AnalysisGuidelines - Revision history

Jstout at 22:26, 17 October 2019

2019-10-17T22:26:46Z

← Older revision		Revision as of 18:26, 17 October 2019
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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

2019-10-16T13:41:32Z

@@ Line 45: / Line 45: @@
 (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'''

2019-10-16T13:16:58Z

← Older revision		Revision as of 09:16, 16 October 2019
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	'''Jupyter Notebook Over a Remote Connection'''<br>		'''Jupyter Notebook Over a Remote Connection'''<br>
	1) Run one terminal to start the notebook:		1) Run one terminal to start the notebook:
	ssh $USER@$REMOTE_HOST		ssh -Y $USER@$REMOTE_HOST
	cd $FOLDER_WITH_CODE		cd $FOLDER_WITH_CODE
	#If necessary: conda activate $CONDA_ENV		#If necessary: conda activate $CONDA_ENV

2019-10-10T14:03:44Z

← Older revision		Revision as of 10:03, 10 October 2019
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	<em>(Replace User and Remote_Host with the appropriate username and ip-address)</em>		<em>(Replace User and Remote_Host with the appropriate username and ip-address)</em>
	ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST		ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST

			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'''

2019-10-10T13:54:53Z

← Older revision		Revision as of 09:54, 10 October 2019
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	'''Jupyter Notebook Over a Remote Connection'''		'''Jupyter Notebook Over a Remote Connection'''<br>
	Run one terminal to start the notebook:		1) Run one terminal to start the notebook:
	ssh $USER@$REMOTE_HOST		ssh $USER@$REMOTE_HOST
	cd $FOLDER_WITH_CODE		cd $FOLDER_WITH_CODE
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	jupyter notebook --no-browser --port=8887		jupyter notebook --no-browser --port=8887

	Run another terminal to forward the port to your local machine		2) Run another terminal to forward the port to your local machine<br>
	(Replace User and Remote_Host with the appropriate username and ip-address)		<em>(Replace User and Remote_Host with the appropriate username and ip-address)</em>
	ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST		ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST

2019-10-10T13:47:40Z

← Older revision		Revision as of 09:47, 10 October 2019
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	~~---~~Anatomy Processing:~~---~~		'''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~~---~~		'''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

2019-10-10T13:37:33Z

← Older revision		Revision as of 09:37, 10 October 2019
Line 21:		Line 21:


	Anatomy Processing:		---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		---Jupyter Notebook---
	Nbdime for notebook version control (a jupyter interface for git)		Nbdime for notebook version control (a jupyter interface for git)

2019-10-10T13:30:11Z

← Older revision		Revision as of 09:30, 10 October 2019
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	Run another terminal to forward the port to your local machine::		Run another terminal to forward the port to your local machine::
	ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST		ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST
	jupyter notebook --no-browser --port=8887		jupyter notebook --no-browser --port=8887

2019-10-10T13:27:47Z

← Older revision		Revision as of 09:27, 10 October 2019
Line 39:		Line 39:

	Run another terminal to forward the port to your local machine::		Run another terminal to forward the port to your local machine::
	ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST		ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST
	jupyter notebook --no-browser --port=8887		jupyter notebook --no-browser --port=8887

2019-10-10T13:27:16Z

← Older revision		Revision as of 09:27, 10 October 2019
Line 39:		Line 39:

	Run another terminal to forward the port to your local machine::		Run another terminal to forward the port to your local machine::
	ssh -N -L localhost:8888:localhost:8887 ~~jstout~~@~~ebi~~		ssh -N -L localhost:8888:localhost:8887 $USER@$REMOTE_HOST
	jupyter notebook --no-browser --port=8887		jupyter notebook --no-browser --port=8887