Dear Mark,
thanks a lot, that is reassuring. I do agree that the correction in the
distorted areas looks good. What I was concerned about is the stretching
outside the brain as I didn't know whether this was indicating a deeper
problem with the fieldmaps.
An experienced opinion on the data is very much what I needed. Thank you
for the intensive and immediate support in this question.
Best regards,
Julia
On 05/23/2014 09:38 AM, Mark Jenkinson wrote:
> Dear Julia,
>
> I've had a look at this data and it all looks good to me.
> The distortions that I saw in your previous images seem to be much
> worse in the original data, and the distortion correction is doing a
> good job of reducing them. In particular, the alignment of the
> anterior regions (ventricles, frontal lobe) is definitely better with
> the distortion correction compared to without the distortion
> correction (see attached images).
>
> In some of the very inferior regions, where the signal loss is quite
> severe, then there is some slightly odd stretching of signal outside
> of the brain, but this is quite minor and in an area where there will
> be no reliable fMRI signal and it will also probably disappear when
> the brain mask is applied.
>
> So unless you have a particular area of concern that you can point
> out, I would say that epi_reg (and hence BBR) is actually doing a good
> job with this data.
>
> All the best,
> Mark
>
>
>
>
> On 21 May 2014, at 14:58, Julia Huntenburg
> <[log in to unmask] <mailto:[log in to unmask]>>
> wrote:
>
>> Dear Mark,
>>
>> thank you.
>>
>> I uploaded a zipped folder called 'epireg_smearing.tar.gz' . As I am
>> not sure from which stage you need to start you find
>> - fsl prepared fieldmap
>> - raw phase image
>> - raw and skullstripped magnitude image
>> - mean epi
>> - anatomy and skullstripped anatomy
>>
>> I also included the epi_reg command I was using and all the output
>> this gave me. This is not the 'worst' subject but quite typical.
>>
>> Maybe you need these informations:
>> echospacing=0.000670 s
>> phase encoding direction = y-
>> deltaTE = 2.46 ms (siemens scanner)
>>
>> Let me know if I can provide any further information or data that
>> might help.
>> Thanks in advance for looking into this.
>>
>> Best regards,
>> Julia
>>
>>
>> 2014-05-21 13:00 GMT+02:00 Mark Jenkinson
>> <[log in to unmask] <mailto:[log in to unmask]>>:
>>
>> Hi,
>>
>> I suspect that the registration is quite good for most of the
>> brain but is applying things inappropriately outside of the valid
>> brain mask. This is an issue with the extrapolation of the
>> fieldmap, which in such extreme angulations does not work well.
>> There might be a workaround for this, and we will implement a
>> better solution in a future release, although this is really only
>> going to be affecting small portions of the image around the edge
>> and will probably not survive the masking in the analyses.
>>
>> So that I can see if an immediate workaround is possible, can you
>> upload the data to the following:
>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>>
>> All the best,
>> Mark
>>
>>
>> On 17 May 2014, at 17:03, Julia Huntenburg
>> <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>>> Hi,
>>>
>>> thanks a lot for the hint, Mark. I had this suspicion too and
>>> had played around with the orientations before. Now I also tried
>>> what you suggested with fslreorient2std -- unfortunately nothing
>>> of it helped.
>>> In terms of the intermediate steps the different registrations
>>> seem to work ok. What looks odd to me though is the
>>> fieldmaprads2str image (see attached). Does that look normal to
>>> you? I'd be very happy for any further hint on what to change
>>> as I start running out of ideas.
