fMRI oriented programs
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<str> |
specify frames-to-count format (default count all) |
-F<str> |
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<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) |
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<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) |
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<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) |
rmspike_4dfp
remove artifact due to k-space DC offset [1]
Usage: rmspike_4dfp <file_4dfp>
Examples:
rmspike_4dfp -n3 -x33 test_b1.4dfp.img
rmspike_4dfp -x33 -F"45(1x6+)" test_b1
Options
-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) |
cross_realign3d_4dfp
motion correct fMRI timeseries within and across runs
Usage: cross_realign3d_4dfp -l<4dfp_list_file> or: cross_realign3d_4dfp <run1_4dfp> <run2_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 |
-@<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 |
t4_xr3d_4dfp
motion correct and resample in atlas space in one step
Usage: t4_xr3d_4dfp [options] <t4file> <input_4dfp_stack>
Examples:
t4_xr3d_4dfp -aatl anat_ave_to_711-2B_t4 b1_rmsp_dbnd
Options
-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
mat2dat
convert cross_realign3d_4dfp mat files to spread sheet format Usage: mat2dat <mat_file>
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 <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
frame_align_4dfp
correct asynchronous slice acquisition
Usage: frame_align_4dfp <(4dfp) input> <frames_to_skip> [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 <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
interp_4dfp
correct asynchronous slice acquisition and resample in time
Usage: interp_4dfp <(4dfp) image> <TR_vol_in> <TR_slice_in> <TR_vol_out>
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) |
-@<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
jitter
optimally distribute n events on m frames
Usage: jitter <(int) nevent> <(int) nframe> <(flt) tr_vol>
Examples:
jitter 20 100 2.0 -s4
Options
-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