Hi Matt,
yes - thanks, I know.
I＊ve talked to Karla and some folks at your end at the time because I was
initially a bit astonished about the LR/RL choice but then I understood.
I think the reasons are also mentioned briefly somewhere in the HCP
documentation.
Cheers,
Andreas
Am 18.09.17, 13:40 schrieb "FSL - FMRIB's Software Library on behalf of
Matt Glasser" unter <[log in to unmask] on behalf of [log in to unmask]>:
>Hi Andreas,
>
>We used LR/RL because we could get the echo spacing down a bit and also
>the TE on the custom HCP scanner. For the standard Prisma this is no
>longer the case, so we are back to AP/PA.
>
>Peace,
>
>Matt.
>
>On 9/18/17, 2:08 AM, "FSL - FMRIB's Software Library on behalf of Andreas
>Bartsch" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>
>>Hi Johan,
>>
>>>while in another subject, the AP encoding made images stretched in this
>>>region
>>
>>Depending on the B0 inhomogeneities from the frontal sinus, this can
>>happen, esp. in the upper part, and then be misleading or confusing.
>>But have a look at the lower part of the frontobasis.
>>Also, the effect on the eyeballs and the pons should be similar for the
>>same phase encoding.
>>
>>>So I don't know whether setting PA encoding will always be the solution.
>>I易ve never had issues with PA while I did occasionally encounter issues
>>with AP.
>>This was, however, primarily in patients with metal artefacts (splinter
>>in
>>subcutaneous fact in the front) or very big frontal sinuses and using a
>>different B0-based correction method I was evaluating for Siemens.
>>For me, topup always performed quite fine - even in rather extreme cases
>>(cf., for example,
>>https://www.radiologie-bamberg.de/images/neuroradiologie/neuroradiologie-
>>2
>>9
>>.jpg) - yet my echo spacing tended to be lower than yours.
>>
>>>Maybe PA works in most cases?
>>
>>Yes, I would say so. I would say if you go for PA it may work for a few
>>cases in which you might encounter issues with AP.
>>I still tend to use PA to largely preserve the left/right symmetry of the
>>brain even though HCP opted for LR/RL for physics reasons.
>>
>>Cheers,
>>Andreas
>>
>>
>>
>>Von: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>>Johan <[log in to unmask]>
>>Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
>>Datum: Montag, 18. September 2017 um 02:02
>>An: <[log in to unmask]>
>>Betreff: Re: [FSL] HCP Topup Unwarping advice
>>
>>
>>Dear Andreas,
>>
>>
>>It makes sense yes. It's much harder to stretch (correct with topup)
>>something that's been compressed, than it is to compress something that's
>>stretched. And this compressing in the uncorrected images is quite big in
>>frontal and less so in posterior regions. And distortion scales (in the
>>sense of amount of voxels) with the in-plane resolution and total readout
>>length. Partial Fourier doesn't seem to affect distortion as much.
>>
>>
>>Funny that I saw is that in one subject, the AP encoding made images
>>frontally compressed, while in another subject, the AP encoding made
>>images stretched in this region. So I don't know whether setting PA
>>encoding will always be the solution. I didn't think anything was too
>>different between the two subjects though. Maybe PA works in most cases?
>>
>>
>>Thanks and best wishes
>>
>>Johan
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>On Thu, Sep 14, 2017 at 7:19 PM, Andreas Bartsch <[log in to unmask]>
>>wrote:
>>
>>Hi Johan,
>>
>>I think I can imagine what is happening and have seen that before:
>>Using A>P phase encoding, the signal of different tissues (brain/skin)
>>are
>>- due to the local B0 field distribution - shifted towards the same
>>geometric position in distorted EPI space. The correction has a hard time
>>to disentangle these and can eventually fail. Using P>A, the same signal
>>contributions are shifted away from each other and can be corrected.
>>In the back part of the skull this isn易t much of a problem because there
>>is no pneumatised sinus, i.e. the local B0 field does not show these
>>inhomogeneities.
>>Does that makes sense?
>>For this very reason, I have always used P>A in GE-EPI.
