DTI

dwi_xalign3d_4dfp

motion compensation for dwi data (single run)

Usage: dwi_xalign3d_4dfp <(4dfp) dwi> <(4dfp) mask>

Examples:

dwi_xalign3d_4dfp hbo08a_dwi1 hbo08a_dwi1_mskt -s -g2-4 -g5,13,18,23

Options

-p planar (2D; disable cross-slice) alignment
-w enable wrap addressing
-s enable cross DWI voxel size adjust (principal axis stretch)
-a compute group arithmeric mean volume (default geometric mean)
-n zero negative values in output image
-I<int> specify volume number of I0 counting from 1 (default 1)
-f<flt> specify pre-blur filter half freq (1/mm) (default none)
-d<flt> specify sampling interval in mm (default=5.0000)
-i<flt> specify displacment search radius in mm (default=3.0000)
-j<flt> specify parameter search object radius in mm (default=40.0000)
-c<int> specify number of within-group cycles (default=3)
-g<int>[-<int>][,<int>[-<int>]][,…] program alignment group

N.B.: <(4dfp) mask> may be “none”
N.B.: I0 should not be named in any programmed alignent group

dwi_cross_xalign3d_4dfp

cross-run motion compensation and averaging of dwi data

Usage: dwi_cross_xalign3d_4dfp <(4dfp) dwi1> <(4dfp) dwi2> <(4dfp) dwin> … <(4dfp) dwi_out>

Examples:

dwi_cross_xalign3d_4dfp -sgmjo_sub2-dwi1_mskt jo_sub2-dwi1 jo_sub2-dwi2 jo_sub2-dwi_all
dwi_cross_xalign3d_4dfp -sgmjo_sub2-dwi1_mskt -ljo_sub2_dwi.lst jo_sub2-dwi_all

Options

-p planar (2D; disable cross-slice) alignment
-w enable wrap addressing
-s enable cross DWI voxel size adjust (principal axis stretch)
-n zero negative values in output image
-z<x|y|z><flt> zoom output x y or z dimension by specified factor
-g use group geometric mean (*_geom) volumes for cross-run registration
-a append successive runs in output (default average)
-m<(4dfp) mask> specify first volume mask
-I<int> specify volume number of I0 counting from 1 (default 1)
-f<flt> specify pre-blur filter half freq (1/mm) (default none)
-d<flt> specify sampling interval in mm (default=5.0000)
-i<flt> specify displacment search radius in mm (default=3.0000)
-j<flt> specify parameter search object radius in mm (default=40.0000)
-l<lst> read input file names from specified file (use before naming output)
-@<b|l> output big or little endian (default input endian)

N.B.: option -I (non-default I0 volume) must be matched according to use of option -g

diff_4dfp

diffusion tensor computation given dwi

Usage: diff_4dfp <prm_file> <file_4dfp> <opt mask_file> <opt CO_file>

Examples:

diff_4dfp tp7_params.dat /data/emotion/data3/track_sub3/track_sub3_DTI_avg

Options

Computational
-N compute D using nonlinear Levenberg-Marquardt (default log linear LS)
-Z use nonlinear approach to repair bad voxels from log linear LS
-c estimate non-mobile diffusion term (applies only to Levenberg-Marquardt algorithm)
-s<int> compute only selected slice for debugging
-v<int> compute only selected voxel for debugging
-B<flt> ignore bad encoding at specified threshold (units = s.d.) (default=3.0)
-b<flt> ignore encodings with noisy background at specified threshold (default=3.0)
-S<flt> subtract a fraction of S0 image from data (def=0.1), not compatible with B,b
-C subtract a CO fraction from data using an imported file, not compatible with B,b
-G<int> Correct tbi data, =1 CCIR remove encode 1, =2 SLCH remove encode 10,22
Masking
-m Use external mask included as third input file
-M compute threshold mask without holes
-t<flt> specify mask threshold as fraction of I0 mode (default=0.1000)
-h<flt> specify minimum I0 mode (default=100.00)
-n<int> specify number of I0 histogram smoothings (default=4)
Output
-a<str> append specified trailer to output fileroots
-p print out pixel numbers for debugging
-D output D tensor
-F output FA (fractional anisotropy)
-E output eigenvalues
-V[int] output [specified number of (default=1)] eigenvectors (principal first)
-P output prolaticity
-R output single residue volume for model
-r output squared residue values for all encodings in a separate file
-o output extra full LM output files (applies only to LM algorithm) (implies -N)
-d debug mode, provide extra volume of output as needed
-@<b|l> output big or little endian (default input endian)

N.B.: the first data volume must have high SNR from b=0 or low b value
N.B.: optional output volumes are appended to MD and RA
N.B.: output order: MD,RA,(Dxx,Dyy,Dzz,Dxy,Dxz,Dyz),(FA),(E123,RD),(CO),(Res),(Evecs),(Prol)
N.B.: -b and -B are independent but can both be applied
N.B.: -b requires -m and mask dimensions must match image dimensions
N.B.: -B, -b parameter useful range is 1.5 to 3
N.B.: eigenvalue ordering is = Eval1 < Eval2 < Eval3
N.B.: -c produces an franctional constant output CO = C/(C+S0)

diffRGB_4dfp

dwi \(\rightarrow\) RGB map

Usage: diffRGB_4dfp <prm_file> <file_4dfp>

Examples:

diffRGB_4dfp -t0.5 -qc1.7 tp7_params.dat /data/DTI_avg

Options

-q scale intesity by sqrt(Asig) instead of Asig
-G change color coding to bgr (default rgb)
-c<flt> specify the intensity scale value (default=1.0000)
-t<flt> specify mask threshold as fraction of I0 mode (default=0.1000)
-T<str> specify t4 file used to transform DWI data
-h<flt> specify minimum I0 mode (default=100.00)
-n<int> specify number of I0 histogram smoothings (default=4)
-D input <file_4dfp> is 8 volume diff_4dfp -D output (Dbar, Asigma, D tensor)
-@<b|l> output big or little endian (default input endian)

N.B.: <prm_file> is ignored with -D option

whisker_4dfp

dwi \(\rightarrow\) whiskers (visualized in Matlab)

Usage: whisker_4dfp <prm_file> <file_4dfp>

Examples:

whisker_4dfp tp7_params.dat -dz3 /data/emotion/data3/track_sub3/track_sub3_DTI_avg

Options

-h<flt> specify minimum I0 mode (default=100.00)
-n<int> specify number of I0 histogram smoothings (default=4)
-t<flt> specify mask threshold as fraction of I0 mode (default=0.1000)
-T<str> specify t4 file used to transform DWI data
-E additionally output eigenvalues
-3 output 3 eigenvectors scaled by eigenvalue
-d<x|y|z><int> specify quiver spacing in pixels (default=1)

N.B.: default output is first two eigenvectors scaled by Asigma