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Thanks Stam, that is really helpful and I will definitely give that a try! 

Best wishes,
Ilse 



On 25 May 2016, at 10:52, Stamatios Sotiropoulos <[log in to unmask]> wrote:

Dear Ilse

I do not think that data can be uploaded through the list, there are certainly no attachments on your email. 

I suggest you download some exemplar data and follow the relevant FSL tutorials. This would give you a very good idea of how to run simple computations like the FA, but also what to expect/ look for in your data. The link is: 

http://fsl.fmrib.ox.ac.uk/fslcourse/

You can go through the Diffusion MRI analysis one and get data from http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz.

Best wishes
Stam


 
On 23 May 2016, at 09:57, Ilse Thompson <[log in to unmask]> wrote:

Hi,

This is the first time I am using FSL, and I am trying to create FA images as part of the preprocessing.

I have a MPRAGE image, and a DTI file – both already converted to NIFTI - and have followed the following steps:

1. Corrected the original data for the effects of head movement and eddy currents using the eddy correct correction function on FSL. Here I have uploaded the DTI file.
2. Then I have created a brain mask, by opening BET brain extraction, and uploaded the MPRAGE data here.
3. I then opened the DFT diffusion function, and chose DTIFIT, and specified the input files manually by

a. Diffusion weighted data – the converted file that is created with the eddy current correction
b. BET binary brain mask – the MPRAGE_brain_mask file that was created with the BET brain extraction
c. Output basename is filled in automatically
d. Gradient directions – added the DTI bvec file
e. B values – added the DTI bval file

All the steps work without any errors, but when I then at the end want to check if everything went okay by clicking the FSLview window and opening the FA data, the brain doesn't load, and instead I can only see a black screen.

Any ideas what I am doing wrong?

Thank you so much,
Ilse