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- <uhrlim>1.4</uhrlim>
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- <species>human</species>
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- <darteltpm>
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- <shootingtpm>
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- <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>
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- <print>2</print>
- <fontsize>10</fontsize>
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- <tr>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
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- <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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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.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/thalamus.nii</td>
- <td>0</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>
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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/aal3.nii</td>
- <td>1</td>
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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</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/anatomy3.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/julichbrain.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_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>/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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- <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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- <td>/var/lib/condor/execute/dir_2498372/ds/code/Tian_Subcortex_S2_7T.nii</td>
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- <item>gm</item>
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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>
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- <tr>
- <td>HCP</td>
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- <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>
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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>
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- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CT>1</CT>
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- <VT>15</VT>
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- <PH>25</PH>
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- </shootingtpms>
- <templates>
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- </templates>
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- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0901422036100002</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0658014714717865</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0626552179455757</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>196.336486816406</res_BB>
- <tissue_mn>[5.23299980163574 128.442993164062 294.216003417969 423.7080078125]</tissue_mn>
- <tissue_mnr>[0.0123504856601357 0.303140342235565 0.694383859634399 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[17.3139104751548 50.9887177696639 40.4032632309705 24.849158028466]</tissue_std>
- <tissue_stdr>[0.041373822838068 0.121844120323658 0.0965488106012344 0.059380266815424]</tissue_stdr>
- <contrast>131.111297607422</contrast>
- <contrastr>0.309437841176987</contrastr>
- <res_ECR>0.301179707050323</res_ECR>
- <NCR>0.131490528583527</NCR>
- <ICR>0.306083649396896</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.43459033966064</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>3.44176578521729</contrastr>
- <NCR>2.21864080429077</NCR>
- <ICR>1.21895742416382</ICR>
- <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0225355509025</SurfaceDefectArea>
- <SurfaceDefectNumber>1.375</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31602942943573</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.25310432910919</SurfacePositionRMSE>
- <SIQR>2.26489608877138</SIQR>
- <IQR>2.12865232897676</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>20231031-000329</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0901422036100002</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0658014714717865</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0626552179455757</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>6</EC_abs>
- <defect_size>0.0901422036100002</defect_size>
- <vol_abs_CGW>[270.886039215686 698.305811764706 527.860274509804 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.327435294117647</vol_abs_WMH>
- <vol_rel_WMH>0.000218720035556832</vol_rel_WMH>
- <surf_TSA>1914.98976508111</surf_TSA>
- <vol_TIV>1497.0521254902</vol_TIV>
- <vol_rel_CGW>[0.180946297462413 0.46645390622992 0.352599796307668 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.6419220110154 0.637870255407195]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.63397789001465 0.770158198201023 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99971895499028 0.253000691707584 0.2876407663071;2.6520214182684 0.184700638483056 0.436075912857884;3.3353565920101 0.27609491206945 0.276283320835016]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.936676761018553 0.340391363589271 0.509970344616014;4.31720426255753 0.335529064437318 0.490029655383986]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.2211398537736</vol_TIV>
- <vol_rel_CGW>[1.09961022741402 6.2272612469454 4.18246760610035 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02187200355568</vol_rel_WMH>
- <surf_TSA>8.6152993568066</surf_TSA>
- <SQR>5.11833251989669</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[8.66976651278409e-08 1 1 11534.335 0.373736570729215]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00147867668420076 0.00136422412469983 0.0283231697976589]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[814.861176470588 473.781725490196 503.300643137255 481.072509803922 860.792996078431 8937.23934901961]</SPMvols0>
- <SPMvols1>[704.649396078431 446.363282352941 307.544780392157 451.769890196078 741.564176470588 8882.56471372549]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[147.252395629883 312.461212158203 412.906707763672]</T3th>
- <Tth>
- <T3th>[-6.24639987945557 -6.24639701843262 3.0160117149353 147.252395629883 312.461212158203 412.906707763672 545.73388671875 1096.24682617188]</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>[0.0201488416641951 0.0723937526345253 0.0796284154057503 0 0]</dtc>
- <ll>[0.0833484455794036 0 0.0833484455794036 0;0.195853683270183 0.0102669096508232 0.206120592921006 2189.39794921875;0.195853683270183 0.0102669096508232 0.206120592921006 2189.39794921875]</ll>
