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
