One advice is to upgrade your scanner with a DTI sequence developed at MGH. Thomas Benner is the contact person. I find it much more research friendly, than the OEM sequence.

pk

----- Original Message -----

From: [log in to unmask]" href="mailto:[log in to unmask]" target="_blank">Markus Gschwind

To: [log in to unmask]" href="mailto:[log in to unmask]" target="_blank">[log in to unmask]

Sent: Tuesday, December 02, 2008 9:15 AM

Subject: Re: [FSL] DTI acquisitions have different A-P distortions

Hi Daniel!

Thank you for your comments.

Actually I am not sure what the sequence within this two acquisitions are.

All I know is that in what I called "interleaved" the multiple averages was chosen to 2 (I believe it is on the card "Diffusion" where also "MDDW" and "free" can be chosen).

When converting the dicoms by MriConvert it comes like this b0 b0 d1 d1 d2 d2 d3 d3  etc
(when converting by dcm2nii it comes like this b0 d1 d2 d3 d4 ... b0 d1 d2 d3 d4 etc.).
I am thus not sure what exactly the scanner is doing (as mentioned it is a TrioTIM Syngo VB15).

Do you know?

Anyway I learned that I should not choose multiple averages within one sequence... but just run the sequence several times.

Thank you!
Markus

2008/12/2 Daniel Gallichan <[log in to unmask]>

Hi Markus

I wasn't quite sure I understand what you mean by 'interleaved' in your case. Do you acquire all slices at one diffusion direction twice in a row? - is that what you then compare with acquiring all slices once at each diffusion direction and then repeating?

If this is the case then perhaps there is some kind of effect where repeating the same diffusion direction over and over causes different heating - and therefore different eddies - to if the diffusion direction is changed after each volume. I suppose this might give the axis that was just being pushed the hardest a 'rest' before it gets pushed again.

Just a thought. 

But it sounds like you've found a way of avoiding the problem anyway so maybe you don't care anymore!

Dan

PS. If this suggestion is the cause - then it may be worthwhile to actually cycle the diffusion direction between each individual slice that's acquired. This would potentially reduce overall eddy-current effects...

On 2 Dec 2008, at 13:59, Markus Gschwind wrote:

Thanks Peter and Matt for suggestions:

I reinspected the data: yes, Matt, indeed there is also a component of position shift of about 2 voxels. After applying eddy-correct (it does a rigid body registration per slice, no?) however it was still of about 1-2 voxels.

Now, after your suggestions I did the direct comparison of

A)
ep2d as I did before in 2 averages (on the sequence card) that come out interleaved as S1b0 S2b0 S1d1 S2d1 S1d2 S2d2 etc.

B)
2 x epd2d in one sigle acquisition and fslmerged them for comparison into the same interleaved order.
This latter one is clearly better! There is hardly any shift and jiggling.

I thus learn form that, that taking multple acquisitons in a Siemens Trio does not improve but rather reduce image quality.
In this case there is appearently no shimming inbetween the two acquisitions.

I also compared "stadard shimming" to "advanced shimming". But no difference, apart form the shimming time.

Does this go with your thoughts?

Thank you a lot,
Markus

2008/11/30 Kochunov, Peter <[log in to unmask]>

Back in the days of passively shielded magnets, these sort of distortions were quite common. Sequences with high gradient cycles would cause a drift in B0, as well as introduce time variable change to the eddy current. Nowadays, these magnets are all but museum pieces, and actively shielded clinical scanners have superb time stability. Thus, Matt's suggestion of inter-run recalibration of shimming/zero frequencies makes the most sense!
pk

________________________________

From: FSL - FMRIB's Software Library on behalf of Matt Glasser
Sent: Sat 11/29/2008 10:42 PM

To: [log in to unmask]

Subject: Re: [FSL] DTI acquisitions have different A-P distortions

Are you sure it is not just a position shift of the images (that simply needs a rigid body registration to correct)?  I believe this can be caused by reshimming between averages.  If the head does not move and the same sequence and gradients are applied, the distortion should not change.



Peace,



Matt.

________________________________

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Markus Gschwind
Sent: Friday, November 28, 2008 6:54 AM
To: [log in to unmask]
Subject: [FSL] DTI acquisitions have different A-P distortions



Dear FSLers!

This is a question for the radiologist or physicists.

I have a DTI sequence where I am taking several acquisitions (non-stop) and I have the problem that systematically the distortion seems different.
That means, the volumes have different length in their AP direction across all gradients, but not in the LR or the IS directions (1. acquisition more anterior, 2. more posterior).
Thus, looking at one acquisition separately, it looks nice, but as soon as they are interleaved there is a shaking in between the acquisitions.

This is only true for the gradient volumes, not for the b0 volume.

It appears consistently in every subject in a similar way.

Applying eddy_correct does not change it.

I tried with applying a fieldmap, but this did not change neither, however I am not sure if I did it correctly.

The sequence is a mono-polar (stejskal-tanner) ep2d dti on a Siemens TrioTIM Syngo VB15 System.

Does anybody know what this could be and what could be done against?
Obviously the problem becomes important when averaging the different acquisitions.

Thanks in advance,
Markus


--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH

Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]

http://labnic.unige.ch <http://labnic.unige.ch/>

--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH

Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch

--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH

Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch