Difference between revisions of "AnalysisGuidelines"
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'''Jupyter Notebook Over a Remote Connection''' |
'''Jupyter Notebook Over a Remote Connection'''<br> |
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Run one terminal to start the notebook: |
1) Run one terminal to start the notebook: |
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ssh $USER@$REMOTE_HOST |
ssh $USER@$REMOTE_HOST |
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cd $FOLDER_WITH_CODE |
cd $FOLDER_WITH_CODE |
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jupyter notebook --no-browser --port=8887 |
jupyter notebook --no-browser --port=8887 |
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Run another terminal to forward the port to your local machine |
2) Run another terminal to forward the port to your local machine<br> |
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(Replace User and Remote_Host with the appropriate username and ip-address) |
<em>(Replace User and Remote_Host with the appropriate username and ip-address)</em> |
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ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST |
ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST |
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Revision as of 09:54, 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
1) 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
2) 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)