|
|
Man /
Pointset2schemeContent-type: text/html pointset2schemeSection: User Commands (1)Index Return to Main Contents NAMEpointset2scheme - Creates scheme files from point sets.SYNOPSISpointset2scheme [options]DESCRIPTIONThis program reads gradient directions and produces a scheme file. It will read files in the text format found in camino/PointSets/Elec???.txt:
Alternatively, the program can read files in the format:
with or without the number of points specified at the top of the file. Gradient directions will be normalized to unit length if non-zero. The program will also read FSL gradient directions in the format
but it does not read the FSL bvals file. To convert FSL bvecs / bvals file to Camino format, see fsl2scheme(1). This program permits you to define new schemes using gradient directions from FSL. Normally, directions will have unit magnitude. If this is not the case, you need to determine whether your scanner incorporates the gradient direction magnitude into account when calculating the diffusion gradients. See the -usegradmod option.
The program produces a scheme file appropriate to the supplied imaging parameters. SCHEME FORMATSAdditional details concerning imaging schemes may be found under SCHEME FILES in camino(1). This section is a quick guide to specifying scheme files using pointset2scheme. This program assumes that measurements either apply zero diffusion weighting, or a fixed non-zero diffusion weighting. If this is not the case, it may be easier to write the scheme by hand. For all schemes created using this program, "zero" measurements, ie those with zero diffusion weighting, should have zero gradient directions. The simplest scheme format is BVECTOR (formerly called version "2"). This has the form
where [x_i y_i z_i] is a gradient direction and b_i the corresponding b-value. To create this scheme file, you need only specify the b-value with the -bvalue option. All non-zero gradient directions will have the specified b-value, and zero gradients will have a zero b-value. The STEJSKALTANNER scheme format is a fully-specified Stejskal-Tanner sequence (formerly version "1"). Its file format is
where |G| is the gradient strength, DELTA is the pulse separation, delta is the pulse duration, and TE is the echo time for the measurement. To create a scheme file in this format, use the -dwparams option and pass (in order) <|G|> <DELTA> <delta> <TE_1>. All non-zero measurements will share these parameters. Zero measurements will have zero |G|, DELTA, and delta, but the same TE. The TRSE scheme format is a fully-specified twice-refocused spin-echo sequence (formerly version "3"). Its file format is
where t_del is the onset and del the duration of a pulse, and there are four pulses per measurement. Details of this scheme may be found in Reese et al, Magn Reson Med, 49(1), 177-82, 2003. This scheme is created by specifying -dwparams followed by (in order) <|G|> <del1> <t_del1> <del2> <t_del2> <del3> <t_del4> <TE>. Zero measurements will have everything but TE set to zero. The scheme version "0" has been deprecated; it is no longer possible to create scheme files in that format. Existing scheme files can still be read by Camino programs that take the -schemefile option. INCLUDING ZERO MEASUREMENTSZero measurements may be placed anywhere in the scheme. A zero measurement is defined as one where the gradient direction is [0 0 0]. If any direction in the input point set is zero, then all diffusion-weighting parameters are also zero for that measurement. Additional zero measurements may be prepended onto the scheme with the -addzeromeas option. COMMENTSComments in scheme files are any line beginning with #. UNITS FOR IMAGING PARAMETERSThe units of the measurements in the scheme file determine the units of the output. By default, Camino prefers to use SI: meters, seconds, Tesla. Other units are permitted, but this will affect the output of Camino programs, and may require you to enter additional options. For the purposes of diffusion tensor reconstruction, non-standard units will scale the diffusion tensors in the output. Thus if you use a BVECTOR scheme with b-values specified in s / mm^2, your diffusivities will be in units of mm^2 / s. Other programs may work with non-standard units if additional options are specified. Check the relevant man page before using non-SI units with camino programs. EXAMPLESCreate a scheme file with 30 measurements at b= 1000 s / mm^2 = 1E9 s / m^2, with 3 unweighted measurements followed by the 30 diffusion-weighted measurements. Gradient directions are chosen from the Camino point sets, which are optimised by electrostatic energy minimization (Jansons and Alexander, Inverse Problems, 19:1031-1046, 2003). Many pre-computed point sets are stored in the camino/PointSets directory.
Same thing, only this time we use a file points.txt that already contains the vector [0 0 0] for the zero measurements. Note that the zero measurements may appear anywhere in the file, the b-value for these measurements will be set to zero.
Create a scheme where all measurements are repeated to improve SNR.
Create the same thing, but acquire the repeat measurements sequentially, rather than in a block, so the measurements go [direction 0, direction 0, direction 1, direction 1,...,direction 32] rather than [direction 0, direction 1,..,direction 32, direction 0, direction 1,..,direction 32]
Use a Camino point set, this time for 60 directions, and specify Stejskal-Tanner sequence parameters.
OPTIONS
AUTHORSPhilip Cook <camino@cs.ucl.ac.uk>SEE ALSOcamino(1), fsl2scheme(1)BUGS
Index
This document was created by man2html, using the manual pages. Time: 02:07:11 GMT, December 04, 2017 |