epi_fieldmap_unwarping
EPI field map unwarp
This page contains information relevant to B0 field map un-warping, using the HUP6, Siemens 3T scanner and FSL FUGUE program.
FSL_FUGUE
Acquiring the b0 field map in the scanner
The b0 field map acquisition is a Gradient Echo fieldmap sequence that takes 1 min. 4 sec. to run. Though this sequence can probably be found in other places, I recommend using the sequence that is in the protocol named below.
- Add the b0 field map sequence to your protocol by copying it over from this protocol: \user\research\thompson-schill\COLORADAPTATIONS_bomap. The name of the sequence is 'B0map“.
- After the sequence has been added to your protocol, make sure that these parameters match (meaning the b0 parameters should match the parameters for your epi runs): (number of) slices, slice thickness, field of view (FoV), and shim mode. All of these can be found on the “Routine” page of the sequence parameters, except for shim mode. Shim mode can be found on the “System” page of the sequence parameters. It should either read “standard” or “advanced”. Most protocols are set to “standard”, but this b0 map sequence is set to “advanced”- It does not need to be. Just make sure that all of the epi runs' shim mode matches the b0 shim mode. Here is an example of the scanner protocol parameters with relevant fields highlighted: b0map.pdf
- Head coil does NOT matter. Use whichever you prefer.
Unwarping using FUGUE
Unwarping at the command line
Below is a sample voxbo script that implements b0 unwarping. Please let me know if you have any questions. apersi@sas.upenn.edu
#========================== # SOFTWARE USAGE # # FSL -- /usr/local/fsl/ # version 4.1 # SPM2 -- /usr/local/spm2/ # # dcm2nii -- /usr/local/mricron-64bit/dcm2nii # # FreeSurfer -- /usr/local/freesurfer_64bit/ # used for the mri_convert command # # Bash shell script -- /jet/rito/migraine/PrepScripts/ASL_scripts/RunPerf.sh # Bash shell script -- /jet/rito/migraine/PrepScripts/ASL_scripts/RunPASL.sh # Bash shell script -- /jet/rito/migraine/PrepScripts/ASL_scripts/RunTransitTime.sh # # IDL # used to implement JJ Wang's perfusion and transit time analysis code # #========================== ####### # Settings ######## LOGGING 2 globals thresh=200 globals xa=1 globals ya=1 globals za=1 globals xf=3 globals yf=3 globals zf=3 globals refvol=/usr/local/spm2/templates/T1.mnc globals paramfile=SPM2_MNI_params.mat globals "bb_anat=[-79,-112,-51;79,76,86]" globals "bb_func=[-78,-111,-50;78,75,85]" globals "bb_disp=[-79,-112,-50;79,76,85]" ####### # Reset any previous attempts to run this script ####### runonce shellcommand "if [ -d Anatomy/raw ]; then mv -f */raw/* ./; fi" runonce shellcommand "if [ -d models ]; then rm -rf models; fi" runonce shellcommand "if [ -d Anatomy ]; then rm -rf Anatomy; fi" rUnonce shellcommand "if [ -d $Subject_* ]; then rm -rf $Subject_*; fi" runonce shellcommand "if [ -d b0map/mag_raw ]; then mv -f */mag_raw/0008* ./; fi" runonce shellcommand "if [ -d b0map/phase_raw ]; then mv -f */phase_raw/0009* ./; fi" runonce shellcommand "if [ -d b0map ]; then rm -rf b0map; fi" runonce