Streamlined and improved. Cluster masks now output with peak coordinate in name.
Small function. Gives mean across ResMS image.
Made meanResMS more general.
Clean up.
Improved documentation and did some light refactoring.
Added roi-to-roi functionality to newLSS_correlation and improved overwriting in generate_spm_singletrial_newLSS. I still don't know how to analyze roi-to-roi results properly, so that hasn't been added yet.
Improved handling of Rissman processing and analysis. I think it's pretty much set short of real roi2roi analysis.
Added erode_image to threshold and erode nifti images.
Update README.md

Formatted README.md to include future improvements for the scripts.
save_clusters_and_effect_size now allows for cluster-extent based thresholding.
It relies on spm_list_edited.
batch_effect_size is an example script to call save_clusters_and_effect_size.
Merge branch 'master' of https://github.com/tsalo/Misc_fMRI_code
Updating generate_spm_singletrial_newLSS and save_clusters_and_effect_size.
Cleaned up spm_list_edited a bit. Also it should now be easier to reorganize the output csv if you want it in a different format.
Fixed some errors with Rissman (multi-regressor) beta series method.
Replaced a bunch of subfunctions with calls to spm_summarise.
Replaced a couple of subfunctions with calls to spm_summarise.
Updated the docstring.
Update erode_image to return the name of the eroded file.
Merge branch 'master' of https://github.com/tsalo/Misc_fMRI_code
It would appear that spm_summarise does not take into header differences into account, while custom functions adjustXyz and roiFindIndex do.