Dear FSL-Experts,
I inherited an older DTI dataset and I am stuck with the preprocessing at the moment. The dataset (recorded on a Siemens Trio 3T) consists of 60 directions and 6 b0's, the bvecs are oriented in a half-sphere and only one PE-polarity was used in the acquisition (A>>P), so unluckily for me the opposite of everything you recommend to pay attention to during acquisition ;) Therefore, I cannot use topup for susceptibility distortion correction. For most of the subjects I simply run the most recent implementation of eddy - the FA maps after dtifit look alright.
Nevertheless, during the acquisition somebody had the glorious idea of recording a gradient field map for the last 10 subjects, which I understand to be another approach of tackling susceptibility distortions. My question is: how?
What I have done so far is preparing the field map using fsl_prepare_fieldmap. For the next steps, I found some old code of Matt Glasser ( https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=FSL&D=0&P=454499 ). Adapting these few lines led to warping of the DTI data, that doesn't seem correct (see attached screenshots). Furthermore, I attached a screenshot of the flirted field map and magnitude image. Do you have any idea about what might have gone wrong or how I could proceed? I am very grateful for every advice!
Greetings from Germany,
Bastian
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