Difference between revisions of "AnalysisGuidelines"

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Anatomy Processing:
---Anatomy Processing:---
The MRI processing starts with anat+orig.BRIK and anat+orig.HEAD format. The datasets are opened using AFNI
The MRI processing starts with anat+orig.BRIK and anat+orig.HEAD format. The datasets are opened using AFNI


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



Revision as of 09:37, 10 October 2019

UNDER CONSTRUCTION
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

fiddist.py fiddist2.py - 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