>>>
>>> Many thanks and all the best,
>>> Julia
>>>
>>>
>>> 2014-05-16 9:55 GMT+02:00 Mark Jenkinson
>>> <[log in to unmask]
>>> <mailto:[log in to unmask]>>:
>>>
>>> Hi,
>>>
>>> The angulation and initial orientation of these images seems
>>> quite extreme, and so my suspicion is that some of the
>>> intermediate steps might not be working correctly. Have you
>>> tried running fslreorient2std on all of your input images
>>> (including the fieldmap)? That might make everything work
>>> better.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 15 May 2014, at 18:13, Julia Huntenburg
>>> <[log in to unmask]
>>> <mailto:[log in to unmask]>> wrote:
>>>
>>>> Hi Mark,
>>>>
>>>> the smearing of signal mostly from OFC and/or brainstem
>>>> occurs in the functional images registered to the
>>>> individual's structural space with epi_reg. I did try to
>>>> optimize the mask size but I cannot completely get rid of
>>>> the smearing. I also tried the epi_reg correction with
>>>> topup derived fieldmaps and have the same problem in
>>>> general. Please find two snapshots of epi_reg outputs
>>>> attached for an impression on what I mean.
>>>>
>>>> I am implementing these corrections for comparison with
>>>> another approach. To make it a fair comparison I am quite
>>>> eager to get the best possible solution. I'm happy to share
>>>> the commands and data if that helps.
>>>>
>>>> Many thanks,
>>>> Julia
>>>>
>>>>
>>>>
>>>> 2014-05-09 21:00 GMT+02:00 Mark Jenkinson
>>>> <[log in to unmask]
>>>> <mailto:[log in to unmask]>>:
>>>>
>>>> Hi,
>>>>
>>>>> thanks again for these clarifications. Do I understand
>>>>> correctly - for distortion correction of functional
>>>>> data with topup I could simply use the topup output
>>>>> field as it is (or the _fieldcoef?) for input to epireg?
>>>>
>>>> You can use the topup output (from --fout) after
>>>> scaling it to rad/s (by multiplying the Hz by 2*pi) as
>>>> the input fieldmap to epi_reg. The only tricky thing
>>>> might be getting a non-brain-extracted magnitude image.
>>>> The unwarped images from topup are good for the
>>>> brain-extracted magnitude image, but you may need to
>>>> either edit the epi_reg script to avoid the
>>>> non-brain-extracted registration step, or to register a
>>>> non-brain-extracted image to the space of the topup
>>>> output to act as a surrogate.
>>>>
>>>>> I can only repeat, this detailed support is highly
>>>>> appreciated.
>>>>> Best, Julia
>>>>>
>>>>> PS on the fieldmaps: when I used too small of a mask
>>>>> for preparing the fieldmap for my data, epireg started
>>>>> to strongly smear the signal in the OFC where the EPI
>>>>> was not covered by the fieldmap. I am just mentioning
>>>>> it, because before it sounded to me like it would
>>>>> always be the better option to use a smaller mask when
>>>>> in doubt. I don't know whether this is just something
>>>>> specific to my data though.
>>>>
>>>> Was this smearing in the outputs registered to
>>>> structural space, or after transforming into standard
>>>> space? It is fairly common to see a bit of smearing in
>>>> standard space, but it isn't common to see in the
>>>> structural space outputs, or the unwarped functionals
>>>> from epi_reg. However, the mask really only needs to
>>>> be made smaller to avoid noisy voxels in the standard
>>>> fieldmap phase images (which are just at the edge of
>>>> the brain). So normally this doesn't make things so
>>>> small that there is a problem. There is a step inside
>>>> the processing that also tries to clean up these noisy
>>>> voxels, but we recommend a tight mask to be a little
>>>> conservative. If you are getting bad results then try
>>>> to run things with a slightly larger mask and see if
>>>> that works better.
>>>>
>>>> All the best,
>>>> Mark
>>>>
>>>>
>>>>
>>>>
>>>>> 2014-05-06 8:39 GMT+02:00 Mark Jenkinson
>>>>> <[log in to unmask]
>>>>> <mailto:[log in to unmask]>>:
>>>>>
>>>>> Hi,
>>>>>
>>>>> What I wanted to make clear here was that topup
>>>>> itself was not performing the distortion
>>>>> correction, like it can for diffusion data (since
>>>>> topup cannot be used in this mode for functional
>>>>> data).
