Hmmm...no I don't think so. Will do and let you know __________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net
> On May 22, 2015, at 3:32 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > > Hi Gaurav, > > Did you look at all 3 warpfield volumes (the second volume, Y, should contain > most of the info)? > > Peace, > > Matt. > > From: Gaurav Patel <gauravpa...@gmail.com> > Date: Friday, May 22, 2015 at 2:28 PM > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] SBref Distortion Correction > > Hi Matt… Juan is working with me at Columbia to get the topups working with > the HCP pipeline. The echo spacing is the same in both scans, as is the > geometry we believe, though we still need to confirm that. The warpfield > images have no information in them that I can tell, as changing the scaling > of the display doesn't reveal anything. Also the shimming should be the same > for all scans. The spin echo and gradient echo images look like they have the > same distortions after they've been rigidly realigned, so we're a little > puzzled as to why the topup procedure is failing. Any help would be > appreciated. Thanks! > > _________________________ > gaurav patel > gauravpa...@gmail.com > www.neurofreak.net > > On May 22, 2015, at 3:00 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > >> It helps to reply to the previous e-mail chain so that all of the info on a >> question is in one place. >> >> Are you sure that those warp fields don’t have data in them, just a bad >> scaling of the display? I don’t think the issue is with the topup >> configuration (we’ve never had to change that, despite using it on scanners >> with different field strengths). >> >> It would be good to check on what I suggested in the previous response. >> While it is undoubtably better to use a proper SBRef generated from the MB >> sequence itself, it should still be possible to do what you are doing. It >> is important that using a rigid registration of the MB to the SBRef results >> in a very precise alignment (the images should have exactly the same >> distortion). >> >> Another question, do you know that your scanner used the same shim for all >> the scans? >> >> Peace, >> >> Matt. >> >> From: Juan Sanchez <sanch...@nyspi.columbia.edu> >> Date: Friday, May 22, 2015 at 8:56 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] SBref Distortion Correction >> >> >> Let us clarify what we are doing exactly here. We are using spin-echo images >> with alternating phase-encoding directions in alternating runs (Topup PA and >> Topup AP, in our case). We also decided to use the corresponding Topup (PA >> or AP) as SBRef instead of an actual single-band reference image because we >> had issues obtaining the single-band image and because the tissue contrast >> in the spin-echo/Topup is pretty good (we tried using as SBRef the first >> frame of the multiband EPI but the spin-echo/Topup definitely works better, >> probably because of its improved tissue contrast). Even though using the >> Topups instead of a B0 map for distortion correction and using the Topup as >> SBRef instead of the first frame of the multiband EPI result in clear >> improvements, the resulting undistorted SBRef is not perfectly aligned to >> the anatomical images. For this reason, we think there's a problem with the >> procedures creating or applying the WarpField (the topup procedure or the >> applyward procedure that uses the WarpField to undistort the SBRef). The >> undistorted SBRef in an example subject from the HCP dataset looks >> noticeably better aligned to the anatomical image than ours. Furthermore, >> the WarpField.nii in that example subject looks very similar to the >> corresponding TopupField.nii (like a scaled version of it). In our data, in >> contrast, the TopupField.nii looks probably like it's supposed to look like >> (with some anatomical information) but the WarpField.nii is totally empty in >> some cases! After realizing this is the case, we think that our (main) >> problem may be in the topup procedure (or maybe the input images it uses or >> some later modification to the WarpField.nii). Could you give us any >> suggestions as to how to fix this issue? Maybe we need to adjust some of the >> configuration files that the topup procedure uses? Did you have to tweak any >> parameters to optimize this for your scanner? >> >> We're attaching one screencapture with the TopupField.nii and the >> WarpField.nii, another image showing the T2 anatomical scan, and a third >> image showing the SBRef (Topup in our case). >> _______________________________________________ >> 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 > > > > 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
