Hi,
This is fine.
Flirt is capable of applying a single matrix to a whole 4D
timeseries using either applyxfm or applyisoxfm (your choice).
The utility applyxfm4D is really there for applying a set
of matrices, where there is a different one for each timepoint.
You usage of -init and -applyisoxfm (or -applyxfm) is perfectly
correct.
I assume this worked OK for you.
All the best,
Mark
On 6 Dec 2008, at 21:26, Patrick Bedard wrote:
> Hi Mark,
>
> So first I used bet on the EPI timeseires
>
> bet subj_EPI subj_EPI_bet -F -f 0.5 -g 0
>
> Then I used these:
>
> flirt -v -searchrx -180 180 -searchry -180 180 -searchrz -180 180 \
> -ref MNI152_T1_1mm_brain.nii \
> -in sub_EPI_bet.nii.gz \
> -omat subj_T2toMNI.mat
>
> flirt -v \
> -ref MNI152_T1_1mm_brain.nii \
> -in subj_EPI_bet.nii.gz \
> -applyisoxfm 3 \
> -init subj_T2toMNI.mat \
> -out subj_EP_MNI
>
> Are these correct or so I need to use the -applyxfm or -applyxfm4D?
> I'm not
> sure how to use the -applyxfm; alone or -applyxfm subj_T2toMNI.mat
>
> Thanks for you help
>
> Pat
>
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