nltools
nltools copied to clipboard
cosanlab
Python toolbox for analyzing imaging data
HI all, I was trying both the [nltools](https://neurolearn.readthedocs.io/en/latest/_modules/nltools/data/adjacency.html#Adjacency.isc) and [Brainiak](https://brainiak.org/docs/brainiak.html#module-brainiak.isc) `brainiak.isc.bootstrap_isc` implementations of ISC, and was getting very different p-values between the two. I was running it on Discovery with...
@Marissa-Clark I think the best place to add the interpolation functionality we discussed is in the `append` or `concatenate` methods. We should have an option to interpolate voxel responses between...
issue appending (adds unwanted rows), using ver 0.3.19 code: `# add motion covariates curr_cov = covs.iloc[time1:time2, :] cov = Design_Matrix(curr_cov, sampling_freq=samp_freq) print(cov.shape) # add polynomial regressors cov_poly = cov.add_poly(order=2, include_lower=True)...
We should add this to nltools `align`. Faster and more memory efficient than ProbSRM https://arxiv.org/pdf/1909.12537.pdf. Looks like it is already implemented in Brainiak.
@ejolly It would be great if `onsets_to_dm` could automatically import a BIDS event file and create a design_matrix. It seems like it should be pretty straightforward to autodetect and read...
@ljchang One issue that's a bit annoying is we haven't enforced a particular code-formatting style for the library. We very loosely adhere to pycodestyle, but it's not consistent across the...
In the specific situation where we estimate an intercept-free regression model, our current estimate of the variance of the residuals (`np.std(res, axis=0, ddof=X.shape[1])`) is biased and will yield slightly lower...
Pretty straightforward, just test which images are multivariate outliers. I have a working example, but we just need to decide how to threshold it. ``` def mahalanobis_distance_outliers(data): '''Calculate mahalanobis distance...
Thresholding method on `Brain_Data` objects vs the `threshold` function behave differently. @ljchang is this intended behavior? For example, a common workflow is to: 1. Compute a stat map and an...
One caveat about the way we handle the 1-tailed option in our `_calc_pvalue` function is that it determines which tail (upper or lower) to compare against based on the sign...