Hi all,
This is my first time using the EDDY command and I am finding the following error.
Could not open matrix file index
eddy: msg=--index must be an 1xN or Nx1 matrix where N is the number of volumes in --imain
terminate called after throwing an instance of 'EDDY::EddyException'
what(): eddy: msg=--index must be an 1xN or Nx1 matrix where N is the number of volumes in --imain
./preprocessDTI.bash: line 7: 11805 Aborted (core dumped) fsl5.0-eddy --imain=${subj}_diffusion --mask=${subj}_unwarped_brain_mask --acqp=bubd_parameters --index=index --bvecs=~/Desktop/DRC/preprocess/${subj}/bvecs --bvals=~/Desktop/DRC/preprocess/${subj}/bvals --topup=${subj}_topup_results --out=${subj}_eddycorrected
I thought I had my "index" text file set up correctly, it is currently a .txt file with 104*1 separated by spaces. Here's the output of fslinfo for the image in case that's helpful to know.
data_type INT16
dim1 104
dim2 104
dim3 72
dim4 105
datatype 4
pixdim1 2.019231
pixdim2 2.019231
pixdim3 2.000000
pixdim4 3.600000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
If anyone has any advice as to what I've done wrong, that would be great. Thank you!
Nicole
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