.0026 0.0780 | 10.4537</item>
- <item>15 | 2.25 | 0.0747 0.0026 0.0773 | 9.5920</item>
- <item>16 | 2.25 | 0.0721 0.0039 0.0760 | 8.8725</item>
- <item>29 | 2.00 | 0.0739 0.0017 0.0757 | 3.3283</item>
- <item>30 | 2.00 | 0.0686 0.0040 0.0726 | 3.1221</item>
- <item>31 | 2.00 | 0.0669 0.0048 0.0717 | 2.9160</item>
- <item>43 | 1.75 | 0.0666 0.0027 0.0693 | 1.5785</item>
- <item>44 | 1.75 | 0.0624 0.0050 0.0674 | 1.5194</item>
- <item>45 | 1.75 | 0.0610 0.0058 0.0668 | 1.4626</item>
- <item>57 | 1.50 | 0.0601 0.0042 0.0643 | 1.0900</item>
- <item>58 | 1.50 | 0.0568 0.0064 0.0631 | 1.0730</item>
- <item>59 | 1.50 | 0.0557 0.0071 0.0627 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 193s</item>
- <item>Prepare output 14s</item>
- <item>206s</item>
- <item>Jacobian determinant (RMS): 0.010 0.037 0.056 0.081 0.107 | 0.113554</item>
- <item>Template Matching: 0.081 0.216 0.201 0.183 0.167 | 0.166982</item>
- <item>Write result maps: 34s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 40s</item>
- <item>CSF distance: 24s</item>
- <item>PBT2x thickness: 72s</item>
- <item>144s</item>
- <item>Create initial surface 126s</item>
- <item>Topology correction: 143s</item>
- <item>Surface refinement: 142s</item>
- <item>Reduction of surface collisions with optimization: 128s</item>
- <item>Spherical mapping with areal smoothing 163s</item>
- <item>Spherical registration 357s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 43s</item>
- <item>CSF distance: 25s</item>
- <item>PBT2x thickness: 71s</item>
- <item>147s</item>
- <item>Create initial surface 120s</item>
- <item>Topology correction: 142s</item>
- <item>Surface refinement: 162s</item>
- <item>Reduction of surface collisions with optimization: 121s</item>
- <item>Spherical mapping with areal smoothing 170s</item>
- <item>Spherical registration 356s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6355 0.6546 mm</item>
- <item>Surface intensity / position RMSE: 0.0796 / 0.0854</item>
- <item>Euler number / defect number / defect size: 30.0 / 20.0 / 0.85%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/surf/lh.thickness.sub-0025263_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/surf/rh.thickness.sub-0025263_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/sub-0025263_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2551s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 29s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 20s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 23s</item>
- <item>ROI estimation of 'mori' atlas 17s</item>
- <item>ROI estimation of 'anatomy3' atlas 25s</item>
- <item>ROI estimation of 'julichbrain' atlas 33s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 8s</item>
- <item>343s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/report/catreport_sub-0025263_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 67 minute(s) and 8 second(s).</item>
- <item>Image Quality Rating (IQR): 82.15% (B-)</item>
- <item>GM volume (GMV): 55.58% (932.78 / 1678.20 ml)</item>
- <item>GM thickness (GMT): 2.63 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_110230/ds/UPSM_1/sub-0025263/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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