Using fieldmap acquisitions, one can improve the registration of EPI (functional) data to the subject's structural scan.
Preparing Fieldmap Data
The script fmap, which processes the fieldmap data to produce the appropriate files required by FEAT. The fieldmap acquisition on the CUBRIC scanner comprises of two SPGR scans with different echo times (7ms and 9ms). The syntax for fmap is;fmap
From these SPGR scans fmap produces a fieldmap directory containing the following files;
abs_image_brain_mask.nii.gz:
abs_image_brain.nii.gz: Required by FEAT
fieldmap_rad_s.nii.gz: Required by FEAT
fieldmap_uT.nii.gz
phasediff_brain.nii.gz
phasediff.nii.gz
Check the fieldmap_rad_s image using fslview. It should appear something similar to the images below, with values typically in the range -2000 to +2000.
Unwarping EPI data within FEAT
On the Pre-stats tab select B0 unwarping with the following parameters;
Fieldmap: the appropriate fieldmap_rad_s.nii.gz file.
Fieldmap map: the appropriate abs_image_brain.nii.gz file.
EPI echo spacing (ms): 0.32
EPI TE (ms): 35
Unwarp direction: +y
% Signal loss threshold: 10
When unwarping is complete, additional data appear in the Pre-stats section of the FEAT report. Check the quality of the unwarping by looking at the original and unwarped EPI, and the magnitude image of the fielmap data (a low resolotion structural scan). These are all in the whatever.feat/unwarp directory
EF_D_example_func.nii.gz: Original ("distorted") EPI volume
EF_UD_example_func.nii.gz: Unwarped (or "undistorted") EPI image
EF_UD_fmap_mag_brain.nii.gz: Structural image (from fieldmap).
The unwarped image (EF_UD_example_func.nii.gz) should be a better match to the structural image than the original (EF_D_example_func.nii.gz). Look for artefacts in the unwarping, which may be caused by head motion during the fieldmap, or in between the fieldmap and the epi acquisition.
Fieldmap: the appropriate fieldmap_rad_s.nii.gz file.
Fieldmap map: the appropriate abs_image_brain.nii.gz file.
EPI echo spacing (ms): 0.32
EPI TE (ms): 35
Unwarp direction: +y
% Signal loss threshold: 10
When unwarping is complete, additional data appear in the Pre-stats section of the FEAT report. Check the quality of the unwarping by looking at the original and unwarped EPI, and the magnitude image of the fielmap data (a low resolotion structural scan). These are all in the whatever.feat/unwarp directory
EF_D_example_func.nii.gz: Original ("distorted") EPI volume
EF_UD_example_func.nii.gz: Unwarped (or "undistorted") EPI image
EF_UD_fmap_mag_brain.nii.gz: Structural image (from fieldmap).
The unwarped image (EF_UD_example_func.nii.gz) should be a better match to the structural image than the original (EF_D_example_func.nii.gz). Look for artefacts in the unwarping, which may be caused by head motion during the fieldmap, or in between the fieldmap and the epi acquisition.
Images (right) show the typical effect of unwarping on EPI data. Original (red) and unwarped (blue) EPI images are overlaid on top of the fieldmap structural image. Original EPI shows stretching of data in the anterior direction near the frontal pole (A, B), and a movement of the cerebellum and spinal cord in the posterior direction (C). These are corrected in the unwarped version (blue)
