.. include:: ../global.rst fMRI oriented programs ====================== .. _compute_defined_4dfp: compute_defined_4dfp -------------------- generate mask of voxels defined over all frames Usage: compute_defined_4dfp <4dfp|conc input> Options ======= ================================================== -z count zero voxels as undefined (default defined) -f specify frames-to-count format (default count all) -F read frames-to-count format from specified file ======= ================================================== cs2ap_4dfp ---------- Converts cosine and sine amplitude images to amplitude and phase. Primarily used for phase-encoded retinotopy. Usage: cs2ap_4dfp <(4dfp) cos_img> <(4dfp) sin_img> <(4dfp) outroot> Options ======= ============================================================ -t specify amplitude threshold for phase map (default = 0.0000) -w specify pre-blur FWHM in mm (default = 0.0000) -@ output big or little endian (default input endian) ======= ============================================================ .. _normalize_4dfp: normalize_4dfp -------------- scale to achieve mode 1000 Usage: normalize_4dfp <(4dfp) image> Examples:: normalize_4dfp -n3 my_run_4dfp normalize_4dfp -n3 -v2 my_run_4dfp Options ======= =============================================================== -n specify number of pre-functional frames -v0 no frame to frame intensity stabilization -v1 volume based frame to frame intensity stabilization (default) -v2 slice based frame to frame intensity stabilization -s disable mode=1000 normalization -z subtract mean volume from functional frames -h create .hist file suitable for plotting, e.g., with xmgr -a specify trailer (default="norm") -m read specified 4dfp mask (default blur & threshold input image) -@ output big or little endian (default input endian) ======= =============================================================== .. _deband_4dfp: deband_4dfp ----------- correct systematic odd vs. even slice intensity banding Usage: deband_4dfp <(4dfp) image> Examples:: deband_4dfp -n3 mybold deband_4dfp -F"3x125+" mybold Options ======= ========================================================= -e deband by exponential gradient model (default flat model) -g deband by linear gradient model (default flat model) -n specify number of pre-functional frames -F specify complete functional/non-functional format -@ output big or little endian (default input endian) ======= ========================================================= rmspike_4dfp ------------------ remove artifact due to k-space DC offset [1]_ Usage: rmspike_4dfp Examples:: rmspike_4dfp -n3 -x33 test_b1.4dfp.img rmspike_4dfp -x33 -F"45(1x6+)" test_b1 Options ======= ================================================== -n specify number of anatomy frames -x restrict search to specified column -y restrict search to specified row -F specify whole run functional/non-functional format -@ output big or little endian (default input endian) ======= ================================================== .. _cross_realign3d_4dfp: cross_realign3d_4dfp -------------------- motion correct fMRI timeseries within and across runs Usage: cross_realign3d_4dfp -l<4dfp_list_file> |br| or: cross_realign3d_4dfp ... Examples:: cross_realign3d_4dfp run1_4dfp run2_4dfp run3_4dfp cross_realign3d_4dfp -sqwv -lruns_4dfp.lst cross_realign3d_4dfp -pwqsf -n3 -lruns_4dfp.lst Options ======= =================================================================== -d debug mode -@ output big or little endian (default CPU endian) -f force recomputing even if output files exist -g enable linear intensity gradient compensation -c use cross-modal registration always -l specify list file of 4dfp filenames -m specify 4dfp mask to be applied to all runs (default compute) -n specify number of pre-functional frames -b specify pre-blur in reciprocal mm (default=0.06) -p 2D (planar) realignment (default 3D) -q minimize status reporting -r specify non-default reference frame -s enable stretch -v[0|1] disable/enable per frame intensity normalization (default disabled) -w enable wrap addressing -Z output undefined voxels as 0.0 (default 1.0e-37) -R disable resampling ======= =================================================================== .. _t4_xr3d_4dfp: t4_xr3d_4dfp ------------ motion correct and resample in atlas space