Dear Nicole,
> 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 these numbers are all correct, it is quite easy. You have 105 volumes, but 104 ones in your index file.
Jesper
> If anyone has any advice as to what I've done wrong, that would be great. Thank you!
>
> Nicole
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