>>>>>
>>>>> Although there is the option in the HCP scripts to
>>>>> register the SBRef image directly to the spin echo
>>>>> output from topup, then convert the topup-derived
>>>>> fieldmap into a warpfield and apply this directly
>>>>> to the functional scan, I would still advise
>>>>> people to use flirt (or epi_reg) for the
>>>>> distortion correction in general. This is because
>>>>> the registration of the functional image (SBRef)
>>>>> to the spin echo image will only work accurately
>>>>> if (a) the distortions are exactly matched in the
>>>>> acquisitions, which won't typically be the case,
>>>>> and (b) the signal loss in the functional images
>>>>> does not affect the registration accuracy. For
>>>>> the HCP these two conditions will be met, but
>>>>> others would need to carefully check if it was
>>>>> true for their data before using this method.
>>>>> However, the method of using flirt/epi_reg will
>>>>> work even when these conditions are not met and so
>>>>> I would recommend that as the more robust/reliable
>>>>> method in general.
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 5 May 2014, at 13:58, Matt Glasser
>>>>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>>>
>>>>>> Hi Mark,
>>>>>>
>>>>>> In my implementation, the distortion correction
>>>>>> is done before flirt BBR. The reason is that the
>>>>>> gradient echo SBRef and spin echo image of
>>>>>> matching phase are very easy to register to each
>>>>>> other rigidly (because they have the same
>>>>>> resolution, ,FOV, and distortions). The topup
>>>>>> field is output as a FSL warpfield and used the
>>>>>> do the correction.
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> From: Mark Jenkinson
>>>>>> <[log in to unmask]
>>>>>> <mailto:[log in to unmask]>>
>>>>>> Reply-To: FSL - FMRIB's Software Library
>>>>>> <[log in to unmask] <mailto:[log in to unmask]>>
>>>>>> Date: Monday, May 5, 2014 at 5:46 AM
>>>>>> To: <[log in to unmask] <mailto:[log in to unmask]>>
>>>>>> Subject: Re: [FSL] flirt -bbr -fieldmap compared
>>>>>> to flirt -bbr / freesurfer bbregister
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Just to clarify here - for fMRI scans, topup was
>>>>>> used to create a fieldmap which was then used in
>>>>>> BBR to do the distortion correction, as opposed
>>>>>> to using topup itself to do the distortion
>>>>>> correction (as the latter is only possible for
>>>>>> diffusion images, not for functional ones).
>>>>>>
>>>>>> So, in answer to your question about the order of
>>>>>> steps, we do not register the fieldmap to the
>>>>>> functional image directly. We used epi_reg (in
>>>>>> FSL) to register fieldmap to structural and then
>>>>>> functional to structural, with the fieldmap
>>>>>> correction. This step did the distortion
>>>>>> correction. Later on a second BBR step was run
>>>>>> with freesurfer, using the distortion corrected
>>>>>> images as input, that refined the rigid-body
>>>>>> registration between the undistorted functional
>>>>>> image and the structural image.
>>>>>>
>>>>>> All the best,
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>> On 2 May 2014, at 14:41, Matt Glasser
>>>>>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>>>>
>>>>>>> HCP data were corrected with spin echo field
>>>>>>> maps (phase reversed spin echo images) using
>>>>>>> topup before running FLIRT BBR and FreeSurfer BBR.
>>>>>>>
>>>>>>> Peace,
>>>>>>>
>>>>>>> Matt.
>>>>>>>
>>>>>>> From: julia <[log in to unmask]
>>>>>>> <mailto:[log in to unmask]>>
>>>>>>> Reply-To: FSL - FMRIB's Software Library
>>>>>>> <[log in to unmask] <mailto:[log in to unmask]>>
>>>>>>> Date: Friday, May 2, 2014 at 4:24 AM
>>>>>>> To: <[log in to unmask] <mailto:[log in to unmask]>>
>>>>>>> Subject: Re: [FSL] flirt -bbr -fieldmap compared
>>>>>>> to flirt -bbr / freesurfer bbregister
>>>>>>>
>>>>>>> Dear Mark, and also Matt before,
>>>>>>>
>>>>>>> thank you so much for your detailed explanations
>>>>>>> which are extremely valuable to me.
