Summary of models and ROIs 04/20/2018
PPI model is activity (how + why + risk) messages vs rest, which paralells the model used in other papers on this dataset
Seed ROIs
plotting.plot_roi('/fmriDataRaw/fmri_data_raw/DSI_test/AAL626_regions/AAL626_final_195.nii')
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plotting.plot_roi('/fmriDataRaw/fmri_data_raw/DSI_test/AAL626_regions/AAL626_final_198.nii')<nilearn.plotting.displays.OrthoSlicer at 0x7ff4e9aeb9b0>
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plotting.plot_roi('/fmriDataRaw/fmri_data_raw/DSI_test/AAL626_regions/AAL626_final_200.nii')<nilearn.plotting.displays.OrthoSlicer at 0x7ff4e98a7c88>
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plotting.plot_roi('/fmriDataRaw/fmri_data_raw/DSI_test/AAL626_regions/AAL626_final_202.nii')<nilearn.plotting.displays.OrthoSlicer at 0x7ff4e9665f60>
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Predicting sedentary change
ROI 195, sedentary
stepAIC reduced model does not contain PPI terms
ROI 198, sedentary
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_198_sed_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.183366 -0.042460 0.004484 0.037281 0.253873
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.03025 0.01503 2.013 0.04591 *
## sed_percent.pre -0.12422 0.04907 -2.531 0.01240 *
## PPI_Activity3vRest_199 -0.50332 0.28135 -1.789 0.07566 .
## PPI_Activity3vRest_237 0.45938 0.25741 1.785 0.07635 .
## PPI_Activity3vRest_286 -0.28910 0.14168 -2.041 0.04306 *
## PPI_Activity3vRest_74 -1.17379 0.44168 -2.658 0.00873 **
## PPI_Activity3vRest_76 0.47387 0.21816 2.172 0.03143 *
## PPI_Activity3vRest_79 0.73160 0.22579 3.240 0.00147 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.07062 on 149 degrees of freedom
## Multiple R-squared: 0.1208, Adjusted R-squared: 0.07953
## F-statistic: 2.926 on 7 and 149 DF, p-value: 0.006742Reduced model with PPI terms only: cross validation permutation test p<0.01
roilist=[199, 237, 286, 74, 76, 79]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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plotting.plot_prob_atlas(roi_imgs, display_mode='y')/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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ROI 200, sedentary
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_200_sed_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.196406 -0.041736 0.006236 0.035315 0.244112
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.03808 0.01504 2.531 0.01238 *
## sed_percent.pre -0.14100 0.04912 -2.871 0.00468 **
## PPI_Activity3vRest_282 -0.40224 0.20578 -1.955 0.05246 .
## PPI_Activity3vRest_77 -0.53110 0.35285 -1.505 0.13435
## PPI_Activity3vRest_78 0.46916 0.24710 1.899 0.05950 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.07178 on 152 degrees of freedom
## Multiple R-squared: 0.07342, Adjusted R-squared: 0.04904
## F-statistic: 3.011 on 4 and 152 DF, p-value: 0.02001Reduced model with PPI terms only: cross validation permutation test p<0.007
roilist=[282, 77, 78]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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ROI 202, sedentary
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_202_sed_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.22460 -0.03859 0.00778 0.03234 0.27505
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.03432 0.01454 2.359 0.01958 *
## sed_percent.pre -0.14477 0.04862 -2.977 0.00339 **
## PPI_Activity3vRest_282 -0.93828 0.32537 -2.884 0.00450 **
## PPI_Activity3vRest_314 0.84448 0.34085 2.478 0.01433 *
## PPI_Activity3vRest_81 0.78944 0.39604 1.993 0.04802 *
## PPI_Activity3vRest_84 -0.73622 0.33194 -2.218 0.02805 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.07111 on 151 degrees of freedom
## Multiple R-squared: 0.09683, Adjusted R-squared: 0.06693
## F-statistic: 3.238 on 5 and 151 DF, p-value: 0.008322Reduced model with PPI terms only: cross validation permutation test p<0.003
roilist=[282, 314,81,84]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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282 is the only ROI to come up in more than one list
plotting.plot_roi('/fmriDataRaw/fmri_data_raw/DSI_test/AAL626_regions/AAL626_final_282.nii')<nilearn.plotting.displays.OrthoSlicer at 0x7ff4f84657b8>
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Predicting mod-vig change
ROI 195, mod-vig
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_195_mod_vig_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.142547 -0.013117 -0.001390 0.009999 0.141488
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.006545 0.004388 1.491 0.13799
