Dear FSL experts
I am new to fsl and DWI preprocessing. I am trying to do GRE filedmap correction for my DWIs.
I will appreciate if someone indicates the steps that I have taken is correct (specially regarding applywarp).
* _brain: brain extracted using BET
* b0: Nodif
* anat: T1 bias field corrected
* _mc: motion/eddy corrected
* sacnner: SIEMENS
###############################
###### Prepare phase map ######
###############################
fslmaths phase.nii -mul 3.14159265 -div 4096 fm_phase_rad -odt float
prelude -p fm_phase_rad -a mag_brain -o u_fm_phase_rad
fslmaths u_fm_phase_rad -div 0.00246 fmap_rads -odt float
#################################
###### Calculating the warps ####
#################################
epi_reg --epi=b0_brain.nii --t1=anat.nii --t1brain=anat_brain.nii.gz --out=b0_brain_2_anat --fmap=fmap_rads --fmapmag=mag.nii --fmapmagbrain=mag_brain.nii.gz --echospacing=0.000345 --pedir=-y
#####################################
## APPLY FIELDMAP TO DWI ##
#####################################
applywarp --ref=b0_brain.nii.gz --in=dwi_mc.nii --warp=b0_brain_2_anat_warp.nii.gz --postmat=b0_brain_2_anat_inv.mat --out=dwi_mc_epi.nii.gz
Many thanks for the help.
Cheers,
H
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