fsl flirt
#!/bin/sh
: <<COMMENTBLOCK
Purpose: Run flirt to reslice an image into a new space
Input: img = image to be resliced,
ref = a reference image (we will reslice INTO this new space)
-init mat = a mat (matrix) file that expresses the relationship between
the input space and the output space
Output: -out = image in new space
COMMENTBLOCK
flirt -in img -datatype float -ref ${ref} -init ${mat} \
-applyxfm -out ${output}fsl flirt
#!/bin/sh
# Use FSL flirt to register label masks
# with nearest neighbor interpolation.
# because the label values should never be interpolated.
# This example assumes:
# an existing 0.5mm standard brain (MNI152_T1_0.5mm_brain)
# an existing flirt matrix from 1 mm to 0.5 mm (stand1stand0.5.mat)
flirt -in atlas -datatype int -ref MNI152_T1_0.5mm_brain \
-interp nearestneighbour \
-init stand1stand0.5.mat -applyxfm -out atlas_0.5mmfsl flirt
#!/bin/sh
# Some viewers (like MRIcron) do not handle anisotropic voxels well.
# FSL can easily convert an image with anisotropic voxels into one
# with isotropic voxels in the same space using -applyisoxfm
# reslice current image into 1mm isotropic
flirt -in anat_CT_axial -ref anat_CT_axial -applyisoxfm 1 -out anat_CT_axial_1mm
# reslice current image into 0.5 mm isotropic voxels.
flirt -in anat_CT_axial -ref anat_CT_axial -applyisoxfm 0.5 -out anat_CT_axial_0.5mmCopyright © 2021 Codeinu
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