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Hey Matt, Jesper, Thanks for the help! I managed to get the C2P going on our scanner and performed some further testing. If you want to see some slides, msg me so I can send it over! My conclusions so far: 1) The scanning sequence that we're trying to correct has a quite long readout duration (~79 msec) - this might cause some problems with topup using the (matched) SE AP/PA scans, especially distortion-correction of more frontal brain regions. Maybe topup is finding a local minimum like Jesper said. 2) Using the GE AP/PA and topup SEEMS to do fine - or better - regarding the frontal corrections, but in my testing I found that the contrast between WM and GM in the GE-topup-corrected images seems to have been reduced. Like it has 'smeared' too much. 3) Using 'standard' B0 fieldmaps (dual-echo) seems to be relatively robust and doesn't suffer from the contrast loss in (2). 4) Using the HCP C2P SE AP/PA fieldmaps in our case does a little bit better than our WIP SE AP/PA fieldmaps. But the SE fieldmaps look really really similar. The C2P fieldmaps might have slightly better contrast, but this is just visual impression - I didn't test. So I will recommend to my group to use the B0 dual-echo fieldmap, but acquire the rest as well. If anything doesn't work as planned, the B0 fieldmap with prelude/fugue would be a good option to fall back on in case things don't work well. Thanks Best wishes Johan On Fri, Aug 25, 2017 at 8:32 PM, Matt Glasser <[log in to unmask]> wrote: > Remember that the distortion scales with the echo spacing, so 0.78 is > quite a bit worse than 0.58 and may simply be too high for topup as Jesper > says. I think the solution will be to change your protocol to match the > HCP’s CCF/lifespan protocol. I believe there is Lifespan pilot 1b data > available from the HCP with roughly the same parameters, but you might want > to re-ask this question on the HCP list. > > 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: Thursday, August 24, 2017 at 11:44 PM > > To: <[log in to unmask]> > Subject: Re: [FSL] HCP Topup Unwarping advice > > 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/> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>> >> >