podismine / falff_cifti

This includes code to calculates fALFF.

fractional Amplitude Low Frequency Fluctuations (fALFF)

Delaney Johnston April 2019

Running ciftify_clean_img.py and falff_nifti.py script on data using cleaned_and_falff_practice.sh

cleaned_and_falff_practice.sh

Module load python and connectome-workbench. Input the following to cleaned_and_falff_practice.sh: a directory for fMRI pre-processed dtseries.nii files (fMRIprep), an output directory for the calculated falff values, and a file with the chosen configurations. Clean output files from ciftify_clean_img.py will be inputted to falff_nifti.py and saved in the given output directory as dscalar.nii falff files.

For Example: './cleaned_and_falff_practice.sh /scratch/colin/MST_open/fmriprep_ciftify /scratch/djohnston/faLFF/practice /scratch/djohnston/faLFF/MST_study/prefALFF_globalsignal.json'

Options for the falff_nifti.py script can be entered by editing the cleaned_and_falff_practice.sh script following the docopt options.

Running pre- and post-treatment difference calculation using prepost_scan_diff.sh

prepost_scan_diff.sh

Module load connectome_workbench. Input the following: an output directory for difference values and an input pre- and post-treatment scan directory. The scan directory must contain variable x as the post-treatment (ses-02) scan dscalar.nii falff file and variable y as the pre-treatment (ses-01) scan dscalar.nii falff file.