>>>>>>>
>>>>>>> As a last tiny follow-up: For the HCP data, did
>>>>>>> you register the fieldmap to the functional
>>>>>>> data, unwarped and then registered to anatomy?
>>>>>>> Or did you rather pre-register to anatomy (w/o
>>>>>>> bbr option?) both the fieldmap and the
>>>>>>> functional image, unwarped and then finetuned
>>>>>>> with bbr?
>>>>>>>
>>>>>>> Thanks a lot for being so helpful,
>>>>>>> Julia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 05/02/2014 10:14 AM, Mark Jenkinson wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>>> thank you so much for your comprehensive
>>>>>>>>> answer and sorry for not being clear enough on
>>>>>>>>> my question about the "magic". I am interested
>>>>>>>>> in the additional benefit of using the
>>>>>>>>> fieldmap within flirt bbr. Or: what is the
>>>>>>>>> difference between the workflow in epi_reg and
>>>>>>>>> an alternative workflow where everything is
>>>>>>>>> equal apart from the fact that the fieldmap
>>>>>>>>> (registered to anatomy) is applied to unwarp
>>>>>>>>> the EPI (pre-registered to anatomy with normal
>>>>>>>>> flirt like it is done in epi_reg) /before/
>>>>>>>>> running flirt bbr (without fieldmap) instead
>>>>>>>>> of /simultaneous/ unwarping and bbr
>>>>>>>>> registration (flirt -bbr -fieldmap). Assuming
>>>>>>>>> the transformations would be combined in the
>>>>>>>>> end to avoid multiple interpolations.
>>>>>>>>
>>>>>>>> That is a tricky question, although the short
>>>>>>>> answer is probably "not much". The use of bbr
>>>>>>>> in the first step will already register to the
>>>>>>>> structural image, so you are never avoiding
>>>>>>>> that, but running things in the second stage,
>>>>>>>> with an unwarped functional image as input can
>>>>>>>> change things subtly.
>>>>>>>>
>>>>>>>> The long answer is that the main difference
>>>>>>>> will be that the second stage of the
>>>>>>>> non-simultaneous version will need to use an
>>>>>>>> interpolated image as the input image to work
>>>>>>>> with. When we investigated this for the HCP,
>>>>>>>> we ended up using such a strategy with the
>>>>>>>> non-fieldmap bbr step being run by freesurfer,
>>>>>>>> and hence fed with an unwarped (and
>>>>>>>> interpolated) image. When I fed the same image
>>>>>>>> into flirt (as a two-stage process, so
>>>>>>>> replacing the freesurfer bbr with flirt) I
>>>>>>>> found that there was very little difference
>>>>>>>> between the freesurfer and two-stage flirt
>>>>>>>> results (less than comparing to simultaneous
>>>>>>>> flirt). However, because we wanted to use the
>>>>>>>> freesurfer segmentations for the best GM-WM
>>>>>>>> edges, then we just stuck with freesurfer for
>>>>>>>> the second bbr step, although I found that with
>>>>>>>> the same input (surface and unwarped image)
>>>>>>>> there was almost no difference between flirt
>>>>>>>> and freesurfer bbr. The difference between
>>>>>>>> using flirt with the two stages rather than
>>>>>>>> simultaneous is probably about slight smoothing
>>>>>>>> benefits from the unwarping step, which on HCP
>>>>>>>> data matter more than I suspect they do in most
>>>>>>>> other data. You could try this yourself and
>>>>>>>> see. It is likely to be hard to see the
>>>>>>>> differences, and the exact benefit/detriment
>>>>>>>> will probably be highly dependent on the
>>>>>>>> quality of the structural, functional and
>>>>>>>> fieldmap images.
