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Dear Matt, The particular sequence I sent was done in a couple of other subjects, and distortion correction didn't seem optimal in those as well. The echo spacing in our case is a bit worse - 0.78 msec. It's possible that the gradients system can handle more, though - I remember that back when the sequence was put in, the TR was made a bit longer. Im trying to get the C2P HCP sequences running and compare outcome of those what what we get right now. Do you have some images that you could possibly send to us - so we can figure out what kind of quality and image features we should be aspiring to? Thanks Johan On Thu, Aug 24, 2017 at 9:52 PM, Matt Glasser <[log in to unmask]> wrote: > Has this issue reproduced across subjects? Have you tried using the HCP’s > CCF protocol (http://protocols.humanconnectome.org/CCF/) for the Prisma? > It looks like that is what you are trying to do and we have gotten fine > results with 2mm data on the Prisma. Some important differences: 1) We are > not using any partial fourier (which does not reduce distortion but does > increase dropout). 2) Are you achieving an echo spacing of 0.58ms? > > I do not recommend GRAPPA at 3T for fMRI, this will lose you a lot of SNR. > > > Peace, > > Matt. > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > Johan <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Wednesday, August 23, 2017 at 10:24 PM > > To: <[log in to unmask]> > Subject: Re: [FSL] HCP Topup Unwarping advice > > Dear Matt, > > The scanner is Magnetom Prisma, Software Version E11 (B) > > Of the fieldmaps: > Resolution is 106x106 2mm^2, slice thickness 2 mm, 72 slices. Partial > Fourier 6/8, and no iPat and no MB. > The functionals have MB 8. > > > This issue regarding the SE fieldmap performing worse than the GE versions > - we have it not only for this scan (A) - but also for other scan versions, > even when we use iPat of 2 (row D). Of course, distortions in iPat > accelerated scans are less bad. The last column RelDist is just based on > visual inspection. > > > Scan Type MB Grappa Matrix VoxSize (mm) Slices SliceTh (mm) TR (sec) FA > (deg) NVOL Task RelDist (voxels) > A 8 1 106 2 72 2 *0.81* 53 *450* 3.4 > B 4 1 96 2.21 60 2.2 *1.24* 53 *310* 2.39 > C 8 1 88 2.4 64 2 *0.735* 52 *490* 2.6 > D 3 2 86 2.5 60 2.5 *1.2* 67 *295* 1 > > > Therefore some data where we could see SE fieldmaps, as they should look > like - would be really valuable. > > Thanks > Johan > > > > > > On Thu, Aug 24, 2017 at 11:07 AM, Matt Glasser <[log in to unmask]> wrote: > >> What scanner and resolution are you using? >> >> Peace, >> >> Matt. >> >> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of >> Johan <[log in to unmask]> >> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >> Date: Wednesday, August 23, 2017 at 7:59 PM >> >> To: <[log in to unmask]> >> Subject: Re: [FSL] HCP Topup Unwarping advice >> >> Dear Jesper, >> >> Thanks for looking at it! >> >> Do you have a data sample (of preferably a Prisma scanner) of how things >> (EPI, SE Fieldmaps) should look like? Otherwise its not clear what quality >> we should be aiming for. It'd be tremendously helpful if I can run >> comparisons what we have with something like a 'gold standard'. >> >> What I can try today is to use iPat of 2 for our current SE fieldmaps, >> and then take care of the discrepancy with the functional using the >> readoutlength as defined in the parameters file that topup uses like you >> suggested. If iPat of 2 exactly halves the readout time, then topup should >> solve for a less-distorted solution and applytopup could interpolate >> accordingly in the functionals. It'll still be helpful to have something to >> check our scans against, though. >> >> Thanks and best wishes >> Johan >> >> >> >> PS. It could be that in our case, the total readout time (with 106/106 >> matrix, 6/8th partial F, but no iPat) causes distortions to a higher degree >> (i.e., ~3 voxels... or maybe even higher) than topup can handle. Maybe >> that's the issue with your other dataset - or do you think it's something >> more subtle? >> >> >> >> >> >> >> >> >> >> >> >> >> On Wed, Aug 23, 2017 at 10:54 PM, Jesper Andersson < >> [log in to unmask]> wrote: >> >>> Dear Johan, >>> >>> I have had a look at your data and I am afraid that neither fieldmap >>> (the SE or GE) look very good. I am not 100% sure exactly why that is, but >>> I think that the problem is the very large distortions. It (topup) has come >>> up with a quite creative solution where instead of pushing back all of the >>> frontal intensity that has been pulled out, it pushes back some and leaves >>> some, while doing the opposite for the reverse PE direction. The end result >>> is an image pair (the --iout output) that looks surprisingly sane, but >>> where the field is not what one would expect from a human head. >>> >>> I have only seen this behaviour once before, and I haven’t got a >>> solution for it. Essentially it is a