Learn the theory and practice of using FSL for structural, functional and diffusion image analysis. The course is designed for people at all skill levels, from those with little or no experience through to intermediate users of FSL. It is based around a set of self-paced, hands-on practicals, supported by a broad set of accessible lectures.
Thanks for the video sir. But im stuck after the installation while typing fslmaths/fsl it shows this - "You need to set the FSLDIR environment variable to point to the FSL installation directory before you can run anything." CAN ANYONE HELP ME
I've just followed the scripts you run, but after the second session, I faced an index error: list index out of range but you didn't face this error How can I fix it?
Some updates for window 10. sudo apt install python3 alias python='python3' (Set alias ) export display did not work for window 10. Then I tried export DISPLAY=:0 It worked.
Hello, I followed the updated instructions from the website and also watched this video, but I am unable to run fsleyes command and get this error: "mwaniak@DESKTOP-43L11BF:~$ fsleyes Traceback (most recent call last): File "/home/mwaniak/fsl/bin/fsleyes", line 6, in <module> from fsleyes.filtermain import main File "/home/mwaniak/fsl/lib/python3.11/site-packages/fsleyes/__init__.py", line 374, in <module> from fsleyes.main import embed, shutdown # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/mwaniak/fsl/lib/python3.11/site-packages/fsleyes/main.py", line 35, in <module> import wx File "/home/mwaniak/fsl/lib/python3.11/site-packages/wx/__init__.py", line 17, in <module> from wx.core import * File "/home/mwaniak/fsl/lib/python3.11/site-packages/wx/core.py", line 12, in <module> from ._core import * ImportError: libXxf86vm.so.1: cannot open shared object file: No such file or directory". I can run fsl command which opens the program though. Do you know what could be causing an error?
Hi, I have installed on windows 11. I have even downloaded Xming. However, when I run the fsleyes command, I get the following error Unable to access the X Display, is $DISPLAY set properly? Any ideas?
Thank you this is very helpful! Are there communities in which the ICA maps of the data I am working on can be discussed with some experienced researchers?
Hi Navi, b-value is the level of sensitivity to diffusion, the higher the b-value the signal decay faster for diffusion along the direction of gradient. Its value is decided when the data is acquired and it will be given to you along with the diffusion images. A diffusion dataset might have one or multiple b-values depending on the intended applications.
This video and the tutorial needs to be updated. For example, "python" is no longer an available Linux package. For Windows 10, there is no need to use XLaunch as WSL2 supports GUI on the latest Windows version. For Windows 11, GUI is enabled by default.
Anyone knows how to install FLS in a virtual box Linux? My main operating system is windows 10 and I have a virtual box with Ubuntu. I cannot make sense from the wiki page so far, starting with whether I should follow the Linux instructions or the windows virtual machine ones.
Hi Michael, Yes, you are correct in that registering an atlas mask to the native space can yield a Thalamus (or other structures) mask, as this is the main motivation for "FIRST." However, the problem is that this approach relies solely on the information included in the nonlinear registration to reconstruct the subcortical structures, and therefore it would likely lose a lot of individual variances in the process. The biggest benefit with FIRST, in my opinion, is that using this shape analysis you can reconstruct the structures while keeping more of the individual variation. Also, it can also be useful with vertex analysis, which is not straightforward with a volumetric mask.
I am trying to align rat brain fMRI to P56 Atlas template. And I'm not quite satisfied with the result. What are the tips for rat brains? And more importantly, how can I manually edit transformation matrices, delete skulls etc?
Hi Everyone! Could you help me out? I installed the fsl, but it is not running. This is what I get from the terminal: ,,zsh: command not found: fslview" What could be the solution for this problem?
Thanks for your helpful videos! If I am trying to do two step registration with the first step being linear registration of a T1 image to a T2 image, is it OK to use the FEAT tool and upload the T2 image where you have uploaded the functional data? Then subsequently use FNIRT to perform spatial normalization to MNI space?
What a great video! Hats off to Oxford's WIN team. I wonder how small can the voxels be and if there is a probabilistic estimation method for the error in estimating the fibre orientations
Any recommendations for MacOS Monterey? I've done everything as instructed, but when I check flirt version, it is returned with 'bad CPU in executable:flirt'. Also, miniconda is not installed at the end, so the post install set up always fails..
I agree. It was recorded in front of my old laptop during the pandemic. And with the neighbour's kids home from school and playing in the back gardens. So not ideal :(
