ComputeFM

#!/bin/bash
# CREATING FIELDMAPS FROM SHIM SEQUENCES	
	cd $FM_DIR

### Create MAGNITUDE FM
# Start by registering SHIM1 to T1 using FLIRT
	flirt -in $SHIM1 -ref $T1 -out shim1_reg -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear &

# Create the magnitude fm from the registered shim1 and a mask
	fslmaths $T1 -bin $T1_mask
	wait
	fslmaths $T1_mask -mul shim1_reg.nii.gz fm_mag &

# Also create a brain extracted magnitude fieldmap
# If used as fsl input: brain extracted fielmap must be named fieldmap_brain and be located in the same directory
# same using T1_brain 
	fslmaths $T1_brain -bin ${T1_mask}2.nii.gz
	fslmaths ${T1_mask}2.nii.gz -mul shim1_reg.nii.gz fm_mag_brain &
	echo "========================= done creating magnitude fieldmap ============================"

### Create PHASE FIELDMAP
# Convert SHIM3 to radians
	fslmaths $SHIM3 -mul 123.21408958 -mul 0.0628 fm_rads -odt float

# Register output in radians to T1 using FLIRT
	flirt -in fm_rads -ref $T1 -out fm_rads_reg -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear &
	echo "========================== done creating phase fieldmap ==============================="