Adding T2s and TE-dependence outputs

README.md

@@ -1,6 +1,11 @@
 # Multi-echo ICA (ME-ICA) Processing of fMRI Data
 
-⚠️ **PLEASE NOTE** This code base is currently unmaintained. No new feature enhancements or bug fixes will be considered at this time.
+⚠️ **As of 5/18/22**, this repository has been unarchived to allow some maintenance of this codebase. While [tedana](https://fmriprep.readthedocs.io) and [fMRIPrep](https://fmriprep.readthedocs.io) provide the future-facing implementations of ME-ICA, there are still users of meica.py who would benefit from a maintened version. Reasons include continuity of existing workflows, reproducing preprocessing etc. Updates will include migration of all modules (meica.py, t2smap.py, etc) to Python 3, interaction with afni, general bug fixes. In addition, the outputs of meica.py (in this package) are compatible with tedana, which will hopefully ease transitions.
+
+**Note** that [tedana](https://fmriprep.readthedocs.io) is faster, is built according to test-driven development and distribution, has many developers, has more PCA options that may be have fewer convergence issues, and produces pretty reports. Otherwise, the ICA component outputs between these packages correspond well with each other in normative datasets.
+
+~~This code base is currently unmaintained. No new feature enhancements or bug fixes will be considered at this time.
+⚠️ **PLEASE NOTE** This code base is currently unmaintained. No new feature enhancements or bug fixes will be considered at this time.~~
 
 We encourage prospective users to instead consider [tedana](https://tedana.readthedocs.io),
 which maintains and extends many of the multi-echo-specific features of ME-ICA.
@@ -24,16 +29,16 @@ Install Python and other dependencies. If you have AFNI installed and on your pa
 
 # Important Files and Directories
 
-- `meica.py` : a master script that performs preprocessing and calls the ICA/TE-dependence analysis script `tedana.py`
+- `meica.py` : a master script that performs preprocessing and calls the ICA/TE-dependence analysis script `lib_tedana.py`
 - `meica.libs` : a folder that includes utility functions for TE-dependence analysis for denoising and anatomical-functional co-registration
-- `meica.libs/tedana.py` : performs ICA and TE-dependence calculations
+- `meica.libs/lib_tedana.py` : performs ICA and TE-dependence calculations
 
 # Usage
 
 fMRI data is called: 		rest_e1.nii.gz, rest_e2.nii.gz, rest_e3.nii.gz, etc. 
 Anatomical is:		mprage.nii.gz
 
-meica.py and tedana.py have a number of options which you can view using the -h flag. 
+meica.py and lib_tedana.py have a number of options which you can view using the -h flag. 
 
 Here's an example use: