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" |br| N.B.: I0 should not be named in any programmed alignent group
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
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 |br| N.B.: optional output volumes are appended to MD and RA |br| N.B.: output order: MD,RA,(Dxx,Dyy,Dzz,Dxy,Dxz,Dyz),(FA),(E123,RD),(CO),(Res),(Evecs),(Prol) |br| N.B.: -b and -B are independent but can both be applied |br| N.B.: -b requires -m and mask dimensions must match image dimensions |br| N.B.: -B, -b parameter useful range is 1.5 to 3 |br| N.B.: eigenvalue ordering is = Eval1 < Eval2 < Eval3 |br| N.B.: -c produces an franctional constant output CO = C/(C+S0)
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
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