Difference between revisions of "AnalysisGuidelines"

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'''Version Control for Jupyter Notebook'''
 
'''Version Control for Jupyter Notebook'''
 
Nbdime for notebook version control (a jupyter interface for git)
 
Nbdime for notebook version control (a jupyter interface for git)
  +
  +
  +
'''SAM installation from within NIH'''
  +
git clone -b devel ...@$SERVER:SAMsrcV#
  +
  +
cd SAMsrcV#
  +
make
  +
  +
If errors asking for GSL
  +
#Use either (yum - Centos/redhat), (dnf - fedora) , or (apt-get - ubuntu)
  +
sudo yum install gsl
  +
  +
#Alternatively if Fedora
  +
sudo dnf install gsl
  +
  +
#Alternatively if using Ubuntu
  +
sudo apt-get install gsl

Latest revision as of 18:26, 17 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)


SAM installation from within NIH

 git clone -b devel ...@$SERVER:SAMsrcV#
 cd SAMsrcV#
 make

If errors asking for GSL

 #Use either (yum - Centos/redhat), (dnf - fedora) , or (apt-get - ubuntu)
 sudo yum install gsl
 #Alternatively if Fedora 
 sudo dnf install gsl 
 #Alternatively if using Ubuntu
 sudo apt-get install gsl