search

cosanlab / nltools

Python toolbox for analyzing imaging data
https://nltools.org
MIT License
120 stars 42 forks source link

ttest 'permutation' question #366

Closed dabinyeum closed 3 years ago

dabinyeum commented 3 years ago

Hi all,

I have a question regarding the permutation test in the ttest function.

I was able to run and plot different thresholds of the ttests such as: Comm_v_Stat_avg_stats_unc = Comm_v_Stat_avg.ttest(threshold_dict={'unc':.001}) Comm_v_Stat_avg_stats_fdr = Comm_v_Stat_avg.ttest(threshold_dict={'fdr':.05})

I was trying to run the permutation test under the same function using this code: Comm_v_Stat_avg_stats_perm = Comm_v_Stat_avg.ttest(threshold_dict = {'permutation':'tfce', 'n_permutations':1000}) and got this error message.

Screen Shot 2021-01-11 at 4 46 22 PM

Please provide feedback as to how I can make this code run or if I did anything incorrectly. Thanks for your help!

ljchang commented 3 years ago

hi @dabinyeum, We are planning on updating that feature soon. Currently that method requires that you have the MNE package installed, which is an optional requirement. This method is fairly limited as most computers can't run this on whole brain. We are (slowly) working on adding some of the accelerated bootstrap/permutation methods

dabinyeum commented 3 years ago

hi @dabinyeum, We are planning on updating that feature soon. Currently that method requires that you have the MNE package installed, which is an optional requirement. This method is fairly limited as most computers can't run this on whole brain. We are (slowly) working on adding some of the accelerated bootstrap/permutation methods

Thank you so much for the reply!

ljchang commented 3 years ago

going to remove this now to prevent code rot.

ljchang commented 3 years ago

we have removed the MNE permutation support in #389