situation where the non-linear >>> optimisation (which is what topup does) has two minima, and topup falls >>> into the wrong one. For future acquisitions I would suggest using some IPAT >>> (a factor 2 should be sufficient) to reduce the distortions. For the >>> current data I can only suggest experimenting with the config file to see >>> if you can get it to take a different path and find the other minimum. >>> >>> Sorry I cannot be of more help. >>> >>> Jesper >>> >>> On 23 Aug 2017, at 04:09, Johan <[log in to unmask]> wrote: >>> >>> Dear Matt, >>> >>> I uploaded a tarball (a second one - the first one isn't good) to the >>> FSL upload site for inspection. I also have a screenshot but it's too big >>> for the FSL mailinglist to accept, so I also uploaded it to the FSL upload >>> site. >>> >>> >>> Thanks again and best wishes >>> Johan >>> >>> >>> >>> On Wed, Aug 23, 2017 at 11:48 AM, Matt Glasser <[log in to unmask]> wrote: >>> >>>> The images you sent were not sufficient to evaluate the issue. Perhaps >>>> if you have some mid sagittal slices after distortion correction in which >>>> you can see some clear anatomy and compare the T1w to the fMRI. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of >>>> Johan <[log in to unmask]> >>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >>>> Date: Tuesday, August 22, 2017 at 8:34 PM >>>> >>>> To: <[log in to unmask]> >>>> Subject: Re: [FSL] HCP Topup Unwarping advice >>>> >>>> Dear Matt, >>>> >>>> I did actually carefully check the scans how they compare to the >>>> Anatomy - the T1. I extracted the boundary between WM and GM of the T1 >>>> scan, and compared to that boundary (and also the T1). The thing is I see >>>> too much dropout in a region where normally you wouldn't expect any dropout >>>> normally - it's too much in the 'middle' of the EPI scan. As if somehow >>>> things get too compressed, or something outside of the brain where signal >>>> is more random, gets pushed inside (but this just a guess on my part). Also >>>> when I calculate the match between T1 and EPI, using fsl FLIRT's brr cost >>>> function, I get lower values for the GE-corrected scans, indicating a >>>> better fit. >>>> >>>> I sent an example 'package' of our results (topup files for GE and SE + >>>> instructions), including T1 and T1 boundary to Jesper (well - will do in a >>>> few minutes). If you wish I can also send it to you for inspection. >>>> >>>> Thanks for your time and best wishes >>>> Johan >>>> >>>> >>>> >>>> >>>> >>>> On Wed, Aug 23, 2017 at 11:14 AM, Matt Glasser <[log in to unmask]> wrote: >>>> >>>>> Like I said on the HCP list what is most important is comparing >>>>> anatomy that is within the distorted region but not the dropped out >>>>> region. This is how you evaluate the quality of the distortion correction, >>>>> not on the size of the dropped out region. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf >>>>> of Johan <[log in to unmask]> >>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >>>>> Date: Tuesday, August 22, 2017 at 8:05 PM >>>>> >>>>> To: <[log in to unmask]> >>>>> Subject: Re: [FSL] HCP Topup Unwarping advice >>>>> >>>>> Dear Matt, >>>>> >>>>> We have (tried) to be really contentious w.r.t. matching echo dwell >>>>> time, in-plane resolution, # k-lines (EPI factor or iPat), partial Fourier >>>>> (it matches the EPI), voxel sizes, tot. slices, orientation and bandwidth. >>>>> Anything basically that could taper with the amount of time spent reading >>>>> out one slice of k-space (which is the main thing w.r.t. distortions). We >>>>> also were careful in the analysis w.r.t. possible motion happening between >>>>> acquisition of SE Fieldmap and following functionals too. >>>>> >>>>> The only thing different, as far as we could see, is that we used the >>>>> Scanner's own SE - EPI instead of the HCP SE-EPI. I'm trying to get those >>>>> installed so I can compare those with what we have so far. >>>>> >>>>> I will upload a sample dataset that we have to the URL Jesper gave me! >>>>> >>>>> This scan is, from the 4 scans that we did, the most 'sensitive' to >>>>> distortions (about 2-3 voxels) due to a res of 2mm ^3 and 106x160 matrix. >>>>> Partial F is 6/8th for both fieldmap and functionals. >>>>> >>>>> Thanks and best wishes >>>>> Johan >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, Aug 22, 2017 at 9:55 PM, Matt Glasser <[log in to unmask]> wrote: >>>>> >>>>>> Also, did you match the geometry between SE and GE images and the >>>>>> echo spacing? What kind of scanner do you have? >>>>>> >>>>>> Peace, >>>>>> >>>>>> Matt. >>>>>> >>>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf >>>>>> of Jesper Andersson <[log in to unmask]> >>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >>>>>> Date: Tuesday, August 22, 2017 at 5:04 AM >>>>>> To: <[log in to unmask]> >>>>>> Subject: Re: [FSL] HCP Topup Unwarping advice >>>>>> >>>>>> Dear Johan, >>>>>> >>>>>> that does indeed look unusual. I think the best would be if I could >>>>>> take a look at your data. To do so, can you please send me the input files >>>>>> into topup for the SE and the GE cases and also a small sample (a couple of >>>>>> volumes) of the GE data that you want to correct? Please put all file in a >>>>>> tar-ball and upload it to >>>>>> >>>>>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F >>>>>> >>>>>> Can you please also send me an email with the exact commands you used >>>>>> for running topup and applytopup? >>>>>> >>>>>> Jesper >>>>>> >>>>>> On 22 Aug 2017, at 09:44, Johan <[log in to unmask]> wrote: >>>>>> >>>>>> Dear Jesper, >>>>>> >>>>>> I could send you the Magnitudes that I have for you to inspect. Here >>>>>> the SE stuff does look a bit better/more tidy. However the EPI, when >>>>>> topup-SE-corrected have quite big 'holes' frontally that I really don't >>>>>> trust is normal dropout - or at least, it looks quite unsubtle. >>>>>> >>>>>> >>>>>> This figure is about the EPI - left = SE unwarped right = GE unwarped. >>>>>> >>>>>> <image.png> >>>>>> >>>>>> >>>>>> >>>>>> Best wishes >>>>>> Johan >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Aug 22, 2017 at 6:02 PM, Jesper Andersson < >>>>>> [log in to unmask]> wrote: >>>>>> >>>>>>> Dear Johan, >>>>>>> >>>>>>> what does the --iout output look like for SE and GE-EPI >>>>>>> respectively. I would expect the former to look better, i.e. less >>>>>>> difference between AP and PA after topup. If not, I think something must be >>>>>>> going wrong. >>>>>>> >>>>>>> When then applying these maps to the GE-EPI images those wont _look_ >>>>>>> as good, because the GE-EPI images also has dropout in those same areas as >>>>>>> there are distortions. It can be surprisingly difficult to distinguish >>>>>>> dropout from distortion, no matter how trained your eye. >>>>>>> >>>>>>> Jesper >>>>>>> >>>>>>> On 22 Aug 2017, at 08:33, Johan <[log in to unmask]> wrote: >>>>>>> >>>>>>> Hi Stephen, >>>>>>> >>>>>>> Yes, we did carefully check all major dropout-susceptible regions of >>>>>>> the brain and still found that the GE AP/PA 'way' somehow produced more >>>>>>> 'complete/better looking' EPIs. The output we get from the GE AP/PA looks >>>>>>> quite reasonable, whereas the SE AP/PA produced scans looking actually a >>>>>>> bit worse with more dropout where we didn't suspect it. We got the same >>>>>>> kind of result for four different kinds of EPI scans, making me thing that >>>>>>> either our SE AP/PA protocol isn't optimal in some way (or I am just doing >>>>>>> something wrong in the analysis). >>>>>>> >>>>>>> But I still wish to figure out what's the deal with our SE AP/PA >>>>>>> scans (se_ep2d based), exactly because in theory SE approach should work >>>>>>> better due to absence of signal dropout in the AP and PA scans. >>>>>>> >>>>>>> In our analysis, we just used basic topup to get the unwarping data >>>>>>> - then did applytopup to unwarp functionals - being careful about >>>>>>> orientation issues. Just as written in the tutorials. We didn't mask or >>>>>>> anything. >>>>>>> >>>>>>> Could I possibly as a test obtain one of your SpinEchoFieldMap AP/PA >>>>>>> scans as well as a functional (and how it should be looking once it's >>>>>>> unwarped)? >>>>>>> >>>>>>> Thanks and best wishes >>>>>>> Johan >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Aug 22, 2017 at 4:00 PM, Stephen Smith <[log in to unmask] >>>>>>> > wrote: >>>>>>> >>>>>>>> Hi - GE AP/PA data is not recommended because this has the serious >>>>>>>> dropouts in the areas being most affected also by distortions - have you >>>>>>>> checked in those areas for performance of the unwarping? >>>>>>>> >>>>>>>> This email list is the best venue for sending these questions, >>>>>>>> Cheers, Steve. >>>>>>>> >>>>>>>> >>>>>>>> On 22 Aug 2017, at 06:54, Johan <[log in to unmask]> wrote: >>>>>>>> >>>>>>>> Dear experts, >>>>>>>> >>>>>>>> If I have a rather complicated question regarding Topup, SpinEcho >>>>>>>> Fieldmaps with AP / PA phase encoding directions, who would you suggest I >>>>>>>> contact? >>>>>>>> >>>>>>>> I have some data that i'd like to send. We obtained GE and SE AP >>>>>>>> and PA scans, and although SE AP/PA combination pair is recommended, for >>>>>>>> our case GE AP/PA seems to work better. We're not confusing this with the >>>>>>>> dual-echo B0 Fieldmaps. >>>>>>>> >>>>>>>> Thanks and best wishes >>>>>>>> Johan >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------ >>>>>>>> --------------- >>>>>>>> Stephen M. Smith, Professor of Biomedical Engineering >>>>>>>> Head of Analysis, Oxford University FMRIB Centre >>>>>>>> >>>>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>>>>>> +44 (0) 1865 222726 <+44%201865%20222726> (fax 222717) >>>>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>>>>>>> ------------------------------------------------------------ >>>>>>>> --------------- >>>>>>>> >>>>>>>> Stop the cultural destruction of Tibet <http://smithinks.net/> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >>> >> >