Some problems can arrise if the NIFTI files are unexpectedly manipulated
prior gradient_unwarp. Two things to check:

1. dcm2nii and dcm2niix has options to perform additional processing like
reorienting or cropping, some of which may be enabled by default. Make sure
those are all DISABLED. (for dcm2niix add "-x n" and for dcm2nii you can
add "-x N -r N"
2. We also usually use "fslreorient2std <origT1> <origT1>_new and then
gradient_unwarp.py on <origT1>_new

-Keith


On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe <k...@kristianloewe.com>
wrote:

> Hi,
>
> I would like to use gradunwarp for offline gradient nonlinearity
> correction of some data acquired on our local Siemens scanners. I used
> dcm2niix to convert the dicom data to nifti format. After applying
> gradunwarp to a T1 image in nifti format (the one that originally has
> the _ND suffix), I proceeded to compare the result with the
> Siemens-corrected T1 image. I expected that they would look very
> similar but in fact they look quite different. I am wondering if this
> is to be expected to some degree because of differences in the
> correction algorithms or what else might be the reason for this. Could
> it be the case, for example, that the wrong center is being used for
> some reason?
>
> I have tried this for a T1 image acquired on a Verio and another one
> from a Prisma using
>
>    gradient_unwarp.py T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS097.grad
> -n
>
> and
>
>    gradient_unwarp.py T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS82.grad -n
>
> respectively.
>
> I would really appreciate any help or advice you can provide.
>
> Cheers,
>
> Kristian
>
>
> Quoting Keith Jamison <kjami...@umn.edu>:
>
> > FYI, when available, you can enable it on the scanner in the
> > "Resolution->Filter" tab with the "Distortion Correction" checkbox.  It's
> > often used for structural scans like MPRAGE, where you will see two DICOM
> > folders in the output: <scanname> and <scanname>_ND.  ND means "No
> > Distortion [Correction]".. .A very confusing choice of acronym.  You can
> > then compare the online corrected (not _ND) and offline using gradunwarp.
> >
> > -Keith
> >
> >
> > On Wed, Oct 19, 2016 at 4:44 PM, Glasser, Matthew <glass...@wustl.edu>
> > wrote:
> >
> >> Some do for some sequences, but because it is not uniformly applied and
> >> because they are likely not to use optimal interpolation algorithms, we
> >> prefer to do offline correction.
> >>
> >> Peace,
> >>
> >> Matt.
> >>
> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Antonin
> Skoch <
> >> a...@ikem.cz>
> >> Date: Wednesday, October 19, 2016 at 4:27 PM
> >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> >> Subject: [HCP-Users] gradient nonlinearity correction question
> >>
> >> Dear experts,
> >>
> >> during the set-up of gradunwarp scripts, it came to my mind, why scanner
> >> vendors standardly do not perform gradient nonlinearity correction
> directly
> >> on the scanner as part of on-line image reconstruction system (i.e. ICE
> in
> >> Siemens)?
> >>
> >> Regards,
> >>
> >> Antonin Skoch
> >>
> >>
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