in one step Usage: t4_xr3d_4dfp [options] Examples:: t4_xr3d_4dfp -aatl anat_ave_to_711-2B_t4 b1_rmsp_dbnd Options ======= =============================================================== -a specify outfile name trailer (default = "xr3d") -c scale output by specified factor -N output undefined voxels as NaN -Z output undefined voxels as 0 -E output undefined voxels as 1.e-37 (default) -v[0|1] set per frame intensity equalization mode (default = OFF) -@ output big or little endian (default input endian) -f fast (linear interpolation resample instead of 3D cubic spline) -e echo mat file to stdout frame by frame (verbose mode) -O111 output in 111 space -O222 output in 222 space -O333.n output in 333.n space (y shifted up by n pixels) -O output image dimensions according to .4dfp.ifh ======= =============================================================== N.B.: default output format = 333.0 .. _mat2dat: mat2dat ------- convert cross_realign3d_4dfp mat files to spread sheet format Usage: mat2dat Examples:: mat2dat atten5_b1_rms4_dbnd_xr3d[.mat] Options ============= ====================================================================== -I save trajectory as 4dfp -R save trajectory relative to run mean (remove accumulated movememnt) -D save differentiated trajectory -L write local (in $cwd) (default write parallel to ) -n specify number of pre steady state frames (default=0) -l lowpass filter (< 0.1 Hz) specified motion parameter (counting from 1) TR_vol= specify TR_vol in sec (required only with option -l) -r specify head radius in mm for total motion computation (default=50mm) -f specify frames to count format, e.g., "4x120+4x76+" ============= ====================================================================== N.B.: -f option overrides -n .. _frame_align_4dfp: frame_align_4dfp ---------------- correct asynchronous slice acquisition Usage: frame_align_4dfp <(4dfp) input> [options] Examples:: frame_align_4dfp bold_run.4dfp.img 4 -TR_vol 2.5 -TR_slc .136 -d 1 frame_align_4dfp bold_run.4dfp.img 4 -TR_vol 2.5 -TR_slc .136 -seqstr 1,8,5,2,9,6,3,10,7,4 Options ============= ============================================================================================== -N enable interleaved order 2,4,6,...,1,3,5,... for even total slice counts -S specify sequential slice acquisition (default interleaved) -d <0|1> specify slice acquisition direction (0:Inf->Sup; 1:Sup->Inf) (default=0) -m specify multi-band factor) (default=1) -seqstr specify [MB] slice sequence (counting from 1) as a comma-separated (no spaces) integer string -TR_vol specify frame TR in sec (default=2.36) -TR_slc specify slice TR in sec (default=TR_vol/nslice) ============= ============================================================================================== N.B.: space between option and value interp_4dfp ----------- correct asynchronous slice acquisition and resample in time Usage: interp_4dfp <(4dfp) image> Examples:: interp_4dfp bold_run[.4dfp[.img]] 2.25 .136 2.5 Options ======= ======================================================================== -d<0|1> specify slice acquisition direction (0:Inf->Sup; 1:Sup->Inf) (default=1) -@ output big or little endian (default input endian) ======= ======================================================================== N.B.: if is input as 0 slices are spaced evenly on TR_vol jitter ------ optimally distribute n events on m frames .. TODO: add Avi's thoughts on randomization Usage: jitter <(int) nevent> <(int) nframe> <(flt) tr_vol> Examples:: jitter 20 100 2.0 -s4 Options ======= ============================================================================= -r specify randomization seed (default=0) -s add specified number of skip frames to output event series (default=0) -g specify max interval in sec (t_max; default=30.00) (ignored when -F specfied) -m specify min interval in sec (t_min; default=tr_vol) -o output named fidl-type event file -v verbose mode -F use flat distribution of delay intervals (default Poisson process) ======= ============================================================================= N.B: nevent must be at least 3 |br| N.B: first event is ALWAYS on frame skip; last event is ALWAYS on frame skip + nframe, duration = Inf; fMRI run should include additional frames at end |br| .. [1] Only needed for older sequences