Hi Nicole,
> Perfusion Subtraction
> rather than the Full Model, since I'm using a TE of 3ms.
Wow, an echo time of 3ms seems unfeasibly low. That said, I am not
sure how that relates to the choice of full model versus subtraction.
A low TE just means that when you are doing the full model approach
there is less need to have an EV to model the BOLD signal (see the
webpage help http://www.fmrib.ox.ac.uk/fsl/feat5/perfusion.html).
> My most significant issue is that there is no activation when using
> the
> perfusion subtraction in FSL. When I had been performing the
> subtraction in
> Matlab, then processing in FSL, I had clear motor activation and
> well-formed
> time courses. I have tried looking at the perfusion_subtract script,
> but
> unfortunately, I cannot follow it. I realize this is a broad issue
> to be
> asking about, but I really do not know where I'm going wrong.
Is there plausible activation, but just at lower z-stats, or nothing
coherent at all?
Worth double checking all of the timings:
- have you got the TR set correctly (should be the time taken for
acquiring a tag OR control)
- ideally the model should be shifted forward by TR/2 to adjust to the
way in which the sinc interpolation is done (e.g. reduce your 3 col
format custom timings by TR/2)
- have you set the "First timepoint is tag" option correctly - it is
worth checking negative contrasts as well
> Other than this most prominent problem, I was also wondering why
> your images
> do not turn out grainy as mine do, and why in the FSL output, there
> are
> black areas around the edges of my images.
Have not seen grainy images. But note that the default settings in
Feat will do a small amount of spatial smoothing.
> Finally, I question how one can perform motion correction on
> perfusion data
> at all, given the alternation between tag and control.
In our experience, this works fine. There is enough common contrast
between the tag and control to allow this to work. Some people have
reported it working better on unBET-ed images, so try with and
without. It may be trickier if there is background suppression, but we
have seen that work OK as well. Best thing to do is to take a look at
the motion corrected data and see if it looks alright.
Cheers, Mark.
----
Dr Mark Woolrich
EPSRC Advanced Research Fellow University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
On 14 May 2009, at 18:14, Nicole Pelot wrote:
> Hello,
>
> I have multiple perfusion datasets. Up to this point, I have been
> performing
> the subtraction in Matlab prior to feeding the data to FSL. However,
> the
> Matlab subtraction produces very grainy images, preventing both motion
> correction and registration from working properly since - to the
> best of my
> understanding - these are both based on image intensity.
>
> Given this problem, I am trying to use FSL's perfusion subtraction.
> I have
> read the relevant documentation, and am opting for the Perfusion
> Subtraction
> rather than the Full Model, since I'm using a TE of 3ms. Hence, I have
> formatted my data into a single timecourse, with datapoints
> alternating
> between tagged and control. I've attached my NIFTI file.
>
> My most significant issue is that there is no activation when using
> the
> perfusion subtraction in FSL. When I had been performing the
> subtraction in
> Matlab, then processing in FSL, I had clear motor activation and
> well-formed
> time courses. I have tried looking at the perfusion_subtract script,
> but
> unfortunately, I cannot follow it. I realize this is a broad issue
> to be
> asking about, but I really do not know where I'm going wrong.
>
> Other than this most prominent problem, I was also wondering why
> your images
> do not turn out grainy as mine do, and why in the FSL output, there
> are
> black areas around the edges of my images.
>
> Finally, I question how one can perform motion correction on
> perfusion data
> at all, given the alternation between tag and control.
>
> Thanks so much,
>
> Nicole
>
> P.S.: Please let me know if any images (to show graininess,
> blackened areas,
> time courses, etc.) would be useful; they are too large in their
> current state.
>
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