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FSL Course
Великобритания
Добавлен 12 май 2017
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.
Probabilistic Functional Modes (PFM) pre-practical video
Probabilistic Functional Modes (PFM) pre-practical video
Просмотров: 402
Видео
FSLnets practical intro (updated 2023)
Просмотров 456Год назад
This updated FSLnets practical intro video shows the new python implementation of FSLnets.
Probabilistic Functional Modes (Part 3)
Просмотров 1 тыс.2 года назад
Probabilistic Functional Modes (Part 3)
Probabilistic Functional Modes (Part 1)
Просмотров 1,2 тыс.2 года назад
Probabilistic Functional Modes (Part 1)
Probabilistic Functional Modes (Part 2)
Просмотров 6642 года назад
Probabilistic Functional Modes (Part 2)
11. FMRI1: Introduction to Task FMRI Experiments and Analysis (Fmri1 E1)
Просмотров 6 тыс.3 года назад
11. FMRI1: Introduction to Task FMRI Experiments and Analysis (Fmri1 E1)
22. FMRI3: Pipeline Overview (Fmri3 E1)
Просмотров 2,2 тыс.3 года назад
22. FMRI3: Pipeline Overview (Fmri3 E1)
8. Segmentation: Subcortical Brain Structures and FIRST (Struc E2)
Просмотров 5 тыс.3 года назад
Subcortical Brain Structures and FIRST
5. Registration: EPI Distortion Correction and Registration (Reg E5)
Просмотров 8 тыс.3 года назад
EPI Distortion Correction and Registration
26. FMRI3: Advanced Analysis, Factorial Designs and Interactions (Fmri3 E5)
Просмотров 1,7 тыс.3 года назад
FSL FMRI Advanced Analysis, Factorial Designs and Interactions
2. Registration: Image Spaces and Spatial Transformations (Reg E2)
Просмотров 17 тыс.3 года назад
Image Spaces and Spatial Transformations
16. FMRI2: Examples of Group FMRI Analysis (Fmri2 E2)
Просмотров 3,2 тыс.3 года назад
Examples of Group FMRI Analysis
9. Segmentation: White Matter Hyper-intensities and BIANCA (Struc E3)
Просмотров 4,9 тыс.3 года назад
9. Segmentation: White Matter Hyper-intensities and BIANCA (Struc E3)
33. Resting State: Network Modelling Analysis, Node Definition and Edge Calculation (Nets E2)
Просмотров 3 тыс.3 года назад
33. Resting State: Network Modelling Analysis, Node Definition and Edge Calculation (Nets E2)
10. Segmentation: Structural Analysis using FSL VBM and SIENA (Struc E4)
Просмотров 7 тыс.3 года назад
10. Segmentation: Structural Analysis using FSL VBM and SIENA (Struc E4)
18. FMRI2: Inference, Null Hypothesis Testing, and Multiple Comparisons (Fmri2 E4)
Просмотров 2,5 тыс.3 года назад
18. FMRI2: Inference, Null Hypothesis Testing, and Multiple Comparisons (Fmri2 E4)
13. FMRI1: Introduction to Single Session Analysis and GLM Basics (Fmri1 E3)
Просмотров 6 тыс.3 года назад
13. FMRI1: Introduction to Single Session Analysis and GLM Basics (Fmri1 E3)
14. FMRI1: Modelling and Statistics (Fmri1 E4)
Просмотров 3,8 тыс.3 года назад
14. FMRI1: Modelling and Statistics (Fmri1 E4)
4. Registration: Single Stage and Multi-Stage Applications (Reg E4)
Просмотров 7 тыс.3 года назад
4. Registration: Single Stage and Multi-Stage Applications (Reg E4)
3. Registration: Cost Functions, Interpolation and Masks (Reg E3)
Просмотров 9 тыс.3 года назад
3. Registration: Cost Functions, Interpolation and Masks (Reg E3)
21. FMRI2: Threshold Free Cluster Enhancement and False Discovery Rate (Fmri2 E7)
Просмотров 3 тыс.3 года назад
21. FMRI2: Threshold Free Cluster Enhancement and False Discovery Rate (Fmri2 E7)
20. FMRI2: Parametric Vs. Non-parametric Tests (Fmri2 E6)
Просмотров 2,4 тыс.3 года назад
20. FMRI2: Parametric Vs. Non-parametric Tests (Fmri2 E6)
15. FMRI2: Group Analysis, Fixed/Mixed Effects, FLAME and OLS (Fmri2 E1)
Просмотров 4,4 тыс.3 года назад
15. FMRI2: Group Analysis, Fixed/Mixed Effects, FLAME and OLS (Fmri2 E1)
For me it's stuck at 0% when it comes to this line: "Installing FSL into /Users/fsl..." No progress after half an hour has passed. I'm on Sonoma.
I get an error, when I type python "/mnt/c/Users/<WindowsUserName>/Downloads/fslinstaller.py" that phyton is not found
Thank you!! It helps a lot!!😁
Amazing talks!
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
Any sources please for the math and derivations behind it?
Trying to work out if the accent New Zealand, Australian, or either and influenced by time spent in England.
Perfect lecture. Thank you for this comprehensive explanation of tractography.
every time i try intalling fsl it fails:(
Really Helpful, Thanks!
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.
顶不住了,这口音,快死了
Is there any disease in which water starts to recede from some body structures?
Thank you so much for this. These videos are amazing. You have explained in very simple terms and easily digestible for a beginner in FSL.
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?
I wish the voice was clearer!
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?
I have the same problem did you solve it?
can I get this ppt?
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?
what is a b value?\ great video, thanks!
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.
where can I take the data? i didnt get it
The mixture sounds were screams from hell
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.
woudn't FNIRT + MNI atlas Thalamus mask do the same trick?
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?
Same. And there are no solutions available online.
I have some problems with flirt/fnirt for rat fMRI. Also I cannot import P56 Allen atlas for rat brain. Why is that?
Thanks for the information. I have a question. Are there any other tools specially on windows platform that can generate brain masks ?
please post link here
Hi, what is a wizard button? Thanks!
How can I do the same thing with the multi subject concatenated ICA?
Thanks for the good explanation!
Thanks!
Our lab collected two field maps one in the AP direction and another in the PA direction, how do we combine the two
Did you end up finding a way to process these AP PA field maps?
@@joanahmadzime fslmerge -t AP_PA_b0 <AP input fmap image> <PA input fmap image>
Brilliant information.
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?
did you ever figure this out?
Hi need a help
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
Life saver! Thanks a bunch.
it could also work on windows 11?
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..
xming is not functional and no GUIs open, I would really appreciate more detail in how to get FSL completely installed and running.
/fslinstaller.py" [FAILED] [Errno -3] Temporary failure in name resolution, please advise on how to address this error.
very bad audio quality!