AnalysisGuidelines: Difference between revisions
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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
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'''Jupyter Notebook Over a Remote Connection'''<br>
ssh -Y $USER@$REMOTE_HOST▼
cd $FOLDER_WITH_CODE
#If necessary: conda activate $CONDA_ENV
jupyter notebook --no-browser --port=8887▼
<em>(Replace User and Remote_Host with the appropriate username and ip-address)</em>
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
'''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'''
Nbdime for notebook version control (a jupyter interface for git)
▲Run one terminal to start the notebook::
▲ssh $USER@$REMOTE_HOST
'''SAM installation from within NIH'''
git clone -b devel ...@$SERVER:SAMsrcV#
▲jupyter notebook --no-browser --port=8887
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
▲Run another terminal to forward the port to your local machine::
sudo apt-get install gsl
▲ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST
▲jupyter notebook --no-browser --port=8887
|
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