Hi experts,
I am working with EPI resting-state fMRI data and I have fieldmaps so I would like to perform distortion correction, however, when I try to use applywarp to register the image to standard space the image is clipped and incorrect (please see the attached image)
Can you please have a look at my steps and see if I have missed something or if I am doing something incorrectly.
Cheers,
Sally
The steps that I have followed are:
1. fsl_prepare_fieldmap with all required data to get outputs (all working well)
2. run epi_reg on my EPI image (my rsfMRI data), as below
epi_reg --epi=ep2d_3_3iso_Resting.nii --t1=t1.nii.gz --t1brain=bet_brain.nii.gz --fmap=fieldmap.nii.gz --fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_BET.nii.gz --echospacing=0.00035 --pedir=-y --out=epi2struc
3. invwarp
invwarp -w epi2struc_warp.nii.gz -o test_warp -r ep2d_3_3iso_Resting.nii
4. applywarp
applywarp --in=epi2struc.nii.gz --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain --out=warped_functional_distortcorrect --warp=test_warp.nii.gz --premat=epi2struc.mat
(output from this step is attached)
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