pandyasneha

[Free|Pet]Surfer by Example

Init FreeSurfer env

At the NIH

Connect to Biowulf via NoMachine
Launch a terminal on Biowulf
Run:

** PLEASE NOTE ***
there are many other solutions for computing SUV, see below link for more info.
https://qibawiki.rsna.org/index.php/Standardized_Uptake_Value_(SUV)

This gist contains code to perform the below with python (3.7).

+ download data from TCIA via tcia-rest api. (download.py, tciaclient.py)

How to mount a GCP compute instance filesystem locally using `sshfs`

This guide assumes that:

you already have an instance set up on GCP that you want to mount locally
the GCP CLI (gcloud) is installed on your local machine
you have authenticated locally to your google account gcloud auth login

make sure your gcloud config is correct for the instance you're trying to access:

	##############
	# pretty prompt and font colors
	##############

	# alter the default colors to make them a bit prettier
	echo -en "\e]P0000000" #black
	echo -en "\e]P1D75F5F" #darkred
	echo -en "\e]P287AF5F" #darkgreen
	echo -en "\e]P3D7AF87" #brown
	echo -en "\e]P48787AF" #darkblue

	"""
	Partial Correlation in Python (clone of Matlab's partialcorr)

	This uses the linear regression approach to compute the partial
	correlation (might be slow for a huge number of variables). The
	algorithm is detailed here:

	http://en.wikipedia.org/wiki/Partial_correlation#Using_linear_regression

	Taking X and Y two variables of interest and Z the matrix with all the variable minus {X, Y},

	"""
	----------------------------------
	jg_MUSC_connectome_tractography.py
	----------------------------------

	Modified version of MUSC connectome (probabilistic) tractography pipeline

	(original code is at bottom of file, plus links to website)

	Modifications:

pandyasneha

[Free|Pet]Surfer by Example

Init FreeSurfer env

At the NIH

How to mount a GCP compute instance filesystem locally using sshfs

How to mount a GCP compute instance filesystem locally using `sshfs`