Dear all,
I am aware that this issue comes around every now and then on the list
but I haven't found a work-around yet...
I have some difficulties with registering 18 functional slices (1mm3
isotropic) to a full brain MPRage anatomy file (also 1mm3 isotropic).
I tried all the obvious methods (i.e. playing around with the degrees
of freedom; use the 'xyztrans' and 'ztransonly' schemes) but no luck
so far.
Although I now know that things may improve by acquiring a full-brain
EPI image I haven't got one for the initial data sets but there is one
option that works: Thankfully, the orientation info from the scanner
is very good at aligning the epi and
mprage and what I do is the following:
flirt -in epi.nii.gz -ref mprage.nii.gz -usesqform -applyxfm -out
func2mprage -omat func2mprage.mat
This creates a good registration!
What I now want is the apply the same transformation in Feat where I
try to register the data to the main structural image (mprage) which
in turn is registered to standard space. Yet seems that I only can use
the normal methods that, in turn, fail. Is there a way to use the
'-usesqform' instead? Alternatively, can I do this afterwards and
combine multiple sessions in a higher-level analysis without feat
nagging about not having registered properly?
Thanks in advance,
Cris Lanting
|