I'm increasingly convinced that a good strategy is to do file management-type things in the script, build the needed (FSL, afni, etc.) command, then send the command directly to the target program (FLS, afni, etc.), rather than use a specialized interface package. There are at least two big advantages to building the actual commands: first, few (if any) dependencies or new syntax are introduced, second, the executed commands are immediately and transparently recoverable. Note that this advice is for analysis scripts, not full-scale pipelines or software.
For example, I needed to run FSL flirt to register around twenty images. This is the only step requiring FSL, and my script is in R. I have a few options, including the FLIRT GUI, generating a text file of the flirt commands and running it at the command line, typing the commands directly at the command line, or running fsl from within R using wrapper functions (e.g., fslr).
This code shows the solution I'm advocating: using R functions for the file-wrangling and command-building parts, and then using system2 to "send" the command to fsl for running. This strategy can be used not only with fsl, but also afni, wb_command, and other command-line programs.
fsl.path <- "/usr/local/pkg/fsl6.0/bin/"; # path to fsl flirt
in.path <- "/data/"; # path to the input images
ref.path <- "/data/"; # path to the reference images
out.path <- "/scratch3/registrations/"; # where to write files
sub.ids <- c(102008, 107321, 814649, 849971); # subject IDs
for (sid in 1:length(sub.ids)) { # sid <- 1;
# make the file names
fname.in <- paste0(in.path, sub.ids[sid], "/T1w/T1w_acpc_dc_restore.nii.gz");
fname.ref <- paste0(ref.path, sub.ids[sid], "/T1w/T1w_acpc_dc_restore.nii.gz");
fname.out <- paste0(out.path, sub.ids[sid], "_T1w.nii.gz");
fname.mat <- paste0(out.path, sub.ids[sid], "_T1w.txt");
# check if the input files exist (and output files do not), then run fsl if so
if (file.exists(fname.in) & file.exists(fname.ref) & !file.exists(fname.out) & !file.exists(fname.mat)) {
system2(paste0(fsl.path, "flirt"), args=paste("-in", fname.in, "-ref", fname.ref, "-out", fname.out, "-omat", fname.mat, "-dof 6"),
stdout=TRUE, env="FSLOUTPUTTYPE=NIFTI_GZ");
}
}
The system2 function "sends" the command to fsl and can be used to check what was done:
- paste0(fsl.path, "flirt") shows which program was run and its location on disk.
- args= has the options sent to the flirt program, as a string. Copying out just the paste(...) part and running it in R will print it for inspection (example below).
- stdout=TRUE tells R to print fsl's messages as it runs (useful to spot any errors)
- env="FSLOUTPUTTYPE=NIFTI_GZ" sets the fsl environment variable FSLOUTPUTTYPE to NIFTI_GZ. Depending on your system and fsl installation you may need to set more (or no) environment variables.
/usr/local/pkg/fsl6.0/bin/flirt -in /data/102008/T1w/T1w_acpc_dc_restore.nii.gz -ref /data/102008/T1w/T1w_acpc_dc_restore.nii.gz -out /scratch3/registrations/102008_T1w.nii.gz -omat /scratch3/registrations/102008_T1w.txt -dof 6
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