fMRI oriented programs


generate mask of voxels defined over all frames

Usage: compute_defined_4dfp <4dfp|conc input>


-z count zero voxels as undefined (default defined)
-f<str> specify frames-to-count format (default count all)
-F<str> read frames-to-count format from specified file


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>


-t<flt> specify amplitude threshold for phase map (default = 0.0000)
-w<flt> specify pre-blur FWHM in mm (default = 0.0000)
-@<b|l> output big or little endian (default input endian)


scale to achieve mode 1000

Usage: normalize_4dfp <(4dfp) image>


normalize_4dfp -n3 my_run_4dfp
normalize_4dfp -n3 -v2 my_run_4dfp


-n<int> 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 <image>.hist file suitable for plotting, e.g., with xmgr
-a<str> specify trailer (default=”norm”)
-m<str> read specified 4dfp mask (default blur & threshold input image)
-@<b|l> output big or little endian (default input endian)


correct systematic odd vs. even slice intensity banding

Usage: deband_4dfp <(4dfp) image>


deband_4dfp -n3 mybold
deband_4dfp -F"3x125+" mybold


-e deband by exponential gradient model (default flat model)
-g deband by linear gradient model (default flat model)
-n<int> specify number of pre-functional frames
-F<str> specify complete functional/non-functional format
-@<b|l> output big or little endian (default input endian)


remove artifact due to k-space DC offset [1]

Usage: rmspike_4dfp <file_4dfp>


rmspike_4dfp -n3 -x33 test_b1.4dfp.img
rmspike_4dfp -x33 -F"45(1x6+)" test_b1


-n<int> specify number of anatomy frames
-x<int> restrict search to specified column
-y<int> restrict search to specified row
-F<str> specify whole run functional/non-functional format
-@<b|l> output big or little endian (default input endian)


motion correct fMRI timeseries within and across runs

Usage: cross_realign3d_4dfp -l<4dfp_list_file>
or: cross_realign3d_4dfp <run1_4dfp> <run2_4dfp> …


cross_realign3d_4dfp run1_4dfp run2_4dfp run3_4dfp
cross_realign3d_4dfp -sqwv -lruns_4dfp.lst
cross_realign3d_4dfp -pwqsf -n3 -lruns_4dfp.lst


-d debug mode
-@<b|l> 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<str> specify list file of 4dfp filenames
-m<str> specify 4dfp mask to be applied to all runs (default compute)
-n<int> specify number of pre-functional frames
-b<flt> specify pre-blur in reciprocal mm (default=0.06)
-p 2D (planar) realignment (default 3D)
-q minimize status reporting
-r<int> 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


motion correct and resample in atlas space in one step

Usage: t4_xr3d_4dfp [options] <t4file> <input_4dfp_stack>


t4_xr3d_4dfp -aatl anat_ave_to_711-2B_t4 b1_rmsp_dbnd


-a<str> specify outfile name trailer (default = “xr3d”)
-c<flt> 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)
-@<b|l> 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<str> output image dimensions according to <str>.4dfp.ifh

N.B.: default output format = 333.0


convert cross_realign3d_4dfp mat files to spread sheet format Usage: mat2dat <mat_file>


mat2dat atten5_b1_rms4_dbnd_xr3d[.mat]


-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 <mat_file>)
-n<int> specify number of pre steady state frames (default=0)
-l<int> lowpass filter (< 0.1 Hz) specified motion parameter (counting from 1)
TR_vol=<flt> specify TR_vol in sec (required only with option -l)
-r<flt> specify head radius in mm for total motion computation (default=50mm)
-f<str> specify frames to count format, e.g., “4x120+4x76+”

N.B.: -f option overrides -n


correct asynchronous slice acquisition

Usage: frame_align_4dfp <(4dfp) input> <frames_to_skip> [options]


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


-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 <int> specify multi-band factor) (default=1)
-seqstr <str> specify [MB] slice sequence (counting from 1) as a comma-separated (no spaces) integer string
-TR_vol <flt> specify frame TR in sec (default=2.36)
-TR_slc <flt> specify slice TR in sec (default=TR_vol/nslice)

N.B.: space between option and value


correct asynchronous slice acquisition and resample in time

Usage: interp_4dfp <(4dfp) image> <TR_vol_in> <TR_slice_in> <TR_vol_out>


interp_4dfp bold_run[.4dfp[.img]] 2.25 .136 2.5


-d<0|1> specify slice acquisition direction (0:Inf->Sup; 1:Sup->Inf) (default=1)
-@<b|l> output big or little endian (default input endian)

N.B.: if <TR_slice_in> is input as 0 slices are spaced evenly on TR_vol


optimally distribute n events on m frames

Usage: jitter <(int) nevent> <(int) nframe> <(flt) tr_vol>


jitter 20 100 2.0 -s4


-r<int> specify randomization seed (default=0)
-s<int> add specified number of skip frames to output event series (default=0)
-g<flt> specify max interval in sec (t_max; default=30.00) (ignored when -F specfied)
-m<flt> specify min interval in sec (t_min; default=tr_vol)
-o<str> 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
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

[1]Only needed for older sequences