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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>
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- <LASstr>0.5</LASstr>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
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- <species>human</species>
- <APP>1070</APP>
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- <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>
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- <reduce_mesh>1</reduce_mesh>
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- <add_parahipp>0.1</add_parahipp>
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- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</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>
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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>
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- <td>
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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>
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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/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>
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- <td>
- <item>gm</item>
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- </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/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>
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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>
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- <td>[false]</td>
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- <tr>
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- <td>1</td>
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- <td>1</td>
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- <tr>
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- <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>
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- <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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- <td>Schaefer2018_400P_17N</td>
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- <td>1</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>
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- </satlas>
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- <VT>15</VT>
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- <PH>25</PH>
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- <shooting>
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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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- <tissue_mnr>[0.00803056452423334 0.225207269191742 0.668712496757507 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[0.883695637897547 22.0987150126767 18.5950709073844 10.4127412576801]</tissue_std>
- <tissue_stdr>[0.00481752539053559 0.120472609996796 0.101372264325619 0.0567657500505447]</tissue_stdr>
- <contrast>61.7571334838867</contrast>
- <contrastr>0.333969444036484</contrastr>
- <NCR>0.13411471247673</NCR>
- <ICR>0.197414100170135</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[6.90941143035889 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.62046815363214 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.07379150390625</contrastr>
- <NCR>2.25631237030029</NCR>
- <ICR>0.949439704418182</ICR>
- <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
- <SurfaceDefectArea>1.19145448954697</SurfaceDefectArea>
- <SurfaceDefectNumber>1.725</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31354284286499</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.34921097755432</SurfacePositionRMSE>
- <IQR>2.15426370593162</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>20220711-083601</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.765817958187874</SurfaceDefectArea>
- <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0656771436333656</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0674605518579483</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>20</EC_abs>
- <defect_size>0.765817958187874</defect_size>
- <vol_abs_CGW>[336.293062745098 776.311019607843 609.584 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.56312156862745</vol_abs_WMH>
- <vol_rel_WMH>0.000907636967555736</vol_rel_WMH>
- <surf_TSA>2244.55589177616</surf_TSA>
- <vol_TIV>1722.18808235294</vol_TIV>
- <vol_rel_CGW>[0.195270810540994 0.450770172876361 0.353959016582646 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.47842888945756 0.56450019206823]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.48036193847656 0.674593755033188 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92730198582918 0.229484733206476 0.281251547651147;2.49166121162045 0.158325825761658 0.448117230791242;3.07171755623718 0.246530228296586 0.270631221557611]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.939200220066074 0.334703515001377 0.526520681265207;3.99490267122065 0.375430917062598 0.473479318734793]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>3.11209642410874</vol_TIV>
- <vol_rel_CGW>[1.35687518931382 5.94558500137142 4.20687888977453 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.09076369675557</vol_rel_WMH>
- <surf_TSA>8.62395713947362</surf_TSA>
- <SQR>4.89926995767894</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.0845044685132576 33 30003 9899.656 0.415705811666974]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00365197705104947 0.002291155513376 0.348032206296921]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[928.800592156863 550.110239215686 559.464341176471 512.756843137255 1813.83823921569 6947.51716862745]</SPMvols0>
- <SPMvols1>[811.589694117647 520.766568627451 349.908733333333 582.294047058823 1701.56876078431 6847.35935294118]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[52.0023002624512 130.393707275391 183.585693359375]</T3th>
- <Tth>
- <T3th>[0 0 3.97684144973755 52.0023002624512 130.393707275391 183.585693359375 249.377380371094 570.131958007812]</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>[0.0194619577378035 0.0665414929389954 0.072764091193676 0 0]</dtc>
- <ll>[0.0823836675783595 0 0.0823836675783595 0;0.201185906491503 0.00907849406852585 0.210264400560029 1935.970703125;0.201185906491503 0.00907849406852585 0.210264400560029 1935.970703125]</ll>
