Difference between revisions of "AnalysisGuidelines"

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---Anatomy Processing:---
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'''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---
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'''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)