- <rmsdtc>[0.0466324836015701 0.0949714109301567 0.105817653238773]</rmsdtc>
- <rmsgdt>[0.03360341116786 0.046323262155056 0.0573064014315605]</rmsgdt>
- <rmsdt>0.105817653238773</rmsdt>
- <dt>0.0796284154057503</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>[0.00851874426007271 0.0307584367692471 0.0434228479862213 0.0510640740394592 0.0570507682859898 0.0633140429854393]</dtc>
- <ll>[0.0819777019299208 0 0.0819777019299208 0;0.213584478021978 0.0127794795482295 0.226363957570208 6541.49609375;0.191974706549286 0.015861253084133 0.207835959633419 11415.5341796875;0.172339183086457 0.0177409288890002 0.190080111975457 19129.546875;0.155635254862798 0.0203712681559982 0.176006523018796 35636.5390625;0.155635254862798 0.0203712681559982 0.176006523018796 35636.5390625]</ll>
- <rmsdtc>[0.00999971199780703 0.0358630530536175 0.0539704412221909 0.0759430453181267 0.0974519774317741 0.10378011316061]</rmsdtc>
- <rmsgdt>[0.00318766641430557 0.0123489750549197 0.0279960539191961 0.0459069013595581 0.0625855773687363 0.0675627589225769]</rmsgdt>
- <rmsdt>0.10378011316061</rmsdt>
- <dt>0.0633140429854393</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025677/ses-1/sub-0025677_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 36s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>29s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 52s</item>
- <item>SPM preprocessing 1 (estimate 2): 53s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 16s</item>
- <item>Update Skull-Stripping 33s</item>
- <item>Update probability maps 8s</item>
- <item>71s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 20s</item>
- <item>Fast Optimized Shooting registration 26s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.14) 10s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 21s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 36s</item>
- <item>90s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 8s</item>
- <item>Blood vessel detection 7s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 17s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>48s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 26s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 3s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>9s</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 | 0.0820 0.0000 0.0820 | 32.0000</item>
- <item>2 | 2.50 | 0.0795 0.0011 0.0806 | 29.4886</item>
- <item>3 | 2.50 | 0.0788 0.0017 0.0805 | 26.9772</item>
- <item>4 | 2.50 | 0.0784 0.0019 0.0803 | 24.6107</item>
- <item>5 | 2.50 | 0.0781 0.0021 0.0802 | 22.6548</item>
- <item>6 | 2.50 | 0.0778 0.0022 0.0800 | 20.6989</item>
- <item>7 | 2.50 | 0.0776 0.0023 0.0798 | 18.9688</item>
- <item>8 | 2.50 | 0.0773 0.0023 0.0796 | 17.4455</item>
- <item>9 | 2.50 | 0.0770 0.0024 0.0794 | 15.9223</item>
- <item>10 | 2.50 | 0.0767 0.0025 0.0792 | 14.6627</item>
- <item>11 | 2.50 | 0.0764 0.0026 0.0790 | 13.4764</item>
- <item>12 | 2.50 | 0.0761 0.0026 0.0787 | 12.3015</item>
- <item>13 | 2.50 | 0.0758 0.0027 0.0785 | 11.3776</item>
- <item>14 | 2.50 | 0.0755 0.0028 0.0783 | 10.4537</item>
- <item>15 | 2.25 | 0.0741 0.0028 0.0769 | 9.5920</item>
- <item>16 | 2.25 | 0.0712 0.0043 0.0755 | 8.8725</item>
- <item>29 | 2.00 | 0.0720 0.0019 0.0739 | 3.3283</item>
- <item>30 | 2.00 | 0.0659 0.0044 0.0703 | 3.1221</item>
- <item>31 | 2.00 | 0.0640 0.0053 0.0693 | 2.9160</item>
- <item>43 | 1.75 | 0.0628 0.0030 0.0659 | 1.5785</item>
- <item>44 | 1.75 | 0.0588 0.0052 0.0639 | 1.5194</item>
- <item>45 | 1.75 | 0.0574 0.0059 0.0634 | 1.4626</item>
- <item>57 | 1.50 | 0.0558 0.0043 0.0600 | 1.0900</item>
- <item>58 | 1.50 | 0.0528 0.0062 0.0590 | 1.0730</item>
- <item>59 | 1.50 | 0.0519 0.0068 0.0587 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 160s</item>
- <item>Prepare output 8s</item>
- <item>168s</item>
- <item>Jacobian determinant (RMS): 0.010 0.036 0.054 0.076 0.097 | 0.103780</item>
- <item>Template Matching: 0.082 0.214 0.192 0.172 0.156 | 0.155635</item>
- <item>Write result maps: 29s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 34s</item>
- <item>82s</item>
- <item>Create initial surface 61s</item>
- <item>Topology correction: 71s</item>
- <item>Surface refinement: 60s</item>
- <item>Reduction of surface collisions with optimization: 49s</item>
- <item>Spherical mapping with areal smoothing 60s</item>
- <item>Spherical registration 219s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 28s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 34s</item>
- <item>78s</item>
- <item>Create initial surface 60s</item>
- <item>Topology correction: 70s</item>
- <item>Surface refinement: 57s</item>
- <item>Reduction of surface collisions with optimization: 50s</item>
- <item>Spherical mapping with areal smoothing 116s</item>
- <item>Spherical registration 244s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6420 0.6378 mm</item>
- <item>Surface intensity / position RMSE: 0.0658 / 0.0627</item>
- <item>Euler number / defect number / defect size: 6.0 / 7.5 / 0.09%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/surf/lh.thickness.sub-0025677_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/surf/rh.thickness.sub-0025677_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/sub-0025677_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1360s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 25s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 93s</item>
- <item>ROI estimation of 'lpba40' atlas 27s</item>
- <item>ROI estimation of 'hammers' atlas 66s</item>
- <item>ROI estimation of 'thalamus' atlas 5s</item>
- <item>ROI estimation of 'ibsr' atlas 24s</item>
- <item>ROI estimation of 'aal3' atlas 40s</item>
- <item>ROI estimation of 'mori' atlas 58s</item>
- <item>ROI estimation of 'anatomy3' atlas 81s</item>
- <item>ROI estimation of 'julichbrain' atlas 102s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 41s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 142s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 164s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 13s</item>
- <item>Write results 15s</item>
- <item>958s</item>
- <item>Quality check: 10s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/report/catreport_sub-0025677_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 52 minute(s) and 22 second(s).</item>
- <item>Image Quality Rating (IQR): 83.71% (B)</item>
- <item>GM volume (GMV): 46.65% (698.31 / 1497.05 ml)</item>
- <item>GM thickness (GMT): 2.64 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2498372/ds/SWU_4/sub-0025677/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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