Dear FSL experts:
I'm using a multi-echo GRE sequence (8 echoes, echo spacing = 4ms, 1st TE = 5.7ms) to calculate QSM. And I'm also using a sequence (2 echoes, echo spacing = 2.46ms, 1st TE=5.19ms, 2nd TE= 7.65ms) for DTI fieldmap correction. Since the multi-echo GRE sequence also generates both magnitude and phase images, I want to use the 8 echo data to correct for distortion. Here are some problems:
1. I tried to use fsl_prepare_fieldmap SIEMENS on my raw 8 echo data to generate fieldmap in rad/s. However, the fieldmap has some phase wrapping still. (Fig. 1)
2. I tried to extract the first two echoes data (fslsplit & fslmerge) from the 8 echo data. The phase wrapping is still there. (Fig. 2)
3, For the above two questions, PRELUDE cannot be used right? Since out data is acquired from a multi-channel head coil.
4, I used the QSM toolbox (http://weill.cornell.edu/mri/pages/qsm.html) to generate a unwrapped fieldmap. The fieldmap is unwrapped but the fieldmap correction is not as good as the 2 echoes one. (Fig.3)
The fieldmap generated from the 2 echo gre sequence, and the fieldmap correction result for DTI data can be found in Fig.4.
The result images can be found here:
https://www.dropbox.com/sh/cbf1cjk4zkjovei/AAATLRPoUg3iJe6J3DhtT0jma?dl=0
Please let me know if you need any other information!
Thank you in advance!
Yuchuan
|