shellcommand "if [ -d DTI ]; then rm -rf DTI; fi" runonce shellcommand "if [ -d Perfusion_pCASL ]; then rm -rf Perfusion_pCASL; fi" ####### # Prepare Anatomy directory # - Create directories # - Move DICOM images into the raw directory # - Create Functional.cub from ScoutEPI # - Create Anatomical.cub from MPRAGE # - Move "moco" versions of data to "unused_moco" directory ######## runonce shellcommand "mkdir -p Anatomy" runonce shellcommand "mkdir -p Anatomy/raw" runonce shellcommand "mkdir -p b0map" runonce shellcommand "mkdir -p b0map/mag_raw" runonce shellcommand "mkdir -p b0map/phase_raw" runonce shellcommand "mv $b0mag b0map/mag_raw" runonce shellcommand "mv $b0phase b0map/phase_raw" runonce shellcommand "mv $Loc Anatomy/raw" runonce shellcommand "vb2cub $ScoutEPI/* Anatomy/Functional.cub" runonce shellcommand "mv $ScoutEPI Anatomy/raw/" runonce shellcommand "vb2cub $MPRAGE Anatomy/Anatomical.cub" runonce shellcommand "mv $MPRAGE Anatomy/raw/" ####### # Prepare scout images # These are images to be used for co-registration and for # subsequent spatial normalization. They are generated for # the pCASL and DTI data ######## runonce shellcommand "tes2cub $RestpCASL Anatomy/pCASL_scout.cub" runonce shellcommand "tes2cub $DTI1 Anatomy/DTI_scout.cub" ##### # Align origins of functional, perfusion, DTI, and anatomical data ##### runonce shellcommand "setorigin -m Anatomy/Anatomical.cub Anatomy/Functional.cub" runonce shellcommand "setorigin -m Anatomy/Functional.cub Anatomy/Anatomical.cub" runonce shellcommand "setorigin -m Anatomy/Anatomical.cub Anatomy/pCASL_scout.cub" runonce shellcommand "setorigin -m Anatomy/Anatomical.cub Anatomy/DTI_scout.cub" runonce shellcommand "resample Anatomy/Anatomical.cub Anatomy/Display.cub -ra Anatomy/Functional.cub" ##### ## Get b0 field map, to be used later to unwarp the epi runs # Convert Phase images to radians. # Unwrap the phase images # Get the fieldmap in radians ##### ### dicom2niftii runonce shellcommand "/usr/local/mricron-64bit/dcm2nii -o b0map/mag_raw b0map/mag_raw/$b0mag" runonce shellcommand "/usr/local/mricron-64bit/dcm2nii -o b0map/phase_raw b0map/phase_raw/$b0phase" runonce shellcommand "vbconv Anatomy/Functional.cub b0map/functional.nii.gz" runonce shellcommand "vbconv Anatomy/Display.cub b0map/display.nii.gz" runonce shellcommand "mv -f b0map/mag_raw/*1001.nii.gz b0map/b0_mag.nii.gz" runonce shellcommand "rm -f b0map/mag_raw/*2001.nii.gz" runonce shellcommand "mv -f b0map/phase_raw/*1001.nii.gz b0map/b0_phase1.nii.gz" runonce shellcommand "mv -f b0map/phase_raw/*2001.nii.gz b0map/b0_phase2.nii.gz" shellcommand "/usr/local/mricron-64bit/dcm2nii $raw" shellcommand "mv -f $raw/*.nii.gz b0map/$scan.nii.gz" # Convert Phase images to radians. Move orig phase 1 and 2 to raw dir. runonce shellcommand "fslmaths b0map/b0_phase1.nii.gz -mul 3.14159 -div 4096 -sub 3.14159 b0map/phase1_rad.nii.gz -odt float" runonce shellcommand "fslmaths b0map/b0_phase2.nii.gz -mul 3.14159 -div 4096 -sub 3.14159 b0map/phase2_rad.nii.gz -odt float" runonce shellcommand "mv b0map/b0_phase1.nii.gz b0map/phase_raw/b0_phase1.nii.gz" runonce