Difference between revisions of "AnalysisGuidelines"

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addmarkers - necessary to embed the stimulus timing into the CTF dataset
 
addmarkers - necessary to embed the stimulus timing into the CTF dataset
 
 
parsemarks - Combines markers (i.e optical and
+
parsemarks - Combines markers (i.e optical and parallel port)
   
 
newDs -f -filter processing.cfg
 
newDs -f -filter processing.cfg
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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)
  +
  +
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 jstout@ebi
  +
jupyter notebook --no-browser --port=8887

Revision as of 09:26, 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 jstout@ebi jupyter notebook --no-browser --port=8887