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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>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
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- <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>
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- <reduce_mesh>1</reduce_mesh>
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- <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>
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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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- <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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- <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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- <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_2614792/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- </atlas>
- <satlas>
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- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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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>
- </LAB>
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- <shooting>
- <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>0.695065669883862</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0699174702167511</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0662471130490303</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>179.664123535156</res_BB>
- <tissue_mn>[157.591003417969 484.747985839844 1455.15905761719 2354.53393554688]</tissue_mn>
- <tissue_mnr>[0.0669308677315712 0.205878525972366 0.618024230003357 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[62.5839462324004 251.099290096176 257.469483033659 167.9826998761]</tissue_std>
- <tissue_stdr>[0.0284868329763412 0.114294864237309 0.117194436490536 0.076462022960186]</tissue_stdr>
- <contrast>827.520263671875</contrast>
- <contrastr>0.351458191871643</contrastr>
- <res_ECR>0.365829586982727</res_ECR>
- <NCR>0.138422936201096</NCR>
- <ICR>0.269352346658707</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.76443672180176</res_ECR>
- <res_BB>10.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.81146049499512</contrastr>
- <NCR>2.3181586265564</NCR>
- <ICR>1.12785804271698</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.17376641747097</SurfaceDefectArea>
- <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.39834940433502</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.32494223117828</SurfacePositionRMSE>
- <SIQR>2.49471126349515</SIQR>
- <IQR>2.19810062100938</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>20231031-010629</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.695065669883862</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0699174702167511</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0662471130490303</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.695065669883862</defect_size>
- <vol_abs_CGW>[223.819054901961 712.876529411765 471.479145098039 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.625937254901961</vol_abs_WMH>
- <vol_rel_WMH>0.000444502547750898</vol_rel_WMH>
- <surf_TSA>1960.17363272816</surf_TSA>
- <vol_TIV>1408.17472941176</vol_TIV>
- <vol_rel_CGW>[0.158942672544235 0.506241529919766 0.334815797535999 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51363360844763 0.598489870441727]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.49590229988098 0.672994043349358 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95833457315224 0.23670128154045 0.306376787548896;2.52678044960012 0.168101392229013 0.423396231231135;3.1681516460604 0.246620370740116 0.270226981219968]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.971495213758464 0.332350896711839 0.558461538461538;3.9940327870675 0.296702415103349 0.441538461538462]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00159196800515</vol_TIV>
- <vol_rel_CGW>[0.704430182188128 6.94183782183488 3.86307107643676 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04445025477509</vol_rel_WMH>
- <surf_TSA>8.6194034803889</surf_TSA>
- <SQR>5.68329539750809</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10223.616 0.469692478191449]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00173785339575261 0.00140146375633776 0.0695394054055214]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[885.192101960784 409.540098039216 381.736188235294 537.775505882353 960.622294117647 7570.74124705882]</SPMvols0>
- <SPMvols1>[771.960576470588 382.27442745098 221.577133333333 473.516537254902 778.060431372549 7596.25390588235]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[554.095092773438 1558.49267578125 2351.75927734375]</T3th>
- <Tth>
- <T3th>[-30.2894306182861 -30.2894325256348 57.7874946594238 554.095092773438 1558.49267578125 2351.75927734375 3250.59130859375 9833.5595703125]</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>[0.0208398979157209 0.0699876993894577 0.0773398503661156 0 0]</dtc>
- <ll>[0.0854677198027649 0 0.0854677198027649 0;0.205335033183195 0.0100155597975274 0.215350592980723 2135.79809570312;0.205335033183195 0.0100155597975274 0.215350592980723 2135.79809570312]</ll>
- <rmsdtc>[0.0445536188781261 0.0941131338477135 0.105756007134914]</rmsdtc>
- <rmsgdt>[0.0316415391862392 0.0465007796883583 0.0579667165875435]</rmsgdt>
- <rmsdt>0.105756007134914</rmsdt>
- <dt>0.0773398503661156</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>[0.00983836408704519 0.0396578013896942 0.0489608459174633 0.0575310289859772 0.0648753792047501 0.0725372135639191]</dtc>
