Not as far as I can tell. It would help a great deal if you copy/pasted exactly what you typed and the full output produced, so we can try to figure out what might have gone wrong…
foreach command is a convenience script provided with MRtrix3 to help with batch processing – see this page for details.
In this case, it uses a Unix pipeline to feed the output of the first command into the next. This is equivalent to running:
foreach * : dwiextract IN/dwi_denoised_unringed_preproc_unbiased_normalised_upsampled.mif IN/tmp.mif
foreach * : dwi2fod msmt_csd IN/tmp.mif ../group_average_response.txt IN/wmfod.mif -mask IN/dwi_mask_upsampled.mif
with the benefit that there is no need to store the temporary
The only odd things about this command are
the need to use an escape character before the pipe symbol (
|) to prevent the shell from interpreting it.
the use of the special
- character in place of the filename for what would have been the output of the first command and what would have been in the input of the second. More on that in the documentation.