Hi Ben,
> Firstly which is the better method to use - Full perfusion modelling or
> simple subtraction ?
Generally we recommend using full perfusion modelling because it's a
more accurate model of the whole ASL signal, and this lets you get
both the BOLD and ASL signals as different contrasts in a single
analysis, rather than having to do two separate analyses.
> In the simple subtraction case does the phase need to be TR/2 ?
The comment in the balloon help about having to advance your phase by
TR/2 is just a minor correction (1-1.5 sec probably) and it's much
more important for rapid event-related designs than for boxcar
designs. Don't worry about it -- especially because you should be
using full perfusion modelling instead.
> If I need ON OFF ON OFF instead of OFF ON OFF ON would I need to set the
> phase equal to rest period or activity period ( 29.3 secs in my experiment)
> in all the EVs to shift the model forwards ?
Yes -- the default boxcar design is to start with an OFF period, so if
you want to start with an ON period just set the phase equal to the
length of the OFF period. If you only have a single boxcar stimulus
and you use the Model Setup Wizard for your perfusion model, then the
phase is only set in one place (EV2).
> How would this change if I need to include TR/2 in the simple subtraction
> method ? Would it just be rest period + TR/2 ? So say the rest period is
> 29.3 secs , would the phase need to be set 29.3 +14.65 ~ 44 secs ?
TR is not the period of your boxcar -- it is the time between volumes
in your FMRI scan, probably 2-3 seconds. So the TR/2 adjustment is
just a minor correction, to account for the fact that when you do
subtraction, the new timepoint #1 is actually the difference between
the original timepoints #1 and #2. Generally don't worry about this
too much unless you have a very fast design.
> Is there any way to view the subtracted images to see what they look like ?
I think you'll see this in the filtered_func_data.nii.gz in the output
directory. They will probably be very noisy, with lots of
blood-vessel "activity".
> I have used the Full perusion model approach and do not seem to get any
> activation when i view the zstat1 image(perfusion) but get activation in the
> ztat3 image (BOLD) . Strangely, when I used a wrong TR (3 secs instead of
> 2.93) I got a single cluster in the left motor area. I have run MELODIC
> and there seems to be a lot of noise. The Simple subtraction model gives me
> a good result in one case but random blobs in the other
It shouldn't make any difference if you change the TR slightly like
that. However, you should look at your design carefully (with View
Design) and make sure that EV1 is alternating in every scan. If you
use TR=3 in one place and TR=2.93 in another, then your perfusion
signal will flip signs about every 20 timepoints! That would
definitely ruin your ASL results.
> I was wondering how I should choose the components to remove when using the
> MELODIC denoising option. I have around 35 components and in most of them
> the activations seem like artifacts except for one or two where the
> activations are in the left motor cortex(with a lot fo noise). Is there a
> 'rule' for selecting components to discard and retain ? Is there a limit to
> the number of components that can be discraded without causing any
> additional problems in the results ?
I'm not sure about using Melodic on ASL data. I imagine it will pick
out the tag-control contrast very strongly, and if you remove part of
this it will cause you problems in the GLM analysis. It takes a
trained eye to know what's an artifact and what is signal -- don't
remove too much!
Cheers,
Adrian
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