First make sure you're using the right coefficient file, copied directly from the scanner. The Prisma should have a file called coeff_AS82.grad, so the one you used in your *second* command above should be correct.
Second is to be absolutely sure your input is the uncorrected volume (*_ND). If you include some matched screenshots of the uncorrected, offline-corrected, and scanner-corrected volumes, we can maybe help evaluate the difference. On Mon, Apr 9, 2018 at 4:09 AM, Kristian Loewe <k...@kristianloewe.com> wrote: > Thanks Keith, > > Cropping is turned off by default in the version of dcm2niix that I'm > using but I re-ran the conversion with "-x n" anyway. I also used > fslreorient2std as per your suggestion. Unfortunately, the result is still > the same. Do you have any other ideas? > > > Cheers, > > Kristian > > > Quoting Keith Jamison <kjami...@umn.edu>: > > 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 >>> >> >>> >> >>> >> _______________________________________________ >>> >> HCP-Users mailing list >>> >> HCP-Users@humanconnectome.org >>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >>> >> >>> >> ------------------------------ >>> >> >>> >> The materials in this message are private and may contain Protected >>> >> Healthcare Information or other information of a sensitive nature. If >>> you >>> >> are not the intended recipient, be advised that any unauthorized use, >>> >> disclosure, copying or the taking of any action in reliance on the >>> contents >>> >> of this information is strictly prohibited. If you have received this >>> email >>> >> in error, please immediately notify the sender via telephone or return >>> mail. >>> >> >>> >> _______________________________________________ >>> >> HCP-Users mailing list >>> >> HCP-Users@humanconnectome.org >>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >>> > >>> > _______________________________________________ >>> > HCP-Users mailing list >>> > HCP-Users@humanconnectome.org >>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> > > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