>>>>>>>>
>>>>>>>>> Concerning the masking I am a bit confused
>>>>>>>>> now. Within epi_reg, if I see it right, the
>>>>>>>>> mask that is used in the first fugue step is a
>>>>>>>>> multiplication of the binarised magnitude
>>>>>>>>> brain image and the binarised fieldmap:
>>>>>>>>>
>>>>>>>>> $FSLDIR/bin/fslmaths ${fmapmagbrain} -abs -bin
>>>>>>>>> ${vout}_fieldmaprads_mask
>>>>>>>>> $FSLDIR/bin/fslmaths ${fmaprads} -abs -bin
>>>>>>>>> -mul ${vout}_fieldmaprads_mask
>>>>>>>>> ${vout}_fieldmaprads_mask
>>>>>>>>> $FSLDIR/bin/fugue --loadfmap=${fmaprads}
>>>>>>>>> --mask=${vout}_fieldmaprads_mask --unmaskfmap
>>>>>>>>> --savefmap=${vout}_fieldmaprads_unmasked
>>>>>>>>> --unwarpdir=${fdir}
>>>>>>>>>
>>>>>>>>> This would always result in a mask which is as
>>>>>>>>> small as the fieldmap itself or smaller,
>>>>>>>>> right? Where does (or should) the
>>>>>>>>> extrapolation happen then? Maybe I don't
>>>>>>>>> understand the function of the mask in fugue
>>>>>>>>> or am misinterpreting the script?
>>>>>>>>
>>>>>>>> The masking here is done to make sure that only
>>>>>>>> valid fieldmap values are kept within the brain
>>>>>>>> extracted mask. It is usually quite tight and
>>>>>>>> can remove a bit of brain tissue, which is fine
>>>>>>>> as it is better to do that in this context
>>>>>>>> rather than keep in any of the noisy voxels
>>>>>>>> that sit at the brain edge in the fieldmap. So
>>>>>>>> we extrapolate the fieldmap (rad/s) image using
>>>>>>>> fugue (as this always extrapolates internally),
>>>>>>>> and this is explicitly specified via the
>>>>>>>> --unmaskfmap flag (as otherwise the fieldmap
>>>>>>>> would be masked on output). It is important to
>>>>>>>> do it this way to remove these noisy voxels at
>>>>>>>> the brain edge, and because the fieldmap is
>>>>>>>> pretty smooth, extrapolation by a few voxels
>>>>>>>> near the edge is a fairly safe/accurate thing
>>>>>>>> to do.
>>>>>>>>
>>>>>>>> I hope this helps.
>>>>>>>> All the best,
>>>>>>>> Mark
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Many thanks in advance,
>>>>>>>>> Julia
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 04/23/2014 08:41 AM, Mark Jenkinson wrote:
>>>>>>>>>> Dear Julia,
>>>>>>>>>>
>>>>>>>>>> I'm not quite sure what this "magic" is that
>>>>>>>>>> you and Matt are referring to.
>>>>>>>>>> The process inside the epi_reg script is to
>>>>>>>>>> register the fieldmap (which is undistorted)
>>>>>>>>>> to the structural image and then use the
>>>>>>>>>> fieldmap in structural space when doing the
>>>>>>>>>> distortion correction and rigid-body
>>>>>>>>>> registration of the EPI to the structural
>>>>>>>>>> simultaneously. If you are just using the
>>>>>>>>>> flirt command line then you will need to get
>>>>>>>>>> the fieldmap into structural space yourself.
>>>>>>>>>> However, if you've already applied a
>>>>>>>>>> fieldmap distortion-correction step prior to
>>>>>>>>>> flirt then you should not use the fieldmap
>>>>>>>>>> again (as this would overcorrect) and can
>>>>>>>>>> just use the bbr option with the 6 dof
>>>>>>>>>> setting. I wasn't very clear as to your
>>>>>>>>>> pipeline, so I hope this helps explain what
>>>>>>>>>> is appropriate for you.
