Dear Varina,
> 1. To BET the magnitude image, what parameters do you recommend? The standard ones, leave the skull inplace, likely secondary to the lack of contrast between scalp and brain in this image type.
This is very difficult to answer without seeing the images. If you have a lot of scalp/skull/meninges that touches the brain then you may need to do a manual brain extraction. Try different -f options first though, to see if that helps.
> 2. My Field Map image is in Hz, what is the best way to find the appropriate converstion factor to render it in rad/s units?
You need to multiply by 2*pi to convert from Hz to rad/s.
> 3. In using the dcmniigui to convert the original field map dicom images, I have tried various iterations to which Nifti type to convert to with the results:
> - FSL 4D Nii: one big file with the magnitude and Field Map dumped in
> - SPM 3D Nii: two separate files not recognized by fsl programs (.img)
> - 4D Nii/hdr: one big file but recognized by at least BET so far.
>
> Any recommendations?
I'm not very familiar with Philips, so I'm not sure what is best for this and dcm2nii. However, what you
ideally want is a separate image of the magnitude (or maybe two of them) and a separate image of
the phase (or maybe two of them). From the above it sounds like you already have a phase difference
in Hz, so you just want a separate magnitude image(s) in addition. Note that you can always use
fslroi to extract parts of any 4D image that is created.
All the best,
Mark
>
> Thanks in advance,
> Varina
>
|