While that is probably better than not correcting for distortions, it is
also likely worse than what you can do with a field map or reversed phase
encoding directions. The reason is that in addition to geometric
distortions, b0 inhomogeneities also cause intensity modulations where
images are stretched (darker) or compressed (brighter). Also the b0 image
has very different contrast from a T1w image, so nonlinear registration
may be challenging (you would need to use a cross-modal capable similarity
metric which I donıt think FNIRT hasperhaps ANTS has this). FA to T1w
might work better or b0 to T2w.
Also, use of the command line is a basic required skill in neuroimaging in
my view, equivalent to being able to pipette in a wet lab.
Peace,
Matt.
On 6/14/17, 7:09 AM, "FSL - FMRIB's Software Library on behalf of Jonatan
Ottino" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>Dear FSL experts,
>
>I have a DWI dataset with 1 b0 and 30 directions all in A>P. Since I
>haven't a field-map or two opposite b0 I can't apply neither FUGUE or
>TOPUP for correcting epi-distortions.
>
>However, the Enigma protocol says that epi-distortions may be corrected
>by using a T1 sequence. I write down the instructions below from their
>website (http://enigma.ini.usc.edu/protocols/dti-protocols/):
>
>Alternatively, a subjectıs DWI images can be adjusted through high
>dimensional warping of the b0 to a high-resolution structural (T1- or T2-
>weighted) image of the same subject not acquired using EPI. This requires
>multiple steps:
>
>1- Make sure skull-stripping has been performed on both b0 and
>T1-weighted scans.
>2- Make sure T1-weighted scans have undergone inhomogeneity (NU)
>correction (note: USING fsl FAST I GUESS?).
>3- Make sure T1-weighted scans and the DWI are aligned!! Check for L/R
>flipping!!
>4- Linear registration of b0 of DWI and T1-weighted reference together.
>**Due to differences in resolution and further registrations needed
>throughout the workflow we recommend initially aligning the the
>T1-weighted scans to ICBM space (which is the space of the ENIGMA-DTI
>template), then using a linear registration (with NO sheering parameters)
>to align your b0 maps to their respective T1-weighted scans in ICBM
>space**
>5- If using FSLıs flirt for linear registration, sheering can be avoided
>by manually setting the degrees of freedom (default 12) to 9 (flirt -in
>b0.nii.gz -out b02T1w.nii.gz -dof 9 -ref T1w.nii.gz)
>6- Once images are in the same space and linearly alight (visually check
>this!), you can perform non-linear registrations to remove the distortion
>from the b0.
>7- Some possible tools include ANTS , DTI-TK, or BrainSuite.
>8- The deformation fields from the warping should then be applied to all
>volumes in the DWI.
>
>I make my way through step 5. The problem is step 6 and 8, because i have
>no idea how to register (FNIRT?) and unwarp the distortions in the whole
>DWI dataset.
>
>I write the enigma staff and they replied almost immediately suggesting
>me to use a script which needs ANTs (http://stnava.github.io/ANTs/) to
>make the non-linear registration. I'm not a regular linux user, and the
>instructions for installing this software/tool are very hard to follow.
>
>My question then is: Did someone correct the epi-distortions from their
>DWI images using a T1 sequence?
>
>Thanks!
>Jonatan
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