Dear Everyone,
We're happy to announce the release of the updated FieldMap
toolbox version 2.0 for SPM5 which can be downloaded with and
should be run with the latest SPM5 distribution. Please read
through the main changes which are listed below:
1) The convention used to describe the direction of the
k-space traversal is now based on the coordinate system used
by SPM. In this coordinate system, the phase encode direction
corresponds with the y-direction and is defined as positive
from the posterior to the anterior of the head. The x-direction
is defined as positive from left to right and the z-direction
is defined as positive from foot to head. The polarity of the
phase-encode blips describes in which direction k-space is
traversed along the y-axis with respect to the coordinate
system described here. The change in convention means that if
previously the polarity of phase-encode blips in the FieldMap
gui was usually set to be negative, it should now be positive
and vice versa. This also applies to the default value for
pm_def.K_SPACE_TRAVERSAL_BLIP_DIR in the pm_defaults.m file which
should be set to -1 if it was +1 previously and vice versa.
As before, the recommendation is: When you first start using the
toolbox USE THE GUI TO ENSURE YOUR DISTORTION CORRECTIONS GO IN
THE RIGHT DIRECTION.
2) In the previous version of FieldMap, there was a bug in
the application of the Jacobian modulation when using an
EPI-based field map. This has now been fixed. Thankyou to
Xu Ning who first alerted us to the presence of this bug.
3) The toolbox now allows the user to select a specified
defaults file.This means it is possible to have more than one
default file containing different sets of parameters relating
to different field map and /or EPI sequences. This is
particularly useful for sites where more than one sequence is
routinely used.
4) The toolbox can be run using the new SPM5 User Interface.
This will allow FieldMap jobs to be saved serving as a log about
how the data was processed. It will also facilitate scripting
and batching jobs.
5) The toolbox now reads and writes files in nifti format
(as does SPM5).
6) The toolbox now save a vdm5_* file which will also be expected
by Realign & unwarp. If doing Unwarp with multiple sessions, but
a single vdm5_* file, it will be necessary to select this file
for each session.
7) All versions of FieldMap and Unwarp are only designed to work
with images collected with the phase-encode direction in y.
We have tried our best to thoroughly test and validate
the toolbox but please report any problems to us. All the
usual waivers and disclaimers apply.
Good luck
Chloe & Jesper
--
Dr Chloe Hutton
Wellcome Trust Centre for Neuroimaging
Institute of Neurology
University College London
12 Queen Square
London WC1N 3BG
United Kingdom
Tel. +44-20-7833-7478, (internal ext 4368)
Fax +44-20-7813-1420
[log in to unmask]
--
Dr Chloe Hutton
Wellcome Trust Centre for Neuroimaging
Institute of Neurology
University College London
12 Queen Square
London WC1N 3BG
United Kingdom
Tel. +44-20-7833-7478, (internal ext 4368)
Fax +44-20-7813-1420
[log in to unmask]
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