>>>>>>>>>>
>>>>>>>>>> As for the masking issue, it is necessary to
>>>>>>>>>> have a tight mask into the
>>>>>>>>>> fsl_prepare_fieldmap step in order to exclude
>>>>>>>>>> noisy voxels that occur at the edge of the
>>>>>>>>>> brain. However, when applying the fieldmap
>>>>>>>>>> it should not be masked in this way and does
>>>>>>>>>> need to be extrapolated. The "too small"
>>>>>>>>>> hack in the script is not for this
>>>>>>>>>> extrapolation (as this extrapolation is
>>>>>>>>>> easily done with fugue) but is instead there
>>>>>>>>>> to deal with cases where the FOV was cut-off,
>>>>>>>>>> typically in the through-slice direction, by
>>>>>>>>>> a much larger factor that goes beyond what
>>>>>>>>>> the fugue extrapolation was good at dealing with.
>>>>>>>>>>
>>>>>>>>>> Finally, to answer Matt's question, I have
>>>>>>>>>> not added GIFTI input support to FLIRT at
>>>>>>>>>> this stage.
>>>>>>>>>>
>>>>>>>>>> All the best,
>>>>>>>>>> Mark
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 18 Apr 2014, at 17:25, julia
>>>>>>>>>> <[log in to unmask]
>>>>>>>>>> <mailto:[log in to unmask]>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Thanks again!
>>>>>>>>>>> I would be very interested in the "magic" in
>>>>>>>>>>> flirt bbr when used with a field map.
>>>>>>>>>>>
>>>>>>>>>>> If I may I'd have one more question
>>>>>>>>>>> (possibly related to the magic):
>>>>>>>>>>>
>>>>>>>>>>> It is advised to use a rather small mask for
>>>>>>>>>>> fsl_prepare_fieldmap. However, when I apply
>>>>>>>>>>> such a fieldmap directly in fugue (i.e.
>>>>>>>>>>> after unmasking), smaller maps tend to smear
>>>>>>>>>>> the signal in areas that are not covered by
>>>>>>>>>>> the fieldmap.
>>>>>>>>>>> Is this dealt with by the "new hack for
>>>>>>>>>>> extrapolation if fieldmap is too small" part
>>>>>>>>>>> in the epi_reg script? What confuses me is
>>>>>>>>>>> that there, the dilated fieldmap version is
>>>>>>>>>>> only used inside flirt bbr, not for the
>>>>>>>>>>> later warping (if I read it right).
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>> Julia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 04/16/2014 05:49 PM, Matt Glasser wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> 1. FLIRT BBR is a better and more robust
>>>>>>>>>>>> initialization than the other
>>>>>>>>>>>> FreeSurfer initialization methods (so I
>>>>>>>>>>>> actually turn off bbregister’s
>>>>>>>>>>>> initialization).
>>>>>>>>>>>> 2. I don’t think it is possible to give
>>>>>>>>>>>> flirt bbr a GIFTI surface, but perhaps
>>>>>>>>>>>> Mark has made this change by now?
>>>>>>>>>>>> 3. I’m not sure I follow the goal of the
>>>>>>>>>>>> process here, but perhaps Mark does?
>>>>>>>>>>>> Mark will have to explain what happens
>>>>>>>>>>>> inside flirt bbr when used with a field
>>>>>>>>>>>> map, but I think there is some “magic”
>>>>>>>>>>>> in it.
>>>>>>>>>>>>
>>>>>>>>>>>> topup and regular field map corrections
>>>>>>>>>>>> appeared very similar to us, but topup’s
>>>>>>>>>>>> can be acquired faster and has the
>>>>>>>>>>>> advantage I mentioned below in terms of
>>>>>>>>>>>> robustness.
>>>>>>>>>>>>
>>>>>>>>>>>> Peace,
>>>>>>>>>>>>
>>>>>>>>>>>> Matt.
>>>>>>>>>>>>
>>>>>>>>>>>> From: Julia Huntenburg
>>>>>>>>>>>> <[log in to unmask]
>>>>>>>>>>>> <mailto:[log in to unmask]>>
>>>>>>>>>>>> Reply-To: FSL - FMRIB's Software Library
>>>>>>>>>>>> <[log in to unmask]
>>>>>>>>>>>> <mailto:[log in to unmask]>>
>>>>>>>>>>>> Date: Wednesday, April 16, 2014 at 10:36 AM
>>>>>>>>>>>> To: <[log in to unmask]
>>>>>>>>>>>> <mailto:[log in to unmask]>>
>>>>>>>>>>>> Subject: Re: [FSL] flirt -bbr -fieldmap
>>>>>>>>>>>> compared to flirt -bbr / freesurfer bbregister
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks a lot, Matt, that is all extremely
>>>>>>>>>>>> helpful.
>>>>>>>>>>>>
>>>>>>>>>>>> Just three quick follow-ups:
>>>>>>>>>>>>
>>>>>>>>>>>> 1. If freesurfer bbr is more accurate, what
>>>>>>>>>>>> would be the advantage of using flirt bbr
>>>>>>>>>>>> first instead using freesurfer bbr straight
>>>>>>>>>>>> away?
>>>>>>>>>>>> 2. If the segmentation is the main
>>>>>>>>>>>> difference, would it be reasonable to
>>>>>>>>>>>> assume flirt bbr would perform similarly
>>>>>>>>>>>> well when fed with a freesurfer segmentation?
>>>>>>>>>>>> 3. In case I register both EPI and fieldmap
>>>>>>>>>>>> to the anatomy before, then apply the
>>>>>>>>>>>> fieldmap and then do another round of
>>>>>>>>>>>> registration (unwarped EPI to anat) with
>>>>>>>>>>>> bbregister, that would not be different (at
>>>>>>>>>>>> least no disadvantage) to performing this
>>>>>>>>>>>> last step with flirt -bbr -fieldmap (as in
>>>>>>>>>>>> epi_reg)? I.e. there is nothing magical
>>>>>>>>>>>> happening inside flirt -bbr when it is
>>>>>>>>>>>> provided with a fieldmap?
>>>>>>>>>>>>
>>>>>>>>>>>> Also the hints on topup correction are very
>>>>>>>>>>>> valubale for me as I am currently
>>>>>>>>>>>> implementing both methods for distortion
>>>>>>>>>>>> correction for my data to compare them.
>>>>>>>>>>>>
>>>>>>>>>>>> Many thanks again, great help!
>>>>>>>>>>>> Julia
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 2014-04-16 17:17 GMT+02:00 Matt Glasser
>>>>>>>>>>>> <[log in to unmask] <mailto:[log in to unmask]>>:
>>>>>>>>>>>>> FreeSurfer BBR is generally slightly more
>>>>>>>>>>>>> accurate than FLIRT BBR, probably because
>>>>>>>>>>>>> of the much higher quality surface being
>>>>>>>>>>>>> used (i.e. the FLIRT BBR makes a quick
>>>>>>>>>>>>> white matter surface based on a FAST
>>>>>>>>>>>>> segmentation, whereas FreeSurfer’s white
>>>>>>>>>>>>> matter surface is based on a lot more
>>>>>>>>>>>>> processing). For HCP Minimal
>>>>>>>>>>>>> Preprocessing Pipelines where we cared
>>>>>>>>>>>>> about getting the alignment right down to
>>>>>>>>>>>>> submm levels, we used both (FLIRT BBR
>>>>>>>>>>>>> first and then FreeSurfer BBR).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Whether or not it is better to use the
>>>>>>>>>>>>> field map with FLIRT BBR or apply it
>>>>>>>>>>>>> before depends on how good of a field map
>>>>>>>>>>>>> to EPI registration you can get outside of
>>>>>>>>>>>>> FLIRT BBR vs a field map to structural
>>>>>>>>>>>>> registration (and EPI to structural
>>>>>>>>>>>>> registration) inside FLIRT BBR (i.e.
