Difference between revisions of "AnalysisGuidelines"

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(It should look like the below - only copy the portion after the token= )
 
(It should look like the below - only copy the portion after the token= )
 
http://localhost:8887/?token=####HERE_IS_THE_TOKEN_CODE---COPY_THIS_AND_PASTE_INTO_BROWSER
 
http://localhost:8887/?token=####HERE_IS_THE_TOKEN_CODE---COPY_THIS_AND_PASTE_INTO_BROWSER
  +
  +
'''Biowulf Jupyter Notebook Connection'''<br>
  +
1) Run one terminal to access the persistent biowulf node and start jupyter notebook:
  +
#Connect to login node
  +
ssh -Y $USER@biowulf.nih.gov
  +
  +
spersist #This will startup a persistent node
  +
#Alternatively if a persistent node is already running, you can ssh into the persistent node
  +
  +
#In the persistent node
  +
conda activate $CONDA_ENVIRONMENT_NAME
  +
cd $FOLDER_WITH_CODE
  +
jupyter notebook --no-browser --port=8887
  +
  +
2) Run another terminal to forward the port to your local machine<br>
  +
<em>(Replace User and Remote_Host with the appropriate username and ip-address)</em>
  +
<em>(This is a two step process, the notebook port is sent to biowulf first, then to your local computer)</em>
  +
ssh -L localhost:8888:localhost:8888 $USER@biowulf.nih.gov
  +
#In the same ssh terminal from the line above this one, type the following
  +
ssh -N -L localhost:8888:localhost:8887 $USER@$PERSISTENT_NODE
  +
  +
3) In Firefox/Chrome/Etc - Log into localhost:8888 <br>
  +
This will prompt you for a token<br>
  +
<br>
  +
4) In the password/token column, copy the token created in the first terminal<br>
  +
(It should look like the below - only copy the portion after the token= )
  +
http://localhost:8887/?token=####HERE_IS_THE_TOKEN_CODE---COPY_THIS_AND_PASTE_INTO_BROWSER
  +
  +
   
 
'''Version Control for Jupyter Notebook'''
 
'''Version Control for Jupyter Notebook'''

Revision as of 09:41, 16 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 -Y $USER@$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

3) In Firefox/Chrome/Etc - Log into localhost:8888
This will prompt you for a token

4) In the password/token column, copy the token created in the first terminal
(It should look like the below - only copy the portion after the token= )

 http://localhost:8887/?token=####HERE_IS_THE_TOKEN_CODE---COPY_THIS_AND_PASTE_INTO_BROWSER

Biowulf Jupyter Notebook Connection
1) Run one terminal to access the persistent biowulf node and start jupyter notebook:

 #Connect to login node
 ssh -Y $USER@biowulf.nih.gov
 
 spersist #This will startup a persistent node
    #Alternatively if a persistent node is already running, you can ssh into the persistent node
 #In the persistent node
 conda activate $CONDA_ENVIRONMENT_NAME
 cd $FOLDER_WITH_CODE
 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) (This is a two step process, the notebook port is sent to biowulf first, then to your local computer)

 ssh -L localhost:8888:localhost:8888 $USER@biowulf.nih.gov
 #In the same ssh terminal from the line above this one, type the following
 ssh -N -L localhost:8888:localhost:8887 $USER@$PERSISTENT_NODE

3) In Firefox/Chrome/Etc - Log into localhost:8888
This will prompt you for a token

4) In the password/token column, copy the token created in the first terminal
(It should look like the below - only copy the portion after the token= )

 http://localhost:8887/?token=####HERE_IS_THE_TOKEN_CODE---COPY_THIS_AND_PASTE_INTO_BROWSER


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