Dear Jesper,
thank you for your answer!! The images should be uploaded here:
https://kth.app.box.com/s/9aoba8pggx44aekvd4dzs7wpornwgoll
In the case of your description I can already tell the images I computed are not right. If you have any ideas why I get these images or you know how those artefacts emerge, I'd be happy to know!
Karen
________________________________________
Von: FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von Jesper Andersson <[log in to unmask]>
Gesendet: Montag, 26. Februar 2018 11:40
An: [log in to unmask]
Betreff: Re: [FSL] Fieldmap computing / phase unwrapping
Dear Karen,
for some reason the link you sent don’t work for me (actually my mail app don’t show me a link at all), so I can’t see your images.
In general what you expect to see in a fieldmap in the brain is a relatively even field (+-10 Hz) for most of the brain, with a significantly higher field in specific areas around the frontal sinuses and the ear canals. In these areas you expect to see a maximum field deviation of ~150Hz around the sinus and ~100Hz around the ear-canals. Those values are for 3T and scale linearly with your field strength.
I would always use 3D phase unwrapping.
Your 456 microseconds sounds like the “dwell time”, i.e. the time between acquisition of consecutive echoes. This is different to “echo time” which refers to the time between excitation and the point at which one traverses the centre of k-space. The dwell time is what you want to specify on the fugue command line. But note that this is complicated by any in-plane acceleration that you might have in your EPI images. In that case you need to “trick” fugue by dividing that value by the IPAT factor. Unless your vendor has already performed that division for the info in 0043,102c, but that is something you need to look into their documentation to find out.
Jesper
> On 26 Feb 2018, at 09:09, Karen Zantop <[log in to unmask]> wrote:
>
> Dear FSL-experts,
>
> I am having some trouble computing a fieldmap image for unwarping my fMRI data. I have two GE image sets, aquired with a TE of 6.4 and 8.4 ms. Both sets contain a magnitude image and two other images, which I believe are the imaginary and the real part of the image. From them, I calculate two phase images by taking the atan after dividing them. Subsequently, I multiply them by 2 to scale them from [-pi/2, pi/2] to the range of [-p, pi] as asked by prelude. Afterwards, I follow the instructions on the FSL FUGUE/Guide website. For unwrapping the phase, I force prelude to do it in 2D and in step 4(a) I use delta TE = 2ms.
>
> For the unwrapping I already have some questions. Is it in general better to unwrap images in 2D or 3D? My voxel size is 3.0556x3.0556x3.0000.
>
> Afterwards, I have no Idea if the fieldmap I compute is right. I wonder if anyone could give me some advice?
>
> Example-wise I computed 4 fieldmaps in Hz from different patients and in comparison 2 fieldmaps where the phase was unwrapped in 3D (can be found in this link). In those PNGs, the image intensity is limited to the intervals described in the file name. The actual intensity ranges in the fieldmap files are
>
> id [min, max] and unwrapped in 3D: id [min, max]
> ———————— ———————
> 03 [-1288, 366] 03 [0, 4910]
> 04 [-326, 1041] 04 [-219, 1405]
> 05 [-1723, 0]
> 06 [-1125, 0]
>
> Are these values in a realistic range? In the link I included there is also a histogram of one of the fieldmap.
>
> I am concerned about some discontinuities in the images (marked in red). Are these okay?
>
> My dicom-header of the EPI- files give me at (0043,102c) = 456 microseconds. As I understood this is the effective echo time, that I enter in the FEAT GUI with the EPI-TE of 30ms I have. Are the times chosen correctly in general ?
>
>
> Thank you for your help in advance!
>
> Karen Zantop
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