.. include:: ../global.rst 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 specify volume number of I0 counting from 1 (default 1) -f specify pre-blur filter half freq (1/mm) (default none) -d specify sampling interval in mm (default=5.0000) -i specify displacment search radius in mm (default=3.0000) -j specify parameter search object radius in mm (default=40.0000) -c specify number of within-group cycles (default=3) -g[-][,[-]][,...] program alignment group ===================================== ============================================================== N.B.: <(4dfp) mask> may be "none" |br| 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 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 specify volume number of I0 counting from 1 (default 1) -f specify pre-blur filter half freq (1/mm) (default none) -d specify sampling interval in mm (default=5.0000) -i specify displacment search radius in mm (default=3.0000) -j specify parameter search object radius in mm (default=40.0000) -l read input file names from specified file (use before naming output) -@ 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 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 compute only selected slice for debugging -v compute only selected voxel for debugging -B ignore bad encoding at specified threshold (units = s.d.) (default=3.0) -b ignore encodings with noisy background at specified threshold (default=3.0) -S 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 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 specify mask threshold as fraction of I0 mode (default=0.1000) -h specify minimum I0 mode (default=100.00) -n specify number of I0 histogram smoothings (default=4) ------------------------------------------------------------------------------------------ **Output** ------------------------------------------------------------------------------------------ -a 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 -@ 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) diffRGB_4dfp ------------ dwi :math:`\rightarrow` RGB map Usage: diffRGB_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 specify the intensity scale value (default=1.0000) -t specify mask threshold as fraction of I0 mode (default=0.1000) -T specify t4 file used to transform DWI data -h specify minimum I0 mode (default=100.00) -n specify number of I0 histogram smoothings (default=4) -D input is 8 volume diff_4dfp -D output (Dbar, Asigma, D tensor) -@ output big or little endian (default input endian) ======= ========================================================================== N.B.: is ignored with -D option whisker_4dfp ------------ dwi :math:`\rightarrow` whiskers (visualized in Matlab) Usage: whisker_4dfp Examples:: whisker_4dfp tp7_params.dat -dz3 /data/emotion/data3/track_sub3/track_sub3_DTI_avg Options ============== ============================================================== -h specify minimum I0 mode (default=100.00) -n specify number of I0 histogram smoothings (default=4) -t specify mask threshold as fraction of I0 mode (default=0.1000) -T specify t4 file used to transform DWI data -E additionally output eigenvalues -3 output 3 eigenvectors scaled by eigenvalue -d specify quiver spacing in pixels (default=1) ============== ============================================================== N.B.: default output is first two eigenvectors scaled by Asigma