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
inplane_paddedFOV
... 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
-ref.
Any suggestions on how to do this?
Ed
--
Ed Vessel
Center for Brain Imaging
New York University
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4 Washington Place, Rm. 156
New York, NY 10003 http://www.cns.nyu.edu/~vessel
(212) 998-8217
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