eddy_openmp not working

1

Hello everyone,

I have just recently started to work with FSL and I have been facing different errors everyday and learning one by one but I am stuck with this error for almost 4 days now. after doing topup and apply_topup to .dwi dataset. I am trying to run eddy_openmp so I gave the following code in my jupyter notebook

!eddy_openmp\
  --imain=/Users/Documents/Projects/dMRI/data/ds000221/sub-010006/ses-01/dwi/sub-010006_ses-01_dwi.nii.gz \
  --mask=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected/sub-010006/ses-01/dwi/sub-010006_ses-01_brainmask.nii.gz \
  --acqp=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup/sub-010006/ses-01/dwi/work/pedir.txt \
  --index=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup_eddy/sub-010006/ses-01/dwi/work/index.txt \
  --bvecs=/Users/Documents/Projects/dMRI/data/ds000221/sub-010006/ses-01/dwi/sub-010006_ses-01_dwi.bvec \
  --bvals=/Users/Documents/Projects/dMRI/data/ds000221/sub-010006/ses-01/dwi/sub-010006_ses-01_dwi.bval \
  --topup=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup/sub-010006/ses-01/dwi/work/topup \
  --out=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup_eddy/sub-010006/ses-01/dwi/dwi \
  --repol

but I got the error as follows
“zsh:1:command not found: eddy_openmp”

I checked with the FSL version but it looks like it has the latest version. Because I just downloaded it 5 days before and installed it. Then I tried using only eddy instead of eddy_openmp

!eddy\
  --imain=/Users/Documents/Projects/dMRI/data/ds000221/sub-010006/ses-01/dwi/sub-010006_ses-01_dwi.nii.gz \
  --mask=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected/sub-010006/ses-01/dwi/sub-010006_ses-01_brainmask.nii.gz \
  --acqp=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup/sub-010006/ses-01/dwi/work/pedir.txt \
  --index=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup_eddy/sub-010006/ses-01/dwi/work/index.txt \
  --bvecs=/Users/Documents/Projects/dMRI/data/ds000221/sub-010006/ses-01/dwi/sub-010006_ses-01_dwi.bvec \
  --bvals=/Users/Documents/Projects/dMRI/data/ds000221/sub-010006/ses-01/dwi/sub-010006_ses-01_dwi.bval \
  --topup=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup/sub-010006/ses-01/dwi/work/topup \
  --out=/Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup_eddy/sub-010006/ses-01/dwi/dwi \
  --repol

now the error is

EddyInputError:  Error when attempting to read --index file /Users/Documents/Projects/dMRI/data/ds000221/derivatives/uncorrected_topup_eddy/sub-010006/ses-01/dwi/work/index.txt
Terminating program

I am struck and really donno what to do.

can anyone help me on this?

Thank you

1 Like
2

Hello @Paddy ,
It seems like there’s some issue with index.txt. Please make sure to use the equal number of 1 values in index.txt as your dwi volumes.

Suren

3

I think it is more appropriate to direct this question to the FSL mailing list at JISCMail - FSL List at WWW.JISCMAIL.AC.UK