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
