Dear Melissa,
applyxfm4D should be a standalone command, rather than an option to flirt. Assuming the 4D image has already been motion-corrected ( and so is internally aligned ) then your flirt call is fine, however you may find epi_reg ( called with a single example 3D image taken from the 4D image ) generates a better affine matrix. Either way you can use that output with applyxfm4D or applywarp ( via e.g. the --premat option ) to resample to structural space.
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 29 Aug 2022, at 09:07, Thalhammer, Melissa <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear FSL-community,
I want to align a 4D-EPI and a T1w image with flirt (FSL version 6.0.5.1). I have used the following code:
flirt -in ${epi4d} -ref {T1} -omat firstvol2t1.mat -dof 6
In the Terminal, I get the warning: "An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is depricated and will be removed in a future release." Hence, I assume that FSL will register the first EPI volume to T1, which is fine.
Next, I wanted to apply applyxfm4d as stated on the flirt user guide:
flirt -in ${epi4d} -ref {T1} -applyxfm4d -init firstvol2t1.mat -out slomoco2t1.nii
However, I get the following error: "Unrecognised option -applyxfm4d". Has this functionality been removed? What is the recommendation to align a 4D EPI?
Best, Melissa Thalhammer
Melissa Thalhammer, M.Sc.
Neuroscientist, PhD candidate
Neuropsychiatry and Neuroimaging Lab
Klinikum Rechts der Isar der Technischen Universität München
Neuroimaging Center (TUM-NIC)
Department of Neuroradiology
Ismaninger Straße 22
81675 Munich, Germany
Tel.: +49 89 4140 4683
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