Difference between revisions of "AnalysisGuidelines"

From MEG Core
Jump to navigation Jump to search
m
Line 21: Line 21:




---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


Line 28: Line 28:




---Jupyter Notebook---
'''Jupyter Notebook Over a Remote Connection'''
Run one terminal to start the notebook:
Nbdime for notebook version control (a jupyter interface for git)
ssh $USER@$REMOTE_HOST
cd $FOLDER_WITH_CODE
#If necessary: conda activate $CONDA_ENV
jupyter notebook --no-browser --port=8887


Run another terminal to forward the port to your local machine
Jupyter Notebook over remote connection:
(Replace User and Remote_Host with the appropriate username and ip-address)
Run one terminal to start the notebook::
ssh $USER@$REMOTE_HOST
ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST


'''Version Control for Jupyter Notebook'''
In the remote terminal:
Nbdime for notebook version control (a jupyter interface for git)
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

Revision as of 09:47, 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 Over a Remote Connection Run one terminal to start the notebook:

 ssh $USER@$REMOTE_HOST
 cd $FOLDER_WITH_CODE
 #If necessary: conda activate $CONDA_ENV
 jupyter notebook --no-browser --port=8887

Run another terminal to forward the port to your local machine (Replace User and Remote_Host with the appropriate username and ip-address)

 ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST

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