Hi Sandhitsu, 1. You could take a difference between the two images to see if anything beyond the extreme slice is affected much 2. We do really try to avoid trilinear interpolation because of its blurring effect. For offline correction we output the warpfield which allows us to use applywarp from FSL to do a less blurring spline interpolation. Additionally we try to concatenate warpfields/affine matrices so that only a single resampling occurs.
Best, Matt. From: Sandhitsu Das <su...@seas.upenn.edu<mailto:su...@seas.upenn.edu>> Date: Monday, August 7, 2017 at 3:39 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Offline vs. online gradient nonlinearity correction Thank you both for responding, guys! Followup questions: 1) When you say "probably" for 3), whatever is going on, can we assume this will be limited to the last one slice only ? 2) I see your point about interpolation, but I thought you mentioned when you were here that the trilinear is something that you do as well (I see the output files named that way also, or should we be using the "warped" file ?). On Fri, Aug 4, 2017 at 2:34 PM Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: FYI: We are switching over to using ‘dcm2niix’, which is Chris Rorden’s newer, actively maintained conversion tool. -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Friday, August 4, 2017 at 1:21 PM To: Sandhitsu Das <su...@seas.upenn.edu<mailto:su...@seas.upenn.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Offline vs. online gradient nonlinearity correction 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<mailto: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. 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