.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH TFF_GENERATE_TRX_FROM_SCRATCH.PY "1" "July 2024" "tff_generate_trx_from_scratch.py 0.3" "User Commands"
.SH NAME
tff_generate_trx_from_scratch.py \- generate a TRX file from CSV, TXT or NPY files
.SH DESCRIPTION
usage: tff_generate_trx_from_scratch.py [\-h] [\-\-positions POSITIONS]
.TP
[\-\-offsets OFFSETS]
[\-\-positions_csv POSITIONS]
[\-\-space {RASMM,VOXMM,VOX}]
[\-\-origin {NIFTI,TRACKVIS}]
[\-\-positions_dtype {float16,float32,float64}]
[\-\-offsets_dtype {uint32,uint64}]
[\-\-dpv FILE DTYPE] [\-\-dps FILE DTYPE]
[\-\-groups FILE DTYPE]
[\-\-dpg GROUP FILE DTYPE]
[\-\-verify_invalid] [\-f]
reference OUT_TRACTOGRAM
.PP
Generate TRX file from a collection of CSV, TXT or NPY files by individually
specifying positions, offsets, data_per_vertex, data_per_streamlines,
groups and data_per_group. Each file must have its data type specified by the
users.
.PP
A reference file must be provided (NIFTI) and the option \fB\-\-verify_invalid\fR will
remove invalid streamlines (outside of the bounding box in VOX space).
.PP
All dimensions (nbr_vertices and nbr_streamlines) and groups/dpg must match
otherwise the script will (likely) crash.
.PP
Each instance of \fB\-\-dps\fR, \fB\-\-dpv\fR, \fB\-\-groups\fR require 2 arguments (FILE, DTYPE).
\fB\-\-dpg\fR requires 3 arguments (GROUP, FILE, DTYPE).
The choice of DTYPE are:
.IP
\- (u)int8, (u)int16, (u)int32, (u)int64
\- float16, float32, float64
\- bool
.PP
Example command:
tff_generate_trx_from_scratch.py fa.nii.gz generated.trx \fB\-f\fR     \fB\-\-positions\fR test_npy/positions.npy \fB\-\-positions_dtype\fR float16     \fB\-\-offsets\fR test_npy/offsets.npy \fB\-\-offsets_dtype\fR uint32     \fB\-\-dpv\fR test_npy/dpv_cx.npy uint8     \fB\-\-dpv\fR test_npy/dpv_cy.npy uint8     \fB\-\-dpv\fR test_npy/dpv_cz.npy uint8     \fB\-\-dps\fR test_npy/dps_algo.npy uint8     \fB\-\-dps\fR test_npy/dps_cw.npy float64     \fB\-\-groups\fR test_npy/g_AF_L.npy int32     \fB\-\-groups\fR test_npy/g_AF_R.npy int32     \fB\-\-dpg\fR g_AF_L test_npy/dpg_AF_L_mean_fa.npy float32     \fB\-\-dpg\fR g_AF_R test_npy/dpg_AF_R_mean_fa.npy float32     \fB\-\-dpg\fR g_AF_L test_npy/dpg_AF_L_volume.npy float32
.SS "positional arguments:"
.TP
reference
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
.TP
OUT_TRACTOGRAM
Output filename. Format must be one of
trk, tck, vtk, fib, dpy, trx.
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-verify_invalid\fR
Verify that the positions are all valid.
None outside of the bounding box in VOX space.
Requires Dipy (due to use of SFT).
.TP
\fB\-f\fR
Force overwriting of the output files.
.SS "Positions options:"
.TP
\fB\-\-positions\fR POSITIONS
Binary file containing the streamlines coordinates.
Must be Nx3 (.npy)
.TP
\fB\-\-offsets\fR OFFSETS
Binary file containing the streamlines offsets (.npy)
.TP
\fB\-\-positions_csv\fR POSITIONS
CSV file containing the streamlines coordinates.
Rows for each streamlines organized as x1,y1,z1,
x2,y2,z2,...,xN,yN,zN
.TP
\fB\-\-space\fR {RASMM,VOXMM,VOX}
Space in which the coordinates are declared.[RASMM]
Non\-default option requires Dipy.
.TP
\fB\-\-origin\fR {NIFTI,TRACKVIS}
Origin in which the coordinates are declared. [NIFTI]
Non\-default option requires Dipy.
.SS "Data type options:"
.TP
\fB\-\-positions_dtype\fR {float16,float32,float64}
Specify the datatype for positions for trx. [float32]
.TP
\fB\-\-offsets_dtype\fR {uint32,uint64}
Specify the datatype for offsets for trx. [uint64]
.SS "Streamlines metadata options:"
.TP
\fB\-\-dpv\fR FILE DTYPE
Binary file containing data_per_vertex.
Must haveNB_VERTICES as first dimension (.npy)
.TP
\fB\-\-dps\fR FILE DTYPE
Binary file containing data_per_vertex.
Must haveNB_STREAMLINES as first dimension (.npy)
.TP
\fB\-\-groups\fR FILE DTYPE
Binary file containing a sparse group (indices).
Indices should be lower than NB_STREAMLINES (.npy)
.TP
\fB\-\-dpg\fR GROUP FILE DTYPE
Binary file containing data_per_group.
.IP
Must have(1,) as first dimension (.npy)