Hi,

To do the image subtraction I would recommend fslmaths - as you say - although you could also just flick between images in FSLView if you are only going to look at images.  Sometimes looking at the difference image (calculated with fslmaths) can be better though.

The naming conventions are: EF = example_func / FM = fieldmap,  and these refer to the space that this image is in (i.e. the resolution and FOV).  UD = undistorted.  shift=shiftmap (the shift, in units of voxels, recorded at each voxel in the image).
fmap_sigloss is the signal loss image (giving proportion of intensity retained).  The _siglossed images are what you get by applying the sigloss image (to make an image with synthetic signal loss to assist registration).  The sigloss+mag image is an overlay image used for display purposes only.

All the best,
Mark


On 11 Sep 2012, at 17:39, Jeni Chen <[log in to unmask]> wrote:

Dear Mark,

Thank you for the pointer. I will certainly take the advice! 

I'm new to fsl, but from what I gathered, fslmaths could be used to do the image substraction to look at the change in the intensity- am I correct?

Also, about the shiftmap- I looked into the 'unwarp' folder, and saw the following:

EF_UD_shift+mag.nii.gz
FM_UD_fmap_mag_brain_siglossed.nii.gz
FM_UD_fmap_sigloss.nii.gz
FM_UD_fmap2epi_shift.nii.gz
FM_UD_sigloss+mag.nii.gz

Some of them I could guess by looking at either the name or the data in fslview, but just for clarity sake, would you mind telling me what each of these files represents and which is the actual shiftmap or the one depicting the signal loss? Also, to run the stats, is it fslstats that I use?

Thanks again for your help,

Jeni

Hi Jeni,

For signal loss the best way is just to look at the intensity difference.
So I would apply the distortion correction and then subtract the images and look at the intensity changes in various areas on a voxel basis, or get histograms from ROIs of interest.

For the distortion, you can take the shiftmap and calculate appropriate statistics from this - you can measure things like the standard deviation across the shiftmap, which then gives a reasonable measure of how much movement is occurring, or maybe look at certain quantiles, or the histograms.

Hope this helps.
All the best,
	Mark

On 7 Sep 2012, at 03:18, Jeni Chen <[log in to unmask]> wrote:

> Hello!
> 
> I've been trying the fieldmap correction with FUGUE in FEAT, and I'm just wondering whether there is a way of quantifying the amount of distortion or signal loss in the epi images, in addtion to the graphic representation in the report file. Basically we have 2 sets of epi images acquired using different parameters in attempt to reduce the signal loss in the known susceptible areas. So the idea is simply to compare the 2, before and after applying FUGUE, and knowing the amount of distortion and signal loss in each set before the correction would actually quite practical as well. 
> 
> Thank you in advance,
> 
> Jeni