Dear all,
As I have to perform eddy correction on many files, I would really like to speed up this process. Does anyone know a script to automatically run Eddy (from fsl) on multiple files?
This is the script I would now have to run separately on every file ;
eddy --imain=data --mask=my_hifi_b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --out=eddy_corrected_data
Every file has its own brain_mask, bvals, and bvecs, and need to have an individual output file..
Els
Dear Eis Janson,
I suggest you to see links and attached file on subject.
https://mrtrix.readthedocs.io/en/3.0_rc3/dwi_preprocessing/dwipreproc.html
https://github.com/danjonpeterson/dti_preproc
http://www.bic.mni.mcgill.ca/~thayashi/dti.html
https://bookdown.org/u0243256/arc/fsl-eddy.html
http://www.hodaielab.org/wiki/index.php/DWI_motion_correction
Best regards
In the came up with this loop with the help of a colleague that worked perfectly!
Declare -a subj=(1027 1150 1166 1235 etc.) # make a list of the original filenames
for ((i=0;i
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