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- <parameter>
- <opts>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
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- <extopts>
- <uhrlim>1.4</uhrlim>
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- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
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- <WMHC>2</WMHC>
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- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
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- <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>
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- </darteltpm>
- <shootingtpm>
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- </shootingtpm>
- <shootingT1>
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- </shootingT1>
- <brainmask>
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- </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>
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- <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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
- <item>gm</item>
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- <td>[false]</td>
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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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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <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>
- <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>[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>
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- <item>gm</item>
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- <td>[false]</td>
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- <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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- <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>
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- <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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- <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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- <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>
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- <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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- <VT>15</VT>
- <NV>17</NV>
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- <PH>25</PH>
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- <new_release>0</new_release>
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- <shootingtpm>
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- <regstr>0.5</regstr>
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- <optimal>[1 0.3]</optimal>
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- </shootingtpms>
- <templates>
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- <qualitymeasures>
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- <res_BB>0</res_BB>
- <tissue_mn>[2.43899989128113 15.0693216323853 32.7620124816895 58.0107345581055]</tissue_mn>
- <tissue_mnr>[0.0420439392328262 0.259767800569534 0.564757764339447 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[0.941081924442843 9.29594843677101 7.80144577696309 5.54032239780167]</tissue_std>
- <tissue_stdr>[0.0169345419853926 0.167278349399567 0.140385136008263 0.0996967703104019]</tissue_stdr>
- <contrast>19.8666114807129</contrast>
- <contrastr>0.34246438741684</contrastr>
- <NCR>0.160419374704361</NCR>
- <ICR>0.503833889961243</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.875 1.79998779296875 1.875]</res_vx_vol>
- <res_RMS>1.85033384869114</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.57201290130615 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.62289888709515 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.94636750221252</contrastr>
- <NCR>2.63392734527588</NCR>
- <ICR>1.70940947532654</ICR>
- <SurfaceEulerNumber>3.14285714285714</SurfaceEulerNumber>
- <SurfaceDefectArea>1.26742629440607</SurfaceDefectArea>
- <SurfaceDefectNumber>2.075</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.60765528678894</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.72290420532227</SurfacePositionRMSE>
- <IQR>2.43278216402703</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220709-125143</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>44</SurfaceEulerNumber>
- <SurfaceDefectArea>1.06970517762426</SurfaceDefectArea>
- <SurfaceDefectNumber>21.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.080382764339447</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.086145207285881</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>44</EC_abs>
- <defect_size>1.06970517762426</defect_size>
- <vol_abs_CGW>[157.516329974497 677.899273763895 430.138196200132 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.365843796519672</vol_abs_WMH>
- <vol_rel_WMH>0.000289078027767325</vol_rel_WMH>
- <surf_TSA>1885.064075143</surf_TSA>
- <vol_TIV>1265.55379993852</vol_TIV>
- <vol_rel_CGW>[0.124464349111155 0.535654251756681 0.339881399132164 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50982102414076 0.615866785871276]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.52398061752319 0.744359482951312 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92852237430957 0.248119353624195 0.290930910337734;2.53064826767343 0.171569763886196 0.408023315618035;3.14913295708107 0.249052908931841 0.301045774044231]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.848679142264228 0.331594317637898 0.617234281437126;4.05624349313679 0.349587786911708 0.382765718562874]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.41871811918909</vol_TIV>
- <vol_rel_CGW>[0.5 7.47008354448063 3.95404811659777 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02890780277673</vol_rel_WMH>
- <surf_TSA>8.61093142321995</surf_TSA>
- <SQR>6.11346887123326</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.168296873569489 1 1 11037.490605703 0.57500789385964]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0432227849960327 0.0421301871538162 0.138261020183563]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[823.010375941746 385.126988816121 253.669207648074 2643.5370212346 2099.4406414113 7781.79104469811]</SPMvols0>
- <SPMvols1>[727.003528068276 358.143088288833 133.104652122575 1510.33462691851 1550.33810344282 8993.00356265903]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[14.2847995758057 37.2627983093262 56.6035003662109]</T3th>
- <Tth>
- <T3th>[0 0 2.5454409122467 14.2847995758057 37.2627983093262 56.6035003662109 77.7628479003906 214.445526123047]</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>[0.0209913719445467 0.0709104612469673 0.0782854408025742 0 0]</dtc>
- <ll>[0.0814127530895171 0 0.0814127530895171 0;0.190732536911249 0.0103208248784133 0.201053361789662 2200.89526367188;0.190732536911249 0.0103208248784133 0.201053361789662 2200.89526367188]</ll>
- <rmsdtc>[0.0446621552109718 0.0948649495840073 0.106458827853203]</rmsdtc>
- <rmsgdt>[0.0316073335707188 0.0461474843323231 0.0575036481022835]</rmsgdt>
- <rmsdt>0.106458827853203</rmsdt>
- <dt>0.0782854408025742</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>[0.00962300412356853 0.0346413739025593 0.0490411818027496 0.0582980215549469 0.0659139081835747 0.075037807226181]</dtc>
- <ll>[0.0837597511396422 0 0.0837597511396422 0;0.223352411477411 0.0136495688339438 0.237001980311355 6986.873046875;0.203890670851674 0.0171092308451158 0.22099990169679 12313.71875;0.18331296219785 0.0200015862329959 0.203314548430846 21567.150390625;0.166401788975696 0.0236569561360686 0.190058745111764 41384.3671875;0.166401788975696 0.0236569561360686 0.190058745111764 41384.3671875]</ll>
- <rmsdtc>[0.0114137604832649 0.0410135202109814 0.0626659989356995 0.0915564373135567 0.119892433285713 0.128189489245415]</rmsdtc>
- <rmsgdt>[0.00336980051361024 0.0136158913373947 0.0315055586397648 0.0558277666568756 0.077901728451252 0.0847618281841278]</rmsgdt>
- <rmsdt>0.128189489245415</rmsdt>
- <dt>0.075037807226181</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_509750/ds/sub-0737/sub-0737_ses-01_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 187s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 11s</item>
- <item>Estimate background 12s</item>
- <item>Initial correction 23s</item>
- <item>Refine background 6s</item>
- <item>Final correction 12s</item>
- <item>Final scaling 9s</item>
- <item>83s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 26s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 113s</item>
- <item>SPM preprocessing 1 (estimate 2): 89s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 28s</item>
- <item>Update Segmentation 28s</item>
- <item>Update Skull-Stripping 67s</item>
- <item>Update probability maps 14s</item>
- <item>138s</item>
- <item>Global intensity correction: 26s</item>
- <item>SANLM denoising after intensity normalization (medium): 27s</item>
- <item>Fast Optimized Shooting registration 47s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.28) 21s</item>
- <item>Estimate local tissue thresholds (WM) 30s</item>
- <item>Estimate local tissue thresholds (GM) 46s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 66s</item>
- <item>178s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 18s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 37s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 7s</item>
- <item>98s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 42s</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 | 0.0838 0.0000 0.0838 | 32.0000</item>
- <item>2 | 2.50 | 0.0810 0.0012 0.0821 | 29.4886</item>
- <item>3 | 2.50 | 0.0801 0.0018 0.0820 | 26.9772</item>
- <item>4 | 2.50 | 0.0797 0.0021 0.0818 | 24.6107</item>
- <item>5 | 2.50 | 0.0794 0.0022 0.0816 | 22.6548</item>
- <item>6 | 2.50 | 0.0791 0.0023 0.0814 | 20.6989</item>
- <item>7 | 2.50 | 0.0789 0.0024 0.0813 | 18.9688</item>
- <item>8 | 2.50 | 0.0786 0.0025 0.0811 | 17.4455</item>
- <item>9 | 2.50 | 0.0783 0.0026 0.0808 | 15.9223</item>
- <item>10 | 2.50 | 0.0779 0.0027 0.0806 | 14.6627</item>
- <item>11 | 2.50 | 0.0776 0.0028 0.0804 | 13.4764</item>
- <item>12 | 2.50 | 0.0773 0.0028 0.0801 | 12.3015</item>
- <item>13 | 2.50 | 0.0770 0.0029 0.0799 | 11.3776</item>
- <item>14 | 2.50 | 0.0767 0.0030 0.0797 | 10.4537</item>
- <item>15 | 2.25 | 0.0774 0.0031 0.0805 | 9.5920</item>
- <item>16 | 2.25 | 0.0745 0.0045 0.0790 | 8.8725</item>
- <item>29 | 2.00 | 0.0765 0.0021 0.0785 | 3.3283</item>
- <item>30 | 2.00 | 0.0701 0.0047 0.0748 | 3.1221</item>
- <item>31 | 2.00 | 0.0680 0.0057 0.0737 | 2.9160</item>
- <item>43 | 1.75 | 0.0674 0.0033 0.0707 | 1.5785</item>
- <item>44 | 1.75 | 0.0627 0.0058 0.0685 | 1.5194</item>
- <item>45 | 1.75 | 0.0611 0.0067 0.0678 | 1.4626</item>
- <item>57 | 1.50 | 0.0601 0.0049 0.0650 | 1.0900</item>
- <item>58 | 1.50 | 0.0566 0.0071 0.0638 | 1.0730</item>
- <item>59 | 1.50 | 0.0555 0.0079 0.0634 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 194s</item>
- <item>Prepare output 16s</item>
- <item>211s</item>
- <item>Jacobian determinant (RMS): 0.011 0.041 0.063 0.092 0.120 | 0.128189</item>
- <item>Template Matching: 0.084 0.223 0.204 0.183 0.166 | 0.166402</item>
- <item>Write result maps: 38s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 39s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 54s</item>
- <item>119s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 113s</item>
- <item>Surface refinement: 118s</item>
- <item>Reduction of surface collisions with optimization: 75s</item>
- <item>Spherical mapping with areal smoothing 95s</item>
- <item>Spherical registration 344s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 40s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 54s</item>
- <item>120s</item>
- <item>Create initial surface 99s</item>
- <item>Topology correction: 109s</item>
- <item>Surface refinement: 79s</item>
- <item>Reduction of surface collisions with optimization: 72s</item>
- <item>Spherical mapping with areal smoothing 92s</item>
- <item>Spherical registration 336s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5101 0.6157 mm</item>
- <item>Surface intensity / position RMSE: 0.0804 / 0.0861</item>
- <item>Euler number / defect number / defect size: 44.0 / 21.5 / 1.07%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_509750/ds/sub-0737/surf/lh.thickness.sub-0737_ses-01_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_509750/ds/sub-0737/surf/rh.thickness.sub-0737_ses-01_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_509750/ds/sub-0737/sub-0737_ses-01_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 1991s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 47s</item>
- <item>ROI estimation of 'lpba40' atlas 14s</item>
- <item>ROI estimation of 'hammers' atlas 33s</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 44s</item>
- <item>ROI estimation of 'julichbrain' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 90s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 136s</item>
- <item>Write results 137s</item>
- <item>563s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_509750/ds/sub-0737/report/catreport_sub-0737_ses-01_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 66 minute(s) and 51 second(s).</item>
- <item>Image Quality Rating (IQR): 80.67% (B-)</item>
- <item>GM volume (GMV): 53.57% (677.90 / 1265.55 ml)</item>
- <item>GM thickness (GMT): 2.51 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_509750/ds/sub-0737/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_509750/ds/sub-0737/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_509750/ds/sub-0737/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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