Good b-value sensitivity parameter for 2shell


#1

Hello!

I am currently designing a new sequence for DTI and I would like to implement multishell (previously we had only singleshell), but I have a time limitation of 10-15 min maximum for the DTI sequence (but the shorter the better).

So far from what I experimented, I can do multiband factor 4x with good signal, in single shell 64 directions it takes 5 min, so I can do probably 2shells. I saw the thread here that looks similar but it doesn’t address specifically 2shells vs 3shells.

Usually I see that published multishell relies on 3 shells, but is it possible to do 2shells? If so, what would be good b-values? 1000 and 3000, or 1000 and 5000 or something else?

Also I saw that some protocols do 3 shells but with a varying number of directions (I guess to reduce the time of acquisition), is it better then to do 3 shells with varying directions (eg, 30, 48, 64) or 2 shells with maximum directions (64)?

Thank you very much in advance!
Best regards,
Stephen


#2

I’m surprised it would take 5 minutes to acquire 64 directions with MB4. We can already do that many volumes in 10 minutes without MB, I’d expect this to take less than 3 minutes. What resolution / number of slices are you targeting?

In any case, you’ll probably be able to do 3 shells in 10 minutes with that setup. That will allow you to get >128 volumes, which you can split up in a relatively sensible ratio in the region of 10, 18, 32, 68 volumes for b=0, 700, 1200, 2500 s/mm² (or thereabouts, depending on what b-values you eventually decide to settle on).

One thing I would recommend is to spread these b-values around in the time domain (and orientation domain too if you can) – i.e. don’t acquire all your b=0 together, followed by all your b=700 volumes, etc. This brings benefits in terms of making motion correction easier, makes the sequence more resilient to interruptions, lowers gradient heating, and often allows the scanner to run the sequence faster (depending on the exact implementation) – see this paper for a discussion of these issues.

As I’d stated in that thread, I don’t think the matter is settled as to how many shells are optimal… 2 shells (+b=0) allows you to do multi-tissue CSD with 3 tissue types, but that doesn’t mean that future applications won’t benefit from additional shells (e.g. Fig 10 in this paper). I don’t think this is a question we can honestly answer without speculating…

Same with the issue of which b-values are optimal. This is something we’re looking into, but at this stage, I wouldn’t want to give recommendations, other than just to say that the b-values I suggested above would probably be what I’d go for if I was in your shoes (for a 3-shell setup). For 2-shell setup, I’d probably opt for 10, 30, 70 directions at b=0, 1000, 2500-3000 s/mm² or thereabouts – again based purely on gut feeling rather than any formal definition of optimality…

Finally, on the question of how many directions for a given b-value, the only recommendation I can provide is to ensure that have at least enough to capture (the bulk of) the information content in the signal at that b-value – see this paper for details (it’s a single-shell analysis, but the results do apply to this particular problem).


#3

Thank you very much for this great answer and all the references! This is very helpful!

I did not describe our population, but indeed our population consists of patients with brain insults, so motion robustness is a big criteria for us, as well as the possibility to extend multi-shell to a 4th tissue type such as oedemas as was done in the paper you mentioned.

We will try to implement your 3-shells suggestion, but I’m not sure it is possible to implement a flexible temporal scheme on a standard machine (ours is a Siemers Vida 3T).

Also about the speed of acquisitions, unfortunately it is not possible to acquire different b-values with different directions nor different TEs in the same sequence, so the only way to implement that for our machine would be to acquire different sequences.

Is it possible with MRTRIX3 to do multi-shell analysis from multiple DWI sequences? If so, should we reacquire one set of b=0 for each sequence, or we just acquire the 10 b=0 at the first sequence?

Thank you very much for your clarifications!
Best regards,
Stephen


#4

It should be possible to do this if you can provide a DiffusionVectors.txt file. Check with your Siemens applications engineer – we do this very routinely. It used to require a Research Agreement with Siemens, I’m not sure whether this is still the case. Lots more info on that in this thread – take a look, see if it helps.


#5

Thank you very much! I discussed with our Siemens healthineer and we unfortunately don’t have the required the access to these advanced parameters, but we might in the future after someone in my team do the required training.

So I tried to tweak to get 3-shells, but unfortunately multiband x4 was too noisy, so I reduced to x3, and I settled for b1000 + b2000 (instead of b1000 + b3000) as b3000 was noticeably too noisy on our machine, for a total of 11:45min. Here is the result (single-shell vs multi-shell analysis for the same healthy subject):

I don’t have much experience with multi-shell, but I think it looks fine, right? :slight_smile:

I also looked at the possibility to acquire multiple sequences and concatenate as one multishell sequence prior to analysis, but I found a thread that suggest this would then require a normalization and is thus disadvised:

So for the moment I think we will settle with this setting, which seems quite good and way better than what we had before :slight_smile: Thank you very much!


#6

How did you assess this? Looking at the raw images is not the right way to assess SNR in these types of data. There is very strong contrast in the angular domain, which also implies that most of each image will be very low signal – but crucially, those regions where the DW gradient is close to perpendicular to the fibre direction will have relatively high signal. I’d recommend looking at the estimated fODFs to get a feel for the quality.

Well, there’s nothing overtly wrong here, but I find it’s hard to tell from the tractography output. It’ll depend on all kinds of other factors, like the use of ACT, and the threshold used in tractography, and the specific algorithm used to derive the fODF (which I assume was different between the single and multi-shell analyses you’re showing?).

Well, it makes things a bit more complicated, but nothing that can’t be dealt with reasonably easily. You just need to be aware of it and make sure you deal with it appropriately. The new functionality in mrhistmatch was added to deal with precisely this issue.

Also, on a Siemens scanner, you can turn off all the adjustments that would lead to scaling differences – see this post in the thread you mentioned. This means that you can avoid these issues altogether, and concatenate the data without worrying about scaling differences. The trick here though is to make sure that only the first scan is calibrated, with all adjustments turned off for subsequent scans.


#7

Thank you very much for your fast reply!

I am going to try to do multiple single-shell sequences and then concatenate into one multi-shell, I guess I can use mrcat to do this (by first extracting the b-0 and b-xxxx values separately using dwiextract)?

About avoiding the calibration for subsequent scans except the first, yes we can do that :slight_smile: But is it ok if then the scans have different TEs? Indeed, I think the only way we can get a benefit in speed is either to reduce the number of angles or the TE for each scan depending on the b-value, but I’m wondering if changing the TE wouldn’t require a recalibration or is it ok?

About data quality, yes you’re right we were using ACT for the single-shell analysis! I remade quickly a pipeline to do single-shell analysis without ACT (sourcecode here), with the same parameters as multi-shell without ACT (sourcecode here). Here are the results:

The only difference between the single-shell and multi-shell is as you guessed the algorithms: dwi2response dhollander and dwi2fod msmt_csd for multi-shell, dwi2response tournier and dwi2fod csd for single-shell. From this picture, it looks like multi-shell is enhancing the results compared to single-shell, no? :slight_smile:

About b-3000 noise, yes indeed I saw a lot of noise in the source image but I know this produces more noise, however the tractography also contain artifacts:

(Notice the small spurious tracts at the bottom of the trunk tracts. Note also a similar artifact was reproduced on another subject acquired at b-3000).

This was done without ACT, so one can argue that using ACT we could remove this. So from this I guessed that b-3000 was too noisy on our machine and b-2000 was better, but you have more experience so what do you suggest? To keep b-3000 and remove the spurious tracts with ACT or stick to b-2000?

Thank you very much again for all your very helpful guidance! :smiley:


#8

If you’re sure the calibration is identical between scans, you can just mrcat them together – no need to use dwiextract at all. The DW encoding will contain all the information about which scans used which b-values.

Even if you do need to correct for different scaling between acquisitions, there should still be no need to use dwiextract when combining the data.

No, not in general. Most analysis algorithms will assume the exact same acquisition parameters have been used throughout. Interestingly, MSMT-CSD is probably the only method I know of that should be able to handle these types of data, but I’ve not seen anyone do it yet. I’d strongly recommend you use the same TE for all acquisitions you wish to combine, it’ll make your life a lot easier later on, when you come to publish, etc.

The main reason to split your acquisition into separate scans is to allow different numbers of directions per shell. I agree that in theory you could also reduce the TE to boost SNR and reduce acquisition time further, but like I said earlier, it’s not a good idea since it breaks the assumptions of almost all analysis methods you might like to use (outside of MSMT-CSD).

Yes, that’s much more in line with what I was expecting. It’s still not comparing like with like though… :wink:

The dwi2fod csd algorithm produces slightly different outputs than the dwi2fod msmt_csd algorithm, even when set to the same parameters. This is due to the use of a soft non-negativity constraint in the csd variant, as opposed to a hard constraint in msmt_csdsome discussion on this issue here. If you’re really keen on performing a proper head-to-head comparison, you could use the dwi2response dhollander and dwi2fod msmt_csd algorithms for the single-shell analysis also, but only provide WM and CSF responses (and corresponding output files) to the dwi2fod msmt_csd call – as per the same thread.

I assume you’re referring to the cluster of spurious streamlines next to the spinal cord / cortico-spinal tract? That’s most likely simply down to poor masking… I’d expect it would be entirely dealt with using ACT. I certainly wouldn’t take any account of it to assess the quality of the reconstruction, you really need to look at the results within the brain, and preferably in the central deep GM regions / brainstem, where the SNR is typically lowest (furthest from the coils).

Like I said earlier, looking at whole brain tractography as a marker of quality is fraught with difficulties (it annoys me when I see these types of comparisons used as ‘validation’ in papers…). So it’s difficult for me to make any meaningful statement on the quality of your results from what you show. I’d personally use other strategies: you could compare the raw fODFs within the central brain regions, and maybe compare the slab-cropped whole-brain tractography in those regions. But personally, I tend to look at the SNR in the b=0 images, assessed as the voxel-wise standard deviation over repeat b=0 volumes (don’t let it drop too far below 20), inspect the quality of the DW encoding (dirstat provides a lot of information on that front), check that the fODFs look as expected, and verify that there are no obvious artefacts (due to e.g. incomplete fat saturation, ghosting, residual eddy-currents problems, etc). The decision as to which b-value to use should probably be guided by other considerations, but these days I’d advocate somewhere between 2,500 to 3000 s/mm² for the highest shell.

Really, this depends on what you hope to do with the data, and future methods will undoubtedly come up that might require higher b-values, etc. It’s really hard to provide any definitive recommendations for a future-proof acquisition, or even for an optimal acquisition for current methods, there are so many things that can be done with these data, and what’s optimal for one type of analysis may not be for another, etc…