Hi Doug,
Thanks so much for your reply and advice. I may have missed it, but I don't
see any information regarding the --vsm option in mri_vol2surf on the command
line or wiki help. Can you provide any guidance regarding the use of this
option and what the format/units/etc of this vsm should be?
Thanks again for all your help.
Best,
t
Re: [Freesurfer] applying distortion correction output from epi_reg in fsl
to freesurfer
Douglas N Greve Mon, 19 Nov 2012 08:05:18 -0800
Hi Ted, can you use epidewarp.fsl to create the warp field (voxel shift
map (VSM))? If so, you can then use bbregister and mri_vol2surf with the
--vsm option to apply the warp simultaneously with determining or
applying the registration. It might work with the warp field that you
have (since epidewarp.fsl uses fsl to compute the VSM).
doug
________________________________
From: Ted Satterthwaite <ted_s...@yahoo.com>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, November 15, 2012 2:35 PM
Subject: applying distortion correction output from epi_reg in fsl to freesurfer
Hi Bruce, Doug, and FreeSurfer Team,
We have calculated coregistrations between bold timeseries and T1 images using
BBR & distortion correction as implemented in the epi_reg utility in FSL5.
We would like to map our functional timeseries to surface space for
connectivity analyses (analagous to papers by Yeo & Buckner). Normally,
without distortion correction, we would use tkregister tp convert the rigid
body coregistration calculated in fsl by flirt(.mat) to a register.dat file,
and then use mri_vol2surf to birng the data to surface space. However, with
distortion correction, the coregistration between the epi & T1 is represented
as a deformation field (_warp.nii.gz).
Is there a way for FreeSurfer to read this warp and use the information? We
could of course simply do a two-step registration by moving our epi data into
T1 space first using FSL and then use FreeSurfer to get it to the surface, but
that would involve an extra interpolation. Are the ways to do this in one
step using our already-calculated & QA'd deformation fields from FSL?
Thanks so much for your time & advice.
Best,
Ted Satterthwaite
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