shellcommand "mv b0map/b0_phase2.nii.gz b0map/phase_raw/b0_phase2.nii.gz" # Unwrap the phase images runonce shellcommand "prelude -a b0map/b0_mag.nii.gz -p b0map/phase1_rad.nii.gz -o b0map/phase1_unwrapped_rad.nii.gz" runonce shellcommand "prelude -a b0map/b0_mag.nii.gz -p b0map/phase2_rad.nii.gz -o b0map/phase2_unwrapped_rad.nii.gz" runonce shellcommand "mv b0map/phase1_rad.nii.gz b0map/phase_raw/phase1_rad.nii.gz" runonce shellcommand "mv b0map/phase2_rad.nii.gz b0map/phase_raw/phase2_rad.nii.gz" # Get the fieldmap in radians runonce shellcommand "fslmaths b0map/phase2_unwrapped_rad.nii.gz -sub b0map/phase1_unwrapped_rad.nii.gz -mul 1000 -div 2.58 b0map/fieldmap_rads.nii -odt float" runonce shellcommand "mv b0map/phase1_unwrapped_rad.nii.gz b0map/phase_raw/phase1_unwrapped_rad.nii.gz" runonce shellcommand "mv b0map/phase2_unwrapped_rad.nii.gz b0map/phase_raw/phase2_unwrapped_rad.nii.gz" # Unwarp ScoutEPI runonce shellcommand "fugue -i b0map/functional.nii.gz --dwell=.0005 --loadfmap=b0map/fieldmap_rads.nii.gz -u b0map/functional_unwarped.nii.gz --unwarpdir=y-" # Coregister the ScoutEPI to the Anatomical image runonce shellcommand "/home/avants/bin/ants/ANTS 3 -m PR[b0map/display.nii.gz,b0map/functional_unwarped.nii.gz,1,4] --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --rigid-affine true --affine-gradient-descent-option 0.5x0.95x1.e-4x1.e-4 --MI-option 32x16000 -o b0map/antsPR -i 0x0x0 -v -t SyN[0.5]" runonce shellcommand "/home/avants/bin/ants/WarpImageMultiTransform 3 b0map/functional_unwarped.nii b0map/functional_unwarped_antsPR.nii.gz -R b0map/display.nii.gz b0map/antsPRAffine.txt" runonce shellcommand "mv b0map/functional_unwarped_antsPR.nii.gz b0map/functional_unwarped_coreg.nii.gz" runonce shellcommand "rm -f b0map/display.nii.gz" runonce shellcommand "rm -f b0map/functional.nii.gz" runonce shellcommand "resample b0map/functional_unwarped_coreg.nii.gz b0map/functional_unwarped_coreg.nii.gz -xx 0 4 64 -yy 0 4 64" # Unwarp epi runs shellcommand "fugue -i b0map/$scan.nii.gz --dwell=.0005 --loadfmap=b0map/fieldmap_rads.nii.gz -u b0map/$scan_unwarped.nii.gz --unwarpdir=y-" # run motion correction on epis shellcommand "mcflirt -in b0map/$scan_unwarped.nii.gz -o b0map/$scan_unwarped.nii.gz -reffile b0map/functional_unwarped_coreg.nii.gz -plots" # Clean up b0 directory shellcommand "mkdir $Subject_$scan" shellcommand "mkdir $Subject_$scan/raw" shellcommand "mv $raw $Subject_$scan/raw" shellcommand "vbconv b0map/$scan_unwarped.nii.gz $Subject_$scan/$Subject_$scan.tes" shellcommand "vbconv b0map/$scan.nii.gz $Subject_$scan/raw/$Subject_$scan_raw.tes" shellcommand "rm -f b0map/$scan.nii.gz" shellcommand "mv b0map/$scan_unwarped.nii.gz.par $Subject_$scan/$Subject_$scan_motion.par" runonce shellcommand "mv b0map/b0_mag.nii.gz b0map/mag_raw" runonce shellcommand "mkdir b0map/coreg" runonce shellcommand "mv b0map/functional_unwarped_coreg.nii.gz b0map/coreg" runonce shellcommand "mv b0map/antsPRAffine.txt b0map/coreg" ##### # Process the Anatomical volume ##### # Store the original anatomical runonce shellcommand "cp Anatomy/Anatomical.cub Anatomy/OrigAnatomical.cub" # Convert