In my experience (as a Siemen's user, processing Philips data), "fat shift
direction = P" on a Philips machine is equivalent to "Phase enc. dir = P
>> A" on a Siemen's machine. Regardless, the accuracy of the shift
>>direction is easy to test empirically by running the correction both
>>ways, and that is what I'd recommend others do as well.
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 8/7/13 10:24 AM, "Franz Liem" <[log in to unmask]> wrote:
>Dear Jesper and Alistair,
>Yesterday, I had a discussion with our MR-Physicist about this topic. I
>can say a little bit about the Phillip information. These are all
>slightly educated guesses, so it would be great if anybody could confirm
>that this information is correct.
>1. fold-over direction = "AP"; only gives you the axis, not the
>direction (i.e. there is no PA option on the console).
>the direction can be found in fat shift direction = "P"; (I guess this
>2. wrt the readout time the following equation seems to give good results
>"For Philips Acheiva, the best equation for echo spacing is
>echo spacing =(1000*wfs)/(434.215 *(etl+1))
>where wfs is the Philips value of water fat shift in pixels
>etl is the echo train length or Philips calls this the epi factor"
>you can obtain wfs and epi factor from your .par files (I am not sure if
>the values of the par files and the sequence are always equal, as
>angulation or other factors? might change wfs)
>Our MR-Physicist measured the echo spacing in the sequence. This
>measurement gave the same value.
>To calculate the total readout time for topup...: ES * (Epi factor - 1)
>Am 07.08.2013 um 16:57 schrieb Jesper Andersson:
>> Dear Alistair,
>> On 30 Jul 2013, at 02:25, Alistair Perry <[log in to unmask]>
>>> Thanks Jesper.
>>> Currently we have 2 studies, one is which is in the process of being
>>>collected on a Phillips 3T scannner. The other, is to be collected on a
>>>Seimens 3T Scanner. Thus, due to the release of the new eddy tool, we
>>>would like to optimally design our diffusion scans.
>>> I retrieved the exam card for both the Phillips and the Seimens (page
>>>6-9) studies, which I have attached and labelled study 1 and study 2
>>>respectively. I find that Phillips does not yield as much information
>>>as Seimens for researchers in terms of acquisition parameters (and
>>>perhaps the phase-encoding is set by default..). Can you find any
>>>indication on the exam cards regarding the phase-encoding direction for
>>>both scanners, and whether the diffusion directions are sampled on the
>> For the Siemens file it is quite clear and the information you need is
>> Phase enc. dir. A >> P
>> Echo spacing 0.73 ms
>> The phillips file looks a little messier to my untrained eye. If I was
>>to guess something I would guess that
>> fold-over direction = "AP";
>> implies A >> P
>> and another guess is that
>> WFS (pix) / BW (Hz) = "14.681 / 29.6";
>> tells you the BW in the PE direction. But I stress that those are only
>>guesses. I suggest you chat to your resident MR physicist about these
>>> Nevertheless, for our second study on the seimens 3T scanner.. At the
>>>moment, we are going to run with 72 directions (8 b0) at a b-value
>>>2700. Would you recommend that instead of using a blip up- blip down
>>>phase encoding, that we instead sample the diffusion directions on the
>>>whole sphere. And if so, how do we ensure this? I have read through the
>>>forums and through the literature that using blip up-blip down is only
>>>suitable for very long acquisition times.
>> The directions in study2vectors are already on the whole sphere. The
>>best way to check this is to read the directions into an nx3 Matlab
>>matrix, plot that matrix using the Matlab command plot3 and then type
>>"rotate3D on" to allow interactive rotation of the resulting
>>point-cloud. I just did that to your directions and when rotating a
>>sphere shape emerges. If it had not been on the whole sphere I would
>>instead have seen a half-sphere (bowl) shape when rotating.
>> I am not sure what you mean by "very long", bit you are probably right
>>that in your case (72 dir) you should not use blip-up-blip-down for all
>>your dwi images. Just make sure that you precede your dwi acquisition
>>with a couple of b=0 scans with reversed blips.
>>> Alistair Perry
>>> On Tue, Jul 16, 2013 at 12:48 AM, Jesper Andersson
>>><[log in to unmask]> wrote:
>>> Dear Alistair,
>>> > I would like to try out the new EDDY tool, as our lab has high
>>>b-value data on a Phillips 3T scanner.
>>> > However, in comparison to the traditional eddy_correct, I noticed
>>>that there are a few extra compulsory arguments that need to be defined.
>>> > For starters, is there any possible way to check the direction of
>>>the phase-encoding and the total readout time, after the scans have
>>>already been collected.
>>> > I have access to the exam card, but the only information I have been
>>>able to obtain is the phase-encoding direction for the y-axis (which is
>>> are all scans collected with the same polarity (i.e. ant->post)? If
>>>so, it is important that the diffusion directions have been sampled on
>>>the whole sphere (N.B. that it is quite common that the directions are
>>>only sampled on the half sphere which give the same diffusion
>>>information but inferior information when it comes to corrections for
>>>eddy current distortions).
>>> You can calculate the total readout time as the dwell time multiplied
>>>by (n-1) where n is the number of echoes of your EPI acquisition. If
>>>you don't have that information you can put any value in there (e.g.
>>>0.1) which means that the fields you calculate will not be scaled
>>>correctly but the distortion correction ail still be the same.
>>> I quite think of eddy as a "prospective tool" in the sense that you
>>>may need to rethink your acquisition protocol (and what information you
>>>record in your scan log) slightly in order to get it to work optimally.
>>> > Thanks
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