- <rmsdtc>[0.0439789965748787 0.0869856402277946 0.0975279361009598]</rmsdtc>
- <rmsgdt>[0.0316260904073715 0.0419409163296223 0.0526705421507359]</rmsgdt>
- <rmsdt>0.0975279361009598</rmsdt>
- <dt>0.072764091193676</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>[0.00881633348762989 0.0313978344202042 0.0440343096852303 0.0525496043264866 0.0589997060596943 0.0658979192376137]</dtc>
- <ll>[0.0828706296172034 0 0.0828706296172034 0;0.221044597069597 0.0116038928952991 0.232648489964896 5939.74267578125;0.20284860906168 0.0152437629782816 0.218092372039962 10971.119140625;0.182705885551141 0.0181620490064195 0.200867934557561 19583.62890625;0.165178193737913 0.0215743111524661 0.186752504890379 37741.0859375;0.165178193737913 0.0215743111524661 0.186752504890379 37741.0859375]</ll>
- <rmsdtc>[0.0104473512619734 0.0370617769658566 0.055231723934412 0.0798491984605789 0.103310897946358 0.110129438340664]</rmsdtc>
- <rmsgdt>[0.00303274835459888 0.011757455766201 0.0267752539366484 0.0471682883799076 0.0649614185094833 0.0701029524207115]</rmsgdt>
- <rmsdt>0.110129438340664</rmsdt>
- <dt>0.0658979192376137</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_24738/ds/sub-23/sub-23_ses-01_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 43s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 6s</item>
- <item>38s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 14s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 65s</item>
- <item>SPM preprocessing 1 (estimate 2): 65s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 17s</item>
- <item>Update Segmentation 19s</item>
- <item>Update Skull-Stripping 38s</item>
- <item>Update probability maps 8s</item>
- <item>82s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 12s</item>
- <item>Fast Optimized Shooting registration 30s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.08) 15s</item>
- <item>Estimate local tissue thresholds (WM) 18s</item>
- <item>Estimate local tissue thresholds (GM) 26s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 34s</item>
- <item>101s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 16s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 32s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>79s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 36s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.04]</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) 2s</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 | 0.0829 0.0000 0.0829 | 32.0000</item>
- <item>2 | 2.50 | 0.0807 0.0011 0.0817 | 29.4886</item>
- <item>3 | 2.50 | 0.0801 0.0016 0.0816 | 26.9772</item>
- <item>4 | 2.50 | 0.0797 0.0018 0.0815 | 24.6107</item>
- <item>5 | 2.50 | 0.0795 0.0019 0.0814 | 22.6548</item>
- <item>6 | 2.50 | 0.0792 0.0020 0.0812 | 20.6989</item>
- <item>7 | 2.50 | 0.0790 0.0021 0.0811 | 18.9688</item>
- <item>8 | 2.50 | 0.0788 0.0021 0.0809 | 17.4455</item>
- <item>9 | 2.50 | 0.0785 0.0022 0.0807 | 15.9223</item>
- <item>10 | 2.50 | 0.0782 0.0023 0.0805 | 14.6627</item>
- <item>11 | 2.50 | 0.0780 0.0024 0.0803 | 13.4764</item>
- <item>12 | 2.50 | 0.0777 0.0024 0.0801 | 12.3015</item>
- <item>13 | 2.50 | 0.0774 0.0025 0.0799 | 11.3776</item>
- <item>14 | 2.50 | 0.0771 0.0025 0.0797 | 10.4537</item>
- <item>15 | 2.25 | 0.0763 0.0026 0.0789 | 9.5920</item>
- <item>16 | 2.25 | 0.0737 0.0039 0.0775 | 8.8725</item>
- <item>29 | 2.00 | 0.0754 0.0017 0.0771 | 3.3283</item>
- <item>30 | 2.00 | 0.0696 0.0041 0.0737 | 3.1221</item>
- <item>31 | 2.00 | 0.0676 0.0051 0.0727 | 2.9160</item>
- <item>43 | 1.75 | 0.0667 0.0029 0.0696 | 1.5785</item>
- <item>44 | 1.75 | 0.0624 0.0052 0.0676 | 1.5194</item>
- <item>45 | 1.75 | 0.0609 0.0061 0.0670 | 1.4626</item>
- <item>57 | 1.50 | 0.0594 0.0044 0.0638 | 1.0900</item>
- <item>58 | 1.50 | 0.0561 0.0065 0.0627 | 1.0730</item>
- <item>59 | 1.50 | 0.0551 0.0072 0.0623 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 165s</item>
- <item>Prepare output 11s</item>
- <item>176s</item>
- <item>Jacobian determinant (RMS): 0.010 0.037 0.055 0.080 0.103 | 0.110129</item>
- <item>Template Matching: 0.083 0.221 0.203 0.183 0.165 | 0.165178</item>
- <item>Write result maps: 24s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 41s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 48s</item>
- <item>113s</item>
- <item>Create initial surface 86s</item>
- <item>Topology correction: 112s</item>
- <item>Surface refinement: 115s</item>
- <item>Reduction of surface collisions with optimization: 93s</item>
- <item>Spherical mapping with areal smoothing 119s</item>
- <item>Spherical registration 306s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 44s</item>
- <item>CSF distance: 19s</item>
- <item>PBT2x thickness: 50s</item>
- <item>119s</item>
- <item>Create initial surface 86s</item>
- <item>Topology correction: 108s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 89s</item>
- <item>Spherical mapping with areal smoothing 101s</item>
- <item>Spherical registration 311s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4785 0.5645 mm</item>
- <item>Surface intensity / position RMSE: 0.0657 / 0.0675</item>
- <item>Euler number / defect number / defect size: 20.0 / 14.5 / 0.77%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_24738/ds/sub-23/surf/lh.thickness.sub-23_ses-01_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_24738/ds/sub-23/surf/rh.thickness.sub-23_ses-01_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_24738/ds/sub-23/sub-23_ses-01_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1942s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 28s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 16s</item>
- <item>ROI estimation of 'anatomy3' atlas 23s</item>
- <item>ROI estimation of 'julichbrain' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s</item>
- <item>Write results 71s</item>
- <item>302s</item>
- <item>Quality check: 5s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_24738/ds/sub-23/report/catreport_sub-23_ses-01_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 52 minute(s) and 13 second(s).</item>
- <item>Image Quality Rating (IQR): 83.46% (B)</item>
- <item>GM volume (GMV): 45.08% (776.31 / 1722.19 ml)</item>
- <item>GM thickness (GMT): 2.48 0.56 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_24738/ds/sub-23/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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