From 1117f0480f01cb7bc5c7864beaf9f91d3f9b73b9 Mon Sep 17 00:00:00 2001 From: jstout211 Date: Fri, 12 Nov 2021 11:23:34 -0500 Subject: [PATCH] Update README.md --- README.md | 36 +++++++++++++++++++++++++++++++++++- 1 file changed, 35 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index bd32a5e..89960eb 100644 --- a/README.md +++ b/README.md @@ -1 +1,35 @@ -#Create MNE transformation matrix from NIMH MEG datasets +Create MNE transformation matrix from NIMH MEG datasets + +## Install: +```pip install git+https://github.com/nih-megcore/nih_to_mne``` + + +## Adds calc_mnetrans.py and bstags.py to the commandline + +``` +usage: calc_mnetrans.py [-h] [-subjects_dir SUBJECTS_DIR] [-anat_json ANAT_JSON] [-tagfile TAGFILE] + [-elec_txt ELEC_TXT] -subject SUBJECT [-afni_mri AFNI_MRI] + [-trans_output TRANS_OUTPUT] -dsname DSNAME [-view_coreg] + +optional arguments: + -h, --help show this help message and exit + -subjects_dir SUBJECTS_DIR + Set SUBJECTS_DIR different from the environment variable. If not set this + defaults to os.environ['SUBJECTS_DIR] + -anat_json ANAT_JSON Full path to the BIDS anatomy json file with the NAS,RPA,LPA locations + -tagfile TAGFILE Tagfile generated by bstags.py + -elec_txt ELEC_TXT Electrode text file exported from brainsight + -subject SUBJECT The freesurfer subject id. This folder is expected to be in the freesurfer + SUBJECTS_DIR + -afni_mri AFNI_MRI Provide a BRIK or HEAD file as input. Data must have the tags assigned to + the header. + -trans_output TRANS_OUTPUT + The output path for the mne trans.fif file + -dsname DSNAME CTF dataset to create the transform + -view_coreg Display the coregistration of MEG and head surface +``` + +``` +usage: bstags.py file.txt + Where file.txt is the saved electrode location output from Brainsight. +```