Install FSL on Fedora Linux

fsl_fedora_install.md

Download the FSL installer (python script) from https://fsl.fmrib.ox.ac.uk/fsldownloads_registration.

Type following commands in a Python interpreter:

from fslinstaller import *
manifest = get_web_manifest(Settings.mirror)
import json
with open('~/manifest.json', 'w') as fp:
  json.dump(manifest, fp)

Open the manifest.json file and look for the filenamename of the latest CentOS FSL version (ending in .tar.gz).

Append this filename to the string in Settings.mirror and paste into your browser: this downloads the required binaries.

# Install dependencies
sudo yum install expat-devel libmng libpng12

# Extract FSL binaries into desired folder (I chose `~/.local`)
cd ~/.local
tar -xzf ~/Downloads/fsl-<fsl_version)-<centos_version>.tar.gz
FSLDIR=`pwd`/fsl
. fsl/etc/fslconf/post_install.sh -f $FSLDIR

Add folowing lines to .bashrc:

FSLDIR=$HOME/.local/fsl
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

Hi, I'm on Fedora 29 attempting to install FSL6.0.1 for Centos7 and when attempting to use the above in a python2 (2.7.15) interpreter, I get

with open('~/manifest.json, 'w') as fp: File "<stdin>", line 1 with open('~/manifest.json, 'w') as fp:
^
SyntaxError: invalid syntax

I assume this is an issue related to which version of python we're running. Could you kindly recommend a fix?

Hi there, it looks like I had a typo in that python snippet where the closing quotation mark around manifest.json was a backtick. Can you try replacing that? I updated it in the gist. Can't test unfortunately at the moment.

Cheers,
Lucas.

Hi Lucas,

Thanks for getting back. Apologies, we now have this problem:

with open('~/manifest.json', 'w') as fp:
... json.dump(manifest, fp)
File "", line 2
json.dump(manifest, fp)
^
IndentationError: expected an indented block

Please forgive my limited knowledge of Linux: am I supposed to tab-over the json.dump? If I enter this, I see another ellipsis. Am I thereafter supposed to use open(manifest.json,rw) in the interpreter?

Big thanks in advance. - Matt

Hi, try using either two or four spaces before the json.dump(...) line. I don't know how many spaces are considered as one indent level in the default python interpreter. Should be pretty flexible as long as there is at least one space.

Hi Lucas,

Again, my apologies, but when I use two spaces, four, or a tab before json.dump(manifest, fp) and hit enter, the command line only returns ". . ." Is this correct?

Thanks again for all the help.

This is normal, just press enter again. When you enter indented multi-line input, you have to finish with an empty line. I suggest playing around a bit in the Python interpreter to get familiar with it.

Hi Lucas,

Hope you're doing well. May I ask you another question? In going back through the interpreter, the following is being reported:

os.getcwd()
'/home/Little.MRI.Lab/Downloads'
dirlist = os.listdir("/home/Little.MRI.Lab/Downloads")
dirlist
['fslinstaller.py', 'matlab_R2019a_glnxa64', 'matlab_R2019a_glnxa64.zip']
from fslinstaller import *
manifest = get_web_manifest(Settings.mirror)
import json
with open('/manifest.json', 'w') as fp:
... json.dump(manifest, fp)
...
Traceback (most recent call last):
File "", line 1, in
IOError: [Errno 2] No such file or directory: '/manifest.json'

Is the path in the open command incorrect? Or is it possible we've picked up an installer with a different file structure? I downloaded FSL 6.0.1 for Centos7. My apologies for being so unfamiliar with the interpreter.

Thanks again,

Matt

the tilde () is vanishing from the previous ('/manifest.json) in both locations (code and error msg)

Hey, how did it go? Did you manage to install it?

Hey guys,

I don't know why the tilde is vanishing in your interpreter but it's not important. Just use any valid file path that is writable to you which let's you open the downloaded json file.

Or even just print out the manifest content in your interpreter using print(manifest) instead of writing it to file.

Cheers,
Lucas.