1. Yes 2. We use dcm2nii. 3. Probably I would use offline so you are sure that all of your images are being corrected the same way and have control over how the resampling is being done (i.e. not adding blurring from trilinear interpolation).
Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Sandhitsu Das <su...@seas.upenn.edu<mailto:su...@seas.upenn.edu>> Date: Friday, August 4, 2017 at 12:06 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Offline vs. online gradient nonlinearity correction This is following up on a thread here https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03502.html We are evaluating online vs. offline correction on our 3T Simens Prisma system using a phantom. I have three questions: 1) Looks like the gradunwarp script is agnostic to the sequence type. Does this mean that we should use it the same way for any sequence (including structural or functional) as a first preprocesing step ? 2) The gradunwarp script takes nifti input. My understanding is that the coefficient file defines the known nonlinearity profile using scanner coordinates. Does this mean the output may be different when using nifti files produced by different dicom converters which can potentially change the coordinate system in some way ? 3) Please see the two attached screenshots that compare online vs. offline corrections. The two images show a middle coronal slice and and a terminal one respectively. Bottom shows original, top left shows online corrected, top right shows offline corrected. While in the middle slice it looks like offline and online produces pretty much the same output (although we didn't quantitatively evaluate yet), there is something funny going on at the terminal slices. Artifact of boundary condition assumptions ? Any help is much appreciated. We can't move on with our studies until we figure out the right way to do this as this is (presumably) the very first pre-processing step. Thanks, Sandy _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