## mod_vig_percent.pre -0.117074 0.039456 -2.967 0.00351 **
## PPI_Activity3vRest_120 -0.312621 0.140724 -2.222 0.02783 *
## PPI_Activity3vRest_14 0.283913 0.167665 1.693 0.09250 .
## PPI_Activity3vRest_38 0.544645 0.226099 2.409 0.01723 *
## PPI_Activity3vRest_39 0.195317 0.109822 1.778 0.07738 .
## PPI_Activity3vRest_40 -0.579294 0.193129 -3.000 0.00317 **
## PPI_Activity3vRest_500 -0.250967 0.122969 -2.041 0.04304 *
## PPI_Activity3vRest_22 0.254425 0.181387 1.403 0.16281
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.02815 on 148 degrees of freedom
## Multiple R-squared: 0.1584, Adjusted R-squared: 0.1129
## F-statistic: 3.483 on 8 and 148 DF, p-value: 0.001036Reduced model with PPI terms only: cross validation permutation test p<0.082
roilist=[14,22,38,39,40,120,500]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
<nilearn.plotting.displays.ZSlicer at 0x7ff4f0a9a908>
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plotting.plot_prob_atlas(roi_imgs, display_mode='x',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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ROI 198, mod-vig
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_198_mod_vig_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.120115 -0.014638 -0.001259 0.012689 0.137839
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.007314 0.004527 1.616 0.10830
## mod_vig_percent.pre -0.110556 0.039109 -2.827 0.00536 **
## PPI_Activity3vRest_14 0.356184 0.145044 2.456 0.01523 *
## PPI_Activity3vRest_222 -0.378174 0.177486 -2.131 0.03478 *
## PPI_Activity3vRest_286 -0.158358 0.059740 -2.651 0.00891 **
## PPI_Activity3vRest_75 0.206694 0.151147 1.368 0.17355
## PPI_Activity3vRest_76 -0.162647 0.077993 -2.085 0.03876 *
## PPI_Activity3vRest_79 0.229619 0.114396 2.007 0.04656 *
## PPI_Activity3vRest_80 -0.163493 0.118073 -1.385 0.16825
## PPI_Activity3vRest_85 0.199955 0.089487 2.234 0.02696 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.02835 on 147 degrees of freedom
## Multiple R-squared: 0.152, Adjusted R-squared: 0.1001
## F-statistic: 2.928 on 9 and 147 DF, p-value: 0.003196Reduced model with PPI terms only: cross validation permutation test p<0.6
roilist=[14,75, 76, 79, 80, 85, 222, 286]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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plotting.plot_prob_atlas(roi_imgs, display_mode='x',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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ROI 14 shows up twice
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ROI 200, mod-vig
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_200_mod_vig_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.132272 -0.014836 -0.000654 0.013342 0.174073
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.007532 0.004607 1.635 0.10412
## mod_vig_percent.pre -0.106999 0.038945 -2.747 0.00674 **
## PPI_Activity3vRest_275 -0.104700 0.076499 -1.369 0.17314
## PPI_Activity3vRest_302 0.219988 0.081248 2.708 0.00756 **
## PPI_Activity3vRest_68 -0.397021 0.164331 -2.416 0.01689 *
## PPI_Activity3vRest_77 0.212676 0.095442 2.228 0.02734 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.02853 on 151 degrees of freedom
## Multiple R-squared: 0.118, Adjusted R-squared: 0.08876
## F-statistic: 4.039 on 5 and 151 DF, p-value: 0.00181Reduced model with PPI terms only: cross validation permutation test p<0.004
roilist=[275,302,68,77]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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plotting.plot_prob_atlas(roi_imgs, display_mode='x',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
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ROI 202, mod-vig
summary(readRDS('~/Desktop/PA2 SF files/ReducedModel_202_mod_vig_percent.rds'))##
## Call:
## lm(formula = formula(PPIFormula), data = mydata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.141385 -0.014144 -0.000863 0.012390 0.104721
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.007291 0.004069 1.792 0.075322 .
## mod_vig_percent.pre -0.122422 0.035693 -3.430 0.000791 ***
## PPI_Activity3vRest_240 0.562694 0.156458 3.596 0.000444 ***
## PPI_Activity3vRest_245 -0.595136 0.150973 -3.942 0.000126 ***
## PPI_Activity3vRest_253 -0.408683 0.143412 -2.850 0.005028 **
## PPI_Activity3vRest_286 -0.366784 0.131932 -2.780 0.006171 **
## PPI_Activity3vRest_289 -0.217004 0.107166 -2.025 0.044749 *
## PPI_Activity3vRest_297 0.210767 0.127281 1.656 0.099947 .
## PPI_Activity3vRest_305 0.591037 0.209914 2.816 0.005561 **
## PPI_Activity3vRest_307 0.199752 0.068995 2.895 0.004389 **
## PPI_Activity3vRest_49 -0.256303 0.136074 -1.884 0.061670 .
## PPI_Activity3vRest_81 0.600233 0.131965 4.548 1.15e-05 ***
## PPI_Activity3vRest_93 -0.386691 0.148681 -2.601 0.010285 *
## PPI_Activity3vRest_95 0.366534 0.216826 1.690 0.093136 .
## PPI_Activity3vRest_97 0.121129 0.080231 1.510 0.133330
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.02549 on 142 degrees of freedom
## Multiple R-squared: 0.338, Adjusted R-squared: 0.2727
## F-statistic: 5.178 on 14 and 142 DF, p-value: 8.04e-08Reduced model with PPI terms only: cross validation permutation test p<0.0001
roilist=[240,245,253,286,289,297,205,307,49,81,93,95,97]
roipathlist=[roidir+'AAL626_final_'+str(x)+'.nii' for x in roilist]
roi_imgs = image.concat_imgs(roipathlist)
plotting.plot_prob_atlas(roi_imgs, display_mode='z',colorbar=True)/usr/local/anaconda3/lib/python3.6/site-packages/numpy/ma/core.py:2766: UserWarning: Warning: converting a masked element to nan.
order=order, subok=True, ndmin=ndmin)
/usr/local/anaconda3/lib/python3.6/site-packages/matplotlib/contour.py:920: UserWarning: linewidths is ignored by contourf
warnings.warn('linewidths is ignored by contourf')
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plotting.plot_prob_atlas(roi_imgs, display_mode='x',colorbar=True)---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-1-9e95a262559a> in <module>()
----> 1 plotting.plot_prob_atlas(roi_imgs, display_mode='x',colorbar=True)
NameError: name 'plotting' is not defined