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
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