>>Cheers,
>>Andreas
>>
>>Von: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>>Johan <[log in to unmask]>
>>Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
>>Datum: Donnerstag, 14. September 2017 um 07:31
>>An: <[log in to unmask]>
>>Betreff: Re: [FSL] HCP Topup Unwarping advice
>>
>>
>>Some further calculations with using topup to reverse-correct the PA GE
>>scans and getting pretty good results would support the notion that I was
>>dealing with something related to signal dropout with AP phase encoding
>>direction in our GE functional scans.
>>
>>
>>So maybe the solution (at least for frontal regions) would be to choose
>>PA
>>phase encoding direction instead of AP. Would this make any sense? In
>>principle I don't really see too big a price to pay in the rest if the
>>brain when switching from AP to PA.
>>
>>
>>Thanks again
>>
>>best wishes
>>
>>Johan
>>
>>
>>
>>
>>
>>
>>
>>
>>On Thu, Sep 14, 2017 at 3:10 PM, Johan <[log in to unmask]> wrote:
>>
>>Hi Matt,
>>
>>
>>I think I understand what the issue is at our site. The SE scans have a
>>rather big hyper-intensity at the boundary region of signal dropout. The
>>GE (and functional) scan here do not have this hyperintensity.
>>
>>
>>
>>The SE scans themselves correct quite nicely, with the hyperintense
>>border
>>region being put into the proper spot (Warpfield) and attenuated
>>(Jacobian) by about 30% (in our case). So topup with SE fieldmaps on SE
>>scans works.
>>
>>
>>The GE scans do not correct nicely, since the warp itself is probably
>>file, but the Jacobian determinant then attenuates the replaced voxels
>>(which already had low-ish signal to begin with) with a factor that is
>>likely too big.
>>
>>
>>The thing is that in the SE fieldmaps, when you 'move across the edge',
>>in
>>P->A direction to frontal, the signal intensity first becomes 10x
>>stronger
>>before it goes down. In the GE scans (to be corrected), the signal
>>intensity becomes 0.5x as strong before going down. This different
>>behaviour isn't accounted for in the Jacobian
>>
>>
>>It could be that it's signal dropout, if you argue that is much harder to
>>push the echo out of a SE k-space acquisition, where the peak is
>>(temporally) in the middle by design, than it is to push it out of a GE
>>acquisition, where the peak will already be at the edge (and be easily
>>pushed over).
>>
>>
>>We did manage to reduce read-out time to about 65 msec this time, but SE
>>fieldmaps issues still persist. I would be appreciative of any thoughts
>>you might have!
>>
>>
>>Best wishes
>>
>>Johan
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>On Thu, Sep 7, 2017 at 12:25 PM, Matt Glasser <[log in to unmask]> wrote:
>>
>>What you can achieve with multi-band will depend on your coil and spatial
>>resolution and what your goals are. We do okay with MB=8 and 2mm voxels
>>with a 32 channel coil, but individual subject subcortical SNR in the
>>very
>>center of the brain isn易t great (that said, you can still see all the
>>functional neuroanatomy at the group level). Some groups have opted for
>>2.4mm as a somewhat more conservative approach. What you need to do is
>>to
>>lower you echo spacing by increasing your bandwidth to fix the distortion
>>issue.
>>
>>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, September 6, 2017 at 7:25 PM
>>To: <[log in to unmask]>
>>Subject: Re: [FSL] HCP Topup Unwarping advice
>>
>>
>>
>>
>>Hi Matt,
>>
>>
>>I think this afternoon we'll try to get/set the echo spacing down a bit,
>>as I think we don't work the gradient system as hard as we could. The
>>general conclusion regarding topup might be that there is some limit
>>w.r.t. total slice readout time (matrix size * echo spacing) where
>>distortions get so out of hand even topup cannot manage properly.
>>
>>Do you know how (high levels of) multiband affects sensitivity (contrast
>>to noise, or T-stats) in subcortical areas - or hippocampus? In your
>>experience, Is it still OK or you think there might be a sensitivity
>>loss?
>>
>>
>>Thanks
>>Johan
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>On Mon, Sep 4, 2017 at 11:17 PM, Matt Glasser <[log in to unmask]> wrote:
>>
>>Did you get the echo spacing down?
>>
>>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: Monday, September 4, 2017 at 12:46 AM
>>To: <[log in to unmask]>
>>Subject: Re: [FSL] HCP Topup Unwarping advice
>>
>>
>>
>>
>>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易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易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易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 <tel:+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/>
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