the Anatomical.cub file to Anatomical.nii runonce shellcommand "vbconv Anatomy/Anatomical.cub -o Anatomy/Anatomical.nii" # Perform noise reduction, skull-stripping and inhomogeneity correction with FSL tools runonce shellcommand "/usr/local/fsl/bin/susan Anatomy/Anatomical.nii 23.3302 3 3D 1 0 Anatomy/susanAnatomical.nii.gz" runonce shellcommand "/usr/local/fsl/bin/bet Anatomy/susanAnatomical.nii.gz Anatomy/susanAnatomical_BET -f 0.5 -g 0 -o -m" runonce shellcommand "gunzip Anatomy/susanAnatomical.nii.gz" runonce shellcommand "gunzip Anatomy/susanAnatomical_BET.nii.gz" runonce shellcommand "gunzip Anatomy/susanAnatomical_BET_mask.nii.gz" runonce shellcommand "/usr/local/fsl/bin/fast --type=1 --class=3 -B --out=Anatomy/susanAnatomical_BET_FAST Anatomy/susanAnatomical_BET" # Gunzip the files runonce shellcommand "gunzip Anatomy/susanAnatomical_BET_FAST_*nii.gz" # Wrap the skull back around the inhomogeneity corrected brain volume runonce shellcommand "vbim -i Anatomy/susanAnatomical_BET_mask.nii -invert -write Anatomy/NotBrain_mask.nii" runonce shellcommand "vbim -i Anatomy/NotBrain_mask.nii Anatomy/susanAnatomical.nii -product -write Anatomy/NotBrain.nii" runonce shellcommand "vbim -i Anatomy/NotBrain.nii Anatomy/susanAnatomical_BET_FAST_restore.nii -sum -write Anatomy/Anatomical_fsl.nii" # Convert the Anatomical.nii file to Anatomical.cub runonce shellcommand "rm Anatomy/Anatomical.cub" runonce shellcommand "vbconv Anatomy/Anatomical_fsl.nii -o Anatomy/Anatomical.cub" runonce shellcommand "vbhdr -c Anatomy/OrigAnatomical.cub Anatomy/Anatomical.cub" # Clean-up runonce shellcommand "mv Anatomy/susanAnatomical_BET_FAST_seg.nii Anatomy/Anatomical_seg.nii" runonce shellcommand "rm Anatomy/Anatomical.nii" runonce shellcommand "rm Anatomy/susanAnatomical.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_overlay.nii.gz" runonce shellcommand "rm Anatomy/susanAnatomical_BET_mask.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_FAST_mixeltype.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_FAST_pve_0.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_FAST_pve_1.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_FAST_pve_2.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_FAST_pveseg.nii" runonce shellcommand "rm Anatomy/susanAnatomical_BET_FAST_restore.nii" runonce shellcommand "rm Anatomy/NotBrain.nii" runonce shellcommand "rm Anatomy/NotBrain_mask.nii" ##### # Create the "Display" volumes for the first MPRAGE ##### runonce shellcommand "resample Anatomy/Anatomical.cub Anatomy/Display.cub -ra Anatomy/Functional.cub" #### # Co-register each of the scout images (pCASL, DTI) to # the functional scout volume # # The header of the Functional.cub must be copied onto the # resliced (coregistered) file to preserve origin info #### runonce shellcommand "vb2img Anatomy/Functional.cub Anatomy/Functional.img" runonce shellcommand "vb2img Anatomy/pCASL_scout.cub Anatomy/pCASL_scout.img" runonce shellcommand "vb2img Anatomy/DTI_scout.cub Anatomy/DTI_scout.img" runonce shellcommand "/usr/local/fsl/bin/flirt -in Anatomy/pCASL_scout.hdr -ref Anatomy/Functional.hdr -out Anatomy/pCASL_scout_Coreg.hdr -omat Anatomy/pCASL_scout_Coreg.