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FSL Cheat Sheet

FSLUTILS - Image and Data Manipulation

Full FSLUTILS descriptions can be found here: http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html

SAMPLE COMMANDS - Image and Data Manipulation

# Resample image into reference image's space (so change matrix dimensions, (image size) and voxel size) 
flirt -ref <image in space you want to be in> -in <input image> -out <input image in new space> -nosearch -interp trilinear

Registration with FNIRT - linear

We have functional data (func.nii) and structrural data (struct.nii) that we want in the MNI152_T1_2mm_brain.nii.gz space

# Register func.nii to struc.nii
flirt -ref struct.nii -in func.nii -omat func2struct.mat -dof 6 

# Output is func2struct.mat, tells how to transform the functional into space of anatomical 
# Now brain extract the anatomical and map struc.nii onto the standard template
# output will be struc2standard_aff.mat - how to map the structural to standard
bet struct.nii struct_bet -ref MNI152_T1_2mm_brain.nii -in struct_bet.nii -omat struct2standard_aff.mat

# Now use with fnirt...
fnirt --ref=MNI152_T1_2mm_brain.nii.gz --in=struct.nii --aff=struct2standard_aff.mat --cout=struct2standard_warp.nii

# Now get functional into standard space
applywarp --ref=MNI152_T1_2mm_brain.nii.gz --in=func.nii --out=func_standard.nii --coef=struct2standard_warp.nii --premat=func2struct.mat

Do a brain extraction on an anatomical, then register functional data to the standard space and the extracted anatomical

#------------------------------------------------------------
# BET Brain Extraction
#------------------------------------------------------------
echo "Performing BET brain extraction on " $ANATFILE
bet $ANATPATH/$ANATFILE.nii.gz $ANATPATH/mprage_bet.nii.gz -S -f .225
#-------------------------------------------------------------
# FLIRT LINEAR REGISTRATION
#-------------------------------------------------------------
echo "Registering " $FUNCDATA " to mprage_bet"
flirt -ref $ANATPATH/mprage_bet.nii.gz -in $FUNCDATA.nii.gz -dof 7 -omat $FUNCDATA"_func2struct.mat";
flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in $ANATPATH/mprage_bet.nii.gz -omat $ANATPATH/affine_trans.mat;
fnirt --in=$ANATPATH/$ANATFILE.nii.gz --aff=$ANATPATH/affine_trans.mat --cout=$ANATPATH/nonlinear_trans --config=T1_2_MNI152_2mm
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=$FUNCDATA.nii.gz --warp=$ANATPATH/nonlinear_trans --premat=$FUNCDATA"_func2struct.mat" --out=$FUNCDATA"_warped_func";

BXH/XCEDE Tools

Tools descriptions by Syam Gadde can be found here: http://www.biac.duke.edu/home/gadde/xmlheader-docs/

Cluster Communication