Hi Colin,
On Oct 24, 2013, at 00:24 , Colin Reveley <cm...@sussex.ac.uk> wrote:
> Hi -
>
> I wonder if anyone has experience in dealing with T1 images where there is
> hyperintenisty of blood vessels?
This looks like receive & transmit surface coil data to me. For
MPRAGEs, in my experience, switching to receive only surface coil (and assuming
a whole body scanner) and the body coil for transmit will darken the the blood
vessels again. Or you could use 8mb/kg bodyweight feraheme to reduce the blood
signal as well. Both methods will obviously not work retrospectively. I have no
experience with MDEFT, so the fereheme might not work. (But if you go that
route: feraheme is an excellent functional contrast agent in NHPs for EPIs)
>
> the data involved is MDEFT scans where only a head coil is used. I read it is
> a long solved problem for acquisition, but these scans do not correct it and
> nor will future scans.
>
> the difficulty is getting 3 classes (CSF,WM,GM) for nu_correct,mri_normalise
> or FSL Fast or whatever.
>
> It's quite a big obstacle for data that is otherwise quite excellent.
>
> One would think one could just threshold it out after brain extraction and to
> an extent one can but it's very imperfect. segmenting 4 classes doesn't
> especially work either (so far)
>
> if anyone has experience segmenting this stuff (especially getting
> mri_normalise to work) I'd be grateful for advice.
How does it affect mri_normalize? I typically used:
mri_normalize -n 1 -no1d -gentle ${src_dir}/${src_vol} ${targ_dir}/${targ_vol}
-v -mprage
on NHPs and:
mri_normalize -f ${controlpoints} ${mri_normalize_options_string} -MASK
${src_dir}/${mask} ${src_dir}/${in_vol} ${targ_dir}/${unmasked_brain} -mprage
for control point based normalization (which does not look required for your
nice data)
I guess for MDEFT I would skip -mprage.
I hope that helps at least some.
best
Sebastian
>
> e.g. attached
>
> Colin Reveley
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