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear -noresample" runonce shellcommand "/usr/local/fsl/bin/flirt -in Anatomy/DTI_scout.hdr -ref Anatomy/Functional.hdr -out Anatomy/DTI_scout_Coreg.hdr -omat Anatomy/DTI_scout_Coreg.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear -noresample" runonce shellcommand "gunzip Anatomy/pCASL_scout_Coreg.nii.gz" runonce shellcommand "gunzip Anatomy/DTI_scout_Coreg.nii.gz" runonce shellcommand "vbconv Anatomy/pCASL_scout_Coreg.nii Anatomy/pCASL_scout_Coreg.cub" runonce shellcommand "vbconv Anatomy/DTI_scout_Coreg.nii Anatomy/DTI_scout_Coreg.cub" runonce shellcommand "vbhdr -c Anatomy/Functional.cub Anatomy/pCASL_scout_Coreg.cub" runonce shellcommand "vbhdr -c Anatomy/Functional.cub Anatomy/DTI_scout_Coreg.cub" runonce shellcommand "rm Anatomy/pCASL_scout.img" runonce shellcommand "rm Anatomy/pCASL_scout.hdr" runonce shellcommand "rm Anatomy/pCASL_scout_Coreg.nii" runonce shellcommand "rm Anatomy/DTI_scout.img" runonce shellcommand "rm Anatomy/DTI_scout.hdr" runonce shellcommand "rm Anatomy/DTI_scout_Coreg.nii" ##### # Perform normalization of anatomicals and scouts (Functional, perfusion, DTI) using SPM2 ##### runonce spm2_norm_calc $DIR/Anatomy/ $paramfile Anatomical.cub $refvol $xa $ya $za $bb_anat runonce spm2_norm_apply3d $DIR/Anatomy $DIR/Anatomy/$paramfile Anatomical.cub nAnatomical.cub $xa $ya $za $bb_anat runonce spm2_norm_apply3d $DIR/Anatomy $DIR/Anatomy/$paramfile Functional.cub nFunctional.cub $xf $yf $zf $bb_func runonce spm2_norm_apply3d $DIR/Anatomy $DIR/Anatomy/$paramfile pCASL_scout_Coreg.cub npCASL_scout_Coreg.cub $xf $yf $zf $bb_func runonce spm2_norm_apply3d $DIR/Anatomy $DIR/Anatomy/$paramfile DTI_scout_Coreg.cub nDTI_scout_Coreg.cub $xf $yf $zf $bb_func runonce spm2_norm_apply3d $DIR/Anatomy $DIR/Anatomy/$paramfile Anatomical.cub nDisplay.cub $xa $ya $zf $bb_disp ####### # Process the pCASL data # - Prepare Perfusion_pCASL directory # - convert non-moco pCASL series to TES file # - Call JJ Wang's IDL code via a bash shell script # - extract the CBF image from the output (the third image of the tes file) # - move the processed files into sub-directories # - convert the CBF volumes to ANALYZE format # - reslice the CBF images to the functional space using FLIRT # - use Freesurfer MRI convert to change the replaced file to ANALYZE # - convert CBF volumes to images, then cubs, and put the processed files away # - spatially normalize the CBF cub images using SPM # - remove the un-needed files ####### runonce shellcommand "mkdir -p Perfusion_pCASL" runonce shellcommand "mkdir -p Perfusion_pCASL/raw" runonce shellcommand "vb2tes $RestpCASL Perfusion_pCASL/$Subject_pCASL_RestingCBF.tes" runonce shellcommand "mv $RestpCASL Perfusion_pCASL/raw/" runonce shellcommand "mv $moco_RestpCASL Perfusion_pCASL/raw/" runonce shellcommand "sh /jet/aguirre/PatientStudies/BlindnessNOS/PrepScripts/ASL_scripts/RunPerf.sh Perfusion_pCASL/$Subject_pCASL_RestingCBF.tes 1650 60 1200 1500" runonce shellcommand "tes2cub Perfusion_pCASL/$Subject_pCASL_RestingCBF.pf.tes