Hi Mark,
Can you please be a bit more detailed in your remark about orientation? As I recall, the program b0calc assumes that B0 is in the z-direction. Are you suggesting that I apply a linear transform to the T1 volume??
For completeness here are the initial segmentation results for Step 1.
https://db.tt/AJFSrOOw
https://db.tt/aoTtQad6 (binarised)
Regards,
Louis.
On Wed, 20 Nov 2013 17:09:54 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>Dear Louis,
>
>I agree with Matt in general, although the extreme superior and inferior portions of your fieldmap do not look that usual. In my experience incorporating other tissue susceptibilities (point 3) is not worth it, as these values are so poorly characterised (especially in bone where the structure of the bone matrix can be significant). Plus, the main departures for you are broad scale, so unlikely to be local tissue. Therefore I suspect the problem is either (i) orientation (and if you reorient your original segmentation input, maybe using information from the DICOM); (ii) shimming, where the only thing you can do is to try adding gradient fields and second-order spherical harmonic field to see if that helps; or (iii) structure beyond the FOV of your segmented image (in particular, the torso and lungs).
>
>I don't have specific details on how to solve these problems, as it depends on what information you have, but hopefully this is enough to help you take the next step.
>
>All the best,
> Mark
>
>
>
>On 19 Nov 2013, at 19:07, Louis Shue <[log in to unmask]> wrote:
>
>> Hi Matt
>>
>> Thanks for the encouragement.
>>
>> My main concern at the moment is that the light/dark areas of the two fieldmaps are not quite consistent which I suspect is related to point 2 you listed. Do you have any suggestions on how I can make use of the orientation to improve the results? I do have access to the original DICOM data.
>>
>> Regards,
>> Louis.
>>
>> On Tue, 19 Nov 2013 10:37:06 -0600, Matt Glasser <[log in to unmask]> wrote:
>>
>>> I agree those files look impressively similar. Some other things that
>>> will influence field maps:
>>>
>>> 1) b0 shimming
>>> 2) Orientation of the head in the b0 field
>>> 3) b0 inhomogeneities due to tissue differences other than air/non-air
>>>
>>> Have you compared your EPI to T1w registrations with and without your
>>> synthetic field maps yet? Perhaps you are already a lot closer than you
>>> were initially. I wouldn't let a desire for perfection get in the way of
>>> a major improvement. I would imagine a lot of people have data for which
>>> they neglected to acquire field maps but wish to register them more
>>> accurately to their structurals and would be interested in your progress
>>> with this.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> On 11/19/13 5:26 AM, "Louis Shue" <[log in to unmask]> wrote:
>>>
>>>> Dear all,
>>>>
>>>> A few months ago, I started looking at the problem of fieldmap-based
>>>> unwarping of EPI when the usual fieldmap sequences (phase-difference
>>>> volumes) were not available. With lots of help from Mark I was able to
>>>> eventually come up with what seemed sensible-looking fieldmaps.
>>>> Essentially the steps I used was
>>>>
>>>> - Extract from T1 a mask to differentiate between air and "everything
>>>> else", i.e. skull+brain+CSF
>>>> - Use b0calc to estiamte the magnetic field variations
>>>> - Scale by 2*pi* gyromanetic ratio
>>>> - Remove spherical harmonics from the resulting volume
>>>>
>>>> Unfortunate after comparing fieldmap determined from this approach with
>>>> fieldmap computed using conventional methods (we were able to acquire
>>>> newer data), there are noticeable differences between the fieldmaps as
>>>> seen in the two files linked below.
>>>>
>>>> Fieldmap computed from phasemap https://db.tt/57Lb8HzM
>>>> Fieldmap computed from T1 volume https://db.tt/Ygte0Zh2
>>>>
>>>> Since we still have substantial data that we would like to process as
>>>> much as reasonably possible, hopefully we can still get something using
>>>> the T1-b0calc approach? I'd really appreciate it if someone can suggest
>>>> where I might be able to improve or where problems might have occurred in
>>>> the above description?
>>>>
>>>> Thanks very much!
>>>>
>>>> Regards,
>>>> Louis.
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