I have two fieldmaps directly converted from DICOM to NIFTI (magnitude image and phase difference image) and I would like to run EPI distortion on the data which I have corrected for eddy currents and subject movement. How do I run it through FSL GUI FEAT Pre-stats? Do i have to first calculate the field map using fsl_prepare_fieldmap?
Hi Gemaine,
Yes, you must create the fieldmap separately before unwarping the distortions. Depending the scanner from which the scans were acquired, the process is slightly different using FSL's prelude and fugue.
Hi Rachelle,
thanks for your response. Yes I have used FSL's fugue to generate the magnitude field map in rads as the scanner used for collection of the field maps and DTI data is Siemens. However, when I tried running the data after placing all the relevant information into FSL GUI FEAT Preprocessing, I got really distorted brains like the image attached when viewed in mricron and fsleyes. Just wondering if you would know what would be the cause of such problems?
Thanks!
Germaine
Hi Germaine,
I had this issue before. It looks like there might be an issue with your fieldmaps. I would recommend checking that your fieldmaps line up with your anatomical and EPI image.
I know this has been a few months -- were you able to solve this already? If so, what was the solution?
Best,
Rachelle
Hi Rachelle,
Both the field maps line up with the anatomical and EPI image so I'm not really sure what could be the issue still.
I was recommended to skip this step and continue on my analysis due to time constraints.
Thank you for your reply!
Germaine
- Badges
- Science topic