Ping ... Got no response on this, just doublechecking to see if there
are any recommendations or if I'm missing something obvious.
On Thu, Jul 30, 2009 at 10:17 AM, Ed Vessel<[log in to unmask]> wrote:
> Hi there -
> I have some EPI and 2D T1 ("inplane") data that were collected with
> the same slice prescription but different fields of view in the image
> plane, and I'm trying to pad my inplane to have the same FOV (without
> changing the NIFTI qform location info).
> The EPI scan is 3x3x3mm, 64x80 voxels (192x240 FOV).
> The 2D T1 inplane is 1.5x1.5x3mm, 128x128 voxels (192x192 FOV).
> I've tried using some flirt commands to do this but can't get it to work right.
> flirt -in inplane -ref EPI -noresample -applyxfm -init yshift.mat -out
> ... does the right thing but the "noresample" tag seems to not have an
> effect and I get 3x3x3 voxels (not 1.5x1.5x3).
> (note, my yshift.mat file is there just to re-center the data in the
> middle of the slice, adding the padding on both sides rather than just
> one side. It contains a 24mm shift in y).
> flirt -in dino_inplane_090729+03+t12Dmprage26sl -ref
> ../04+Online/dino_inplane_090729+04+Online -applyisoxfm 1.5 -init
> yshift.mat -out inplane_paddedFOV2
> ... this resamples in all directions, giving me 1.5x1.5x1.5mm voxels,
> which is no good because now I can't use it as an "inplane" ... it
> doesn't have the same slices as the EPI.
> I've also tried creating a _new_ reference file with the right image
> dimensions (1.5x1.5x3, 128x160 voxels), but have been unsuccessful at
> getting the qform of this new file set correctly, so that it places
> the data in the wrong place in the file when I then use this as the
> Any suggestions on how to do this?
Center for Brain Imaging
New York University
[log in to unmask]
4 Washington Place, Rm. 156
New York, NY 10003 http://www.cns.nyu.edu/~vessel