Thank you very much Mark for elaborating on this.

As a general strategy, low resolution perfusion image on one side and
high resolution T1 image on the other side, what direction would you
chose, T1 -> perf or perf -> T1

What I said in my earlier email was migrating from perfusion resolution
to T1 resolution; by down sampling our grey matter to perfusion
resolution we are sacrificing accuracy of the boundaries, are we not?

Your thoughts on this are appreciated

Thanks

-P




-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Mark Jenkinson
Sent: Tuesday, August 18, 2009 3:24 PM
To: [log in to unmask]
Subject: Re: [FSL] Partial volume segmentation and trilinear
interpolation

Hi,

You will find that when you do substantial downsampling, FLIRT will
apply a pre-smoothing step which tries to incorporate information
over the size of the new voxel, although it is done with a Gaussian
which might be too big in this instance. It is this smoothing (or
blurring)
which is critical though - not the interpolation - as you don't really
want to interpolate single points at the centre of the new voxels,
you want to know what the total PVE is over the whole voxel volume.
No interpolation method will give you the latter without doing
smoothing/blurring.

So if you just want to integrate the intensities from the 1x1x1 voxels
contained in each of the 4x4x6 voxels then the easiest way would
be to do the following:
  - apply any transformation (rotation, etc) but use a reference image
that has 1x1x1 mm voxel sizes and trilinear interpolation
  - convolve this resultant image with a 4x4x6 kernel of all ones
(you can do this with fslmaths and the "-kernel boxv" option)
  - downsample with -noresampblur and trilinear interpolation using
flirt
In both of these cases the use of trilinear interpolation versus any
other interpolation (besides nearest neighbour) won't make much
difference.

I'm not sure how much difference doing it this way will have on
your final results.

All the best,
Mark



On 18 Aug 2009, at 20:19, Mojabi, Pouria wrote:

> Hi Deniz,
>
> FSL only supports {trilinear,nearestneighbour,sinc} with trilinear
> being the default. The best interpolation from my perspective is
> splines, and I switched to SPM in order to get that to work.
>
> For bringing low resolution perfusion to T1 resolution you
> definitely don't want to use tri-linear for interpolation. Try sinc
> and see how it works
>
> The only catch is if you chose interpolation methods other than tri-
> linear it might introduce negative intensities to your image which
> is perfectly normal considering the specs of interpolation. So you
> need to zero them out after interpolation.
>
> Also, (I have tested this) I faced better results breaking down my
> T1 image resolution. Meaning, you can define an intermediate
> resolution, co-register your perfusion to that then co-register to
> final T1 resolution, I observed better alignment doing it this way.
>
> I mean frankly speaking there isn't so much you could do with those
> crappy quality perfusion images!
>
> Hope this helps
>
> -P
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Deniz Ozgen
> Sent: Tuesday, August 18, 2009 9:14 AM
> To: [log in to unmask]
> Subject: [FSL] Partial volume segmentation and trilinear interpolation
>
> Hi,
>
> I have a question about how trilinear interpolation works.
>
> Briefly I am working on perfusion images with a voxel size of 4x4x6
> mm. and T1 images with 1x1x1 mm. I have obtained GM segmentation on
> T1, I have the PVE map. I would like to obtain the perfusion value
> for GM. Therefore I obtained the linear tranformation matrix from T1
> to perfusion image using FLIRT.
>
> I am trying to find percentage volume of GM for a given perfusion
> image voxel. I believe it would NOT be very accurate to transform
> the PVE map to the perfusion image space using ApplyXFM using
> trilinear interpolation.
>
> I understand how trilinear interpolation works while reslicing a low
> resolution image to get a high resolution image. But I am not sure
> how/which the PVE values are combined to obtain the PVE map for a
> lower resolution image using trilinear interpolation.
>
> I hope my question is clear enough.
>
> Thank you very much in advance.
>
> Deniz.
>
>