- Preprocessing Pipeline
- AFNI
- nifti_to_afni_conversion.txt: command line codes to convert between BRIK/HEAD and NIFTI files
- template_afni_proc.py: afni's default pre-processing pipeline template structure, would probably work well with human brains
- Mask_maker
- model_2d_contrast_full_2.h5: deep learning model to generate masks for mice structural images
- T1_RARE_mask_maker.py: code to run the masking model
- binarizer.py: erode and dilate mask to clean it up
- pipeline.py: full pre-processing pipeline from start to finish ***
- random
- collect_filenames.py: collects all filenames in a folder
- graymatter.py: generates gray matter mask from csf, wm, and atlas masks
- restack_slices.py: takes fMRI 3D Volumes and restacks into 4D NIFTI
- separate_slices.py: takes fMRI 4D NIFTI and breaks down into 3D volumes
- T1_resampler.py: resamples T1 images to 0.3mm^3 resolution
- AFNI
- Analysis
- melodic.py: code to run FSL Melodic from terminal (important for mice since it can bypass masking step)
- gift_setup.py: sets up files and filenames for Group ICA of fMRI Toolbox to organize better (important because subjects need to be in their own folder)
- conn_setup.py: sets up files and filenames for Conn Toolbox (*** INCOMPLETE ***)
- batch_test.m: sets up conn to run. Run file in matlab, type conn_batch(BATCH) in matlab terminal, open conn and open project
- NyquistGhost: document containing nyquist ghost research, papers, links to githubs of codes. (Minnesota code is of interest)
- Archive: unnecessary or incomplete scripts
- conn_setup.py: sets up files and filenames for Conn Toolbox (*** INCOMPLETE ***)
- apply_mask.py: applies mask by multiplication between 2 nifti files (*** already part of pipeline.py ***)
- echo_extracting.py: extracts the first of 3 echos of a 4D image and removes the first 4 of those echos (*** already part of pipeline.py ***)
- register_volumes_and_combine.py: registers volumes using ANTs (*** already part of pipeline.py ***)