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Hi Peter! Thank you too! > Interesting. It appears that you have a central frequency drift between > your acquisitions. You can calculate the value of this shift by calculating > the bandwidth in the phase encoding direction - which will be inversly > proportional to your read-out bandwidth. One should look into whether this > drift is outside of the calibration values and might require adjustments. > The Bandwidth is 1396 Hz/Px. Phase encodign is A>>P. How would I calculate what you propose? Could you explain a little bit more, please? 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. > Appearently there was the MGH sequence. They changed then to the monopolar sequence (vibration artifacts, on this list too). But I will go and look for that. Thank you very much, Markus 2008/12/2 Peter Kochunov <[log in to unmask]> > 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:* Markus Gschwind <[log in to unmask]> > *To:* [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 > > -- 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