Perfusion_pCASL/$Subject_pCASL_RestingCBF.cub 3" runonce shellcommand "mkdir Perfusion_pCASL/processed" runonce shellcommand "mv Perfusion_pCASL/$Subject_pCASL_RestingCBF.pf.tes Perfusion_pCASL/processed/" runonce shellcommand "mv Perfusion_pCASL/$Subject_pCASL_RestingCBF.tes Perfusion_pCASL/processed/" runonce shellcommand "vb2img Perfusion_pCASL/$Subject_pCASL_RestingCBF.cub Perfusion_pCASL/$Subject_pCASL_RestingCBF.img" runonce shellcommand "/usr/local/fsl/bin/flirt -in Perfusion_pCASL/$Subject_pCASL_RestingCBF.hdr -ref Anatomy/Functional.hdr -applyxfm -init Anatomy/pCASL_scout_Coreg.mat -out Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.nii.gz" runonce shellcommand64 "export FREESURFER_HOME=/usr/local/freesurfer_64bit;/usr/local/freesurfer_64bit/bin/mri_convert $DIR/Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.nii.gz $DIR/Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.img" runonce shellcommand "vb2cub Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.img Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.cub" runonce spm2_norm_apply3d $DIR/Perfusion_pCASL $DIR/Anatomy/$paramfile $Subject_pCASL_RestingCBF_Coreg.cub n$Subject_pCASL_RestingCBF_Coreg.cub $xf $yf $zf $bb_func runonce shellcommand "rm Perfusion_pCASL/$Subject_pCASL_RestingCBF.img" runonce shellcommand "rm Perfusion_pCASL/$Subject_pCASL_RestingCBF.hdr" runonce shellcommand "rm Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.img" runonce shellcommand "rm Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.hdr" runonce shellcommand "rm Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.nii.gz" runonce shellcommand "rm Perfusion_pCASL/$Subject_pCASL_RestingCBF_Coreg.mat" ####### # Prepare the DTI data # At present, this involves simply # involves moving the data into # a top-level DTI directory ####### runonce shellcommand "mkdir -p DTI" runonce shellcommand "mkdir -p DTI/raw" runonce shellcommand "mv $DTI1 DTI/raw/" runonce shellcommand "mv $DTI2 DTI/raw/" ###################### # process the tes file ###################### shellcommand "sliceacq -i $Subject_$scan/$Subject_$scan.tes -o $Subject_$scan/$Subject_$scan.tes -n" #shellcommand "setorigin -c Anatomy/Functional.cub $Subject_$scan/$Subject_$scan.tes spm2_norm_apply4d $DIR/$Subject_$scan $DIR/Anatomy/$paramfile $Subject_$scan.tes n$Subject_$scan.tes $xf $yf $zf $bb_func shellcommand "vbsmooth -vox 0.5 0.5 0.5 -o $Subject_$scan/$Subject_$scan.tes $Subject_$scan/$Subject_$scan.tes threshold $Subject_$scan/$Subject_$scan.tes $Subject_$scan/$Subject_$scan.tes $thresh calcgs $Subject_$scan/$Subject_$scan.tes calcps $Subject_$scan/$Subject_$scan.tes ###################### # Create a models directory # Create the average power spectrum and one-over-f file ##################### runonce shellcommand "mkdir -p Models" runonce shellcommand "vbfit 3000 150 $Subject_01/$Subject_01_PS.ref $Subject_02/$Subject_02_PS.ref $Subject_03/$Subject_03_PS.ref -o Models/OneOverF.ref"
epi_fieldmap_unwarping.txt · Last modified: 2016/09/15 18:04 (external edit)
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