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DtfitContent-type: text/html dtfitSection: User Commands (1)Index Return to Main Contents NAMEdtfit - Fits the diffusion tensor to diffusion MRI measurements.SYNOPSISdtfit <data file> <scheme file> [-nonlinear] [options]DESCRIPTIONReads diffusion MRI data, acquired using the acquisition scheme detailed in the scheme file, from the data file. For help with scheme files, please see the section "scheme files" in camino(1).The data file stores the diffusion MRI data in voxel order with the measurements stored in big-endian format and ordered as in the scheme file. The default input data type is four-byte float. The default output data type is eight-byte double. See modelfit(1) and camino(1) for the format of the data file and scheme file. The program fits the diffusion tensor to each voxel and outputs the results, in voxel order and as big-endian eight-byte doubles, to the standard output. The program outputs eight values in each voxel: [exit code, ln(S(0)), D_xx, D_xy, D_xz, D_yy, D_yz, D_zz]. An exit code of zero indicates no problems. For a list of other exit codes, see modelfit(1). The entry S(0) is an estimate of the signal at q=0. This program is a simplified wrapper to modelfit. Options other that -nonlinear are documented in modelfit(1). The command
is equivalent to
The command
is equivalent to
To read data from stdin, do:
The handedness of the coordinate system used by the scanner may not agree with that used within Camino. If this happens, the anisotropy and trace of tensors will be correct but the orientations will be incorrect. This problem is often only noticed during tractography. A simple way to check for this is to fit the diffusion tensors and visualize the principal directions with the dtpdview program. If the principal directions appear to be rotated by 180 degrees about the X, Y or Z directions, then the likely cause is that the gradient directions do not agree. This can be remedied by negating the relevant entries in the scheme file. By default, the program uses linear regression to the log measurements, but may also use non-linear fitting to the raw measurements, which is slower but slightly more accurate. If the first command line argument is - the program reads data from the standard input. EXAMPLESFit the diffusion tensor to the data in SubjectA.Bfloat using linear regression to the log measurements:dtfit SubjectA.Bfloat A.scheme > DiffTensorA.Bdouble Equivalently: cat SubjectA.Bfloat | dtfit - A.scheme > DiffTensorA.Bdouble Fit the diffusion tensor to the data in SubjectA.Bfloat using non-linear fitting: dtfit SubjectA.Bfloat A.scheme -nonlinear > DiffTensorA.Bdouble OPTIONS
AUTHORSDaniel Alexander <camino@cs.ucl.ac.uk>SEE ALSOmodelfit(1), twotenfit(1), threetenfit(1), fa(1), trd(1), shfit(1), shanis(1)BUGS
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