Hello Samantha,
the procedure looks correct to me.
did you already check the resulting nodif_brain_mask that you create using BET? Does that look correct?
Cheers,
Matteo
> On 30 Mar 2015, at 15:05, Samantha C. <[log in to unmask]> wrote:
>
> Hello,
> I recently started working with a new set of data and am not able to generate FA maps using the methods that have worked previously.
>
> I am using the following steps with the FDT toolbox:
> 1. Eddy current correction
> 2. Creation of a nodif.nii.gz using fslroi from the corrected "data.nii.gz" dataset
> 3. Creation of nodif_brain and nodif_brain_mask using BET
> 4. DTIFIT
>
> When opening FA or MD files in FSLView, a blank image appears (all black with only crosshairs). I am wondering if the problem is with step #2. In the past, my diffusion data sets have only included 1 b0 image at the beginning of the dataset, so that I use "fslroi data.nii.gz nodif.nii.gz 0 1" to acquire the correct nodif image. In this case, the dataset includes 5 initial b0 images. Since fslroi did not work using timepoints 0 to 1, I tried using timepoints 0 4 (to include all b0 images), but this also produces an empty FA map.
>
> Is there anything else I should be considering?
>
> Thank you for your help!
> Samantha
|