Slicer - Revision history

192.168.1.1: /* Installing Slicer */

2016-10-27T18:34:08Z

Installing Slicer

← Older revision		Revision as of 14:34, 27 October 2016
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	Reload your path by either logging out and logging in again or (quicker):		Reload your path by either logging out and logging in again or (quicker):
	source ~/.bashrc		source ~/.bashrc

			=== Installation Problems ===
			The above instructions work fine for Ubuntu 14.04-LTS. More recent releases (e.g. 16.04) are missing a key shared library (libjsoncpp.so.0) that Slicer relies on. In fact, it's not even an option to install it. Fortunately, there's a workaround that takes advantage of the fact that there is a functionally similar library available in a package that simply may not be installed by default (but can be easily added).

			#install the libjsoncpp-dev package
			sudo apt-get install libjsoncpp-dev
			#This package contains libjsoncpp.so.1, which seems to be compatible
			#with the missing libjsoncpp.so.0 library
			#We can now make a symbolic link (similar to a shortcut) pointing to
			#this compatible file, but give it the name of the library file that
			#Slicer is expecting.
			cd /usr/lib/x86_64-linux-gnu
			sudo ln -s libjsoncpp.so.1 libjsoncpp.so.0
			#now when Slicer looks for libjsoncpp.so.0, it will load in information
			#from libjsoncpp.so.1, which seems to be good enough to get the job done

			For the record, this sort of strategy for dealing with packages that get removed from later releases often handles these sorts of issues.

192.168.1.1: /* Installing Slicer */

2016-10-27T18:07:19Z

Installing Slicer

← Older revision		Revision as of 14:07, 27 October 2016
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	tar -xzvf Slicer-*.tar.gz		tar -xzvf Slicer-*.tar.gz
	Move the unzipped directory to /opt/		Move the unzipped directory to /opt/
	sudo mv Slicer-4.5.0-1-linux-amd64 /opt/		sudo mv Slicer-4.6.0-linux-amd64 /opt/
	Edit your ~/.bashrc file to put the directory in your path		Edit your ~/.bashrc file to put the directory in your path
	PATH=/opt/Slicer-4.5.0-1-linux-amd64:${PATH}		PATH=/opt/Slicer-4.6.0-linux-amd64:${PATH}
	Reload your path by either logging out and logging in again or (quicker):		Reload your path by either logging out and logging in again or (quicker):
	source ~/.bashrc		source ~/.bashrc

192.168.1.1 at 18:06, 27 October 2016

2016-10-27T18:06:51Z

← Older revision		Revision as of 14:06, 27 October 2016
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	Slicer		Slicer
	Alternately, if it’s not, you should be able to run it specifying the complete path, as in the example:		Alternately, if it’s not, you should be able to run it specifying the complete path, as in the example:
	/opt/Slicer-4.5.0-1-linux-amd64/Slicer		/opt/Slicer-4.6.0-linux-amd64/Slicer

	#Open the anatomical file		#Open the anatomical file

192.168.1.1 at 14:44, 6 April 2016

2016-04-06T14:44:31Z

← Older revision		Revision as of 10:44, 6 April 2016
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	#*File > Save (screenshot forthcoming of dialog box: select .mgz filetype, and uncheck the Scene checkbox so that only the file is saved)		#*File > Save (screenshot forthcoming of dialog box: select .mgz filetype, and uncheck the Scene checkbox so that only the file is saved)

	You should now have <code>filename~~.nii~~.mgz</code> alongside the original files		You should now have <code>filename.mgz</code> alongside the original files

	== Installing Slicer ==		== Installing Slicer ==

192.168.1.1 at 14:44, 6 April 2016

2016-04-06T14:44:03Z

← Older revision		Revision as of 10:44, 6 April 2016
Line 7:		Line 7:
	If Slicer is in your path, you can run slicer from the console		If Slicer is in your path, you can run slicer from the console
	Slicer		Slicer
	Alternately, if it’s not, you should be able to run it specifying the complete path:		Alternately, if it’s not, you should be able to run it specifying the complete path, as in the example:
	/opt/Slicer-4.5.0-1-linux-amd64/Slicer		/opt/Slicer-4.5.0-1-linux-amd64/Slicer

192.168.1.1 at 14:43, 6 April 2016

2016-04-06T14:43:09Z

← Older revision		Revision as of 10:43, 6 April 2016
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	#Open the anatomical file		#Open the anatomical file
	#*File > Add Data > choose File(s) to add		#*File > Add Data > choose File(s) to add
	#Navigate to MPRAGE folder select orig.nii or highres00.nii		#*Navigate to MPRAGE folder select the source .nii file
	#Re-save the file as a .mgz file:		#Re-save the file as a .mgz file:
	#*File > Save (screenshot forthcoming of dialog box: select .mgz filetype, and uncheck the Scene checkbox so that only the file is saved)		#*File > Save (screenshot forthcoming of dialog box: select .mgz filetype, and uncheck the Scene checkbox so that only the file is saved)

192.168.1.1: Created page with "Slicer is a graphical linux utility for manipulating structural MRI data. We use it for converting between data formats. It is run from the Linux command-line. To check if it..."

2016-04-05T17:47:03Z

Created page with "Slicer is a graphical linux utility for manipulating structural MRI data. We use it for converting between data formats. It is run from the Linux command-line. To check if it..."

New page

Slicer is a graphical linux utility for manipulating structural MRI data. We use it for converting between data formats. It is run from the Linux command-line.

To check if it is installed, open up a Linux terminal and type:
Slicer
If you get a message indicating that the command can't be found, see the instructions below for installation and/or ask for help from a lab administrator.

If Slicer is in your path, you can run slicer from the console
Slicer
Alternately, if it’s not, you should be able to run it specifying the complete path:
/opt/Slicer-4.5.0-1-linux-amd64/Slicer

#Open the anatomical file
#*File > Add Data > choose File(s) to add
#*Navigate to MPRAGE folder select orig.nii or highres00*.nii
#Re-save the file as a .mgz file:
#*File > Save (screenshot forthcoming of dialog box: select .mgz filetype, and uncheck the Scene checkbox so that only the file is saved)

You should now have <code>filename.nii.mgz</code> alongside the original files

== Installing Slicer ==
Visit http://download.slicer.org/ and get the latest stable build (the examples below assume the most stable build is Slicer-4.5.0-1, so edit the commands below as appropriate). Unzip the tarball
tar -xzvf Slicer-*.tar.gz
Move the unzipped directory to /opt/
sudo mv Slicer-4.5.0-1-linux-amd64 /opt/
Edit your ~/.bashrc file to put the directory in your path
PATH=/opt/Slicer-4.5.0-1-linux-amd64:${PATH}
Reload your path by either logging out and logging in again or (quicker):
source ~/.bashrc