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Analysis Introduction
1) Anatomical Processing
2) MEG Trigger Configuration
3) MEG Inverse Solution (SAM software)
4) Statistical Analysis

Data collection: Exact timing of the experiment can be provided in the data acquisition or a set of smaller trials can be provided

CTF Software: DataEditor -data $DATA

thresholdDetect - Detect changes in the analog inputs to determine onset of stimulus addmarkers - necessary to embed the stimulus timing into the CTF dataset

parsemarks - Combines markers (i.e optical and parallel port)

newDs -f -filter processing.cfg

Anatomy Processing: The MRI processing starts with anat+orig.BRIK and anat+orig.HEAD format. The datasets are opened using AFNI - wrapper that accepts two inputs and provides the difference in distance (e.g. MRI and dataset)

Jupyter Notebook Nbdime for notebook version control (a jupyter interface for git)

Jupyter Notebook over remote connection: Run one terminal to start the notebook:: ssh $USER@$REMOTE_HOST

In the remote terminal: jupyter notebook --no-browser --port=8887

Run another terminal to forward the port to your local machine:: ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST jupyter notebook --no-browser --port=8887