- <ll>[0.0873343129750773 0 0.0873343129750773 0;0.22454594017094 0.0161269707722833 0.240672910943223 8254.9931640625;0.211216800088091 0.017059764443972 0.228276564532063 12278.1171875;0.191802094578177 0.018936649913009 0.210738744491186 20418.859375;0.175177336992591 0.0223083526273714 0.197485689619962 39025.18359375;0.175177336992591 0.0223083526273714 0.197485689619962 39025.18359375]</ll>
- <rmsdtc>[0.0114713348448277 0.0402936972677708 0.0615285150706768 0.0841475278139114 0.108518324792385 0.115462750196457]</rmsdtc>
- <rmsgdt>[0.00316105014644563 0.012331641279161 0.0278472229838371 0.0487947165966034 0.0687777176499367 0.074979193508625]</rmsgdt>
- <rmsdt>0.115462750196457</rmsdt>
- <dt>0.0725372135639191</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027267/ses-2/sub-0027267_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 59s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>31s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 64s</item>
- <item>SPM preprocessing 1 (estimate 2): 52s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 34s</item>
- <item>Update probability maps 7s</item>
- <item>73s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 25s</item>
- <item>Fast Optimized Shooting registration 30s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 13s</item>
- <item>Estimate local tissue thresholds (WM) 16s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 36s</item>
- <item>98s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 15s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 22s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>64s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>11s</item>
- <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
- <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
- <item>1 | 2.50 | 0.0873 0.0000 0.0873 | 32.0000</item>
- <item>2 | 2.50 | 0.0847 0.0012 0.0859 | 29.4886</item>
- <item>3 | 2.50 | 0.0839 0.0018 0.0857 | 26.9772</item>
- <item>4 | 2.50 | 0.0835 0.0020 0.0856 | 24.6107</item>
- <item>5 | 2.50 | 0.0832 0.0022 0.0854 | 22.6548</item>
- <item>6 | 2.50 | 0.0830 0.0023 0.0852 | 20.6989</item>
- <item>7 | 2.50 | 0.0827 0.0024 0.0850 | 18.9688</item>
- <item>8 | 2.50 | 0.0824 0.0025 0.0849 | 17.4455</item>
- <item>9 | 2.50 | 0.0821 0.0025 0.0846 | 15.9223</item>
- <item>10 | 2.50 | 0.0818 0.0026 0.0844 | 14.6627</item>
- <item>11 | 2.50 | 0.0815 0.0027 0.0842 | 13.4764</item>
- <item>12 | 2.50 | 0.0812 0.0028 0.0839 | 12.3015</item>
- <item>13 | 2.50 | 0.0808 0.0029 0.0837 | 11.3776</item>
- <item>14 | 2.50 | 0.0805 0.0030 0.0835 | 10.4537</item>
- <item>15 | 2.25 | 0.0805 0.0030 0.0835 | 9.5920</item>
- <item>16 | 2.25 | 0.0774 0.0045 0.0819 | 8.8725</item>
- <item>17 | 2.25 | 0.0762 0.0051 0.0812 | 8.1530</item>
- <item>18 | 2.25 | 0.0754 0.0053 0.0807 | 7.5234</item>
- <item>19 | 2.25 | 0.0748 0.0054 0.0802 | 6.9630</item>
- <item>29 | 2.00 | 0.0768 0.0027 0.0795 | 3.3283</item>
- <item>30 | 2.00 | 0.0720 0.0049 0.0769 | 3.1221</item>
- <item>31 | 2.00 | 0.0704 0.0057 0.0761 | 2.9160</item>
- <item>43 | 1.75 | 0.0696 0.0032 0.0729 | 1.5785</item>
- <item>44 | 1.75 | 0.0654 0.0055 0.0709 | 1.5194</item>
- <item>45 | 1.75 | 0.0639 0.0063 0.0702 | 1.4626</item>
- <item>57 | 1.50 | 0.0628 0.0046 0.0673 | 1.0900</item>
- <item>58 | 1.50 | 0.0595 0.0067 0.0662 | 1.0730</item>
- <item>59 | 1.50 | 0.0584 0.0074 0.0658 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 176s</item>
- <item>Prepare output 10s</item>
- <item>186s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.062 0.084 0.109 | 0.115463</item>
- <item>Template Matching: 0.087 0.225 0.211 0.192 0.175 | 0.175177</item>
- <item>Write result maps: 32s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 28s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 46s</item>
- <item>96s</item>
- <item>Create initial surface 90s</item>
- <item>Topology correction: 95s</item>
- <item>Surface refinement: 98s</item>
- <item>Reduction of surface collisions with optimization: 70s</item>
- <item>Spherical mapping with areal smoothing 81s</item>
- <item>Spherical registration 296s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 45s</item>
- <item>96s</item>
- <item>Create initial surface 87s</item>
- <item>Topology correction: 92s</item>
- <item>Surface refinement: 103s</item>
- <item>Reduction of surface collisions with optimization: 66s</item>
- <item>Spherical mapping with areal smoothing 78s</item>
- <item>Spherical registration 293s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5136 0.5985 mm</item>
- <item>Surface intensity / position RMSE: 0.0699 / 0.0662</item>
- <item>Euler number / defect number / defect size: 30.0 / 15.5 / 0.70%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/surf/lh.thickness.sub-0027267_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/surf/rh.thickness.sub-0027267_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/sub-0027267_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1734s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 20s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 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 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>349s</item>
- <item>Quality check: 12s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/report/catreport_sub-0027267_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 49 minute(s) and 15 second(s).</item>
- <item>Image Quality Rating (IQR): 83.02% (B-)</item>
- <item>GM volume (GMV): 50.62% (712.88 / 1408.17 ml)</item>
- <item>GM thickness (GMT): 2.51 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|