>>>>>>>>>>>>> epi_reg). Generally one does a better job
>>>>>>>>>>>>> inside of FLIRT BBR, but this is not
>>>>>>>>>>>>> always the case. Also, it can be harder
>>>>>>>>>>>>> to debug what is going wrong when the
>>>>>>>>>>>>> steps are not separated (is my
>>>>>>>>>>>>> registration not good because the
>>>>>>>>>>>>> distortion correction is not good, or
>>>>>>>>>>>>> because the EPI to structural registration
>>>>>>>>>>>>> is not good?).
>>>>>>>>>>>>>
>>>>>>>>>>>>> I actually prefer using spin echo field
>>>>>>>>>>>>> maps (phase reversed spin echo images
>>>>>>>>>>>>> matched to the gradient echo EPI
>>>>>>>>>>>>> acquisition) and topup, as these have the
>>>>>>>>>>>>> same distortion as the gradient echo EPIs
>>>>>>>>>>>>> and can be very precisely registered (EPI
>>>>>>>>>>>>> to matching spin echo image) without the
>>>>>>>>>>>>> complication of using the structural image
>>>>>>>>>>>>> as an intermediate. Then one can use BBR
>>>>>>>>>>>>> on the undistorted EPI image. This keeps
>>>>>>>>>>>>> each step separate for debugging and
>>>>>>>>>>>>> “easy” for the algorithms involved to
>>>>>>>>>>>>> achieve robustly.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Peace,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Matt.
>>>>>>>>>>>>>
>>>>>>>>>>>>> From: Julia Huntenburg
>>>>>>>>>>>>> <[log in to unmask]
>>>>>>>>>>>>> <mailto:[log in to unmask]>>
>>>>>>>>>>>>> Reply-To: FSL - FMRIB's Software Library
>>>>>>>>>>>>> <[log in to unmask]
>>>>>>>>>>>>> <mailto:[log in to unmask]>>
>>>>>>>>>>>>> Date: Wednesday, April 16, 2014 at 9:25 AM
>>>>>>>>>>>>> To: <[log in to unmask]
>>>>>>>>>>>>> <mailto:[log in to unmask]>>
>>>>>>>>>>>>> Subject: [FSL] flirt -bbr -fieldmap
>>>>>>>>>>>>> compared to flirt -bbr / freesurfer bbregister
>>>>>>>>>>>>>
>>>>>>>>>>>>> Dear list,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Concerning the usage of flirt with bbr
>>>>>>>>>>>>> cost function and a fieldmap I was
>>>>>>>>>>>>> wondering if there is any experience on:
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1. how different it is to use the flirt
>>>>>>>>>>>>> -fieldmap option as compared to unwarping
>>>>>>>>>>>>> with the fieldmap first and using flirt
>>>>>>>>>>>>> -bbr afterwards?
>>>>>>>>>>>>> (-- and related: How exactly is the
>>>>>>>>>>>>> fieldmap applied in this implementation?)
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2. how the FSL bbr implementation compares
>>>>>>>>>>>>> to freesurfer bbregister? E.g. if I use
>>>>>>>>>>>>> the freesurfer segmentation with flirt
>>>>>>>>>>>>> -bbr, would that give me similar results
>>>>>>>>>>>>> as bbregister?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Any thoughts or experience (even if
>>>>>>>>>>>>> anecdotal) would be highly appreciated!
>>>>>>>>>>>>> Many thanks,
>>>>>>>>>>>>> Julia
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> <smear1.png><smear2.png>
>>>
>>>
>>>
>>> <epireg_fieldmaprads2str.jpg>
>>
>>
>
