That worked! I've been looking at this error for many hours, so thank you
so much for your time. Also, sorry that it was such a basic mistake.
Thanks,
Nicole
On Tue, Nov 15, 2016 at 11:54 PM, Jesper Andersson <
[log in to unmask]> wrote:
> Hi again,
>
>
> indx=""
> for ((i=1; i<=105; i+=1)); do indx="$indx 1"; done
> echo $indx > index.txt
>
>
> yes, that looks about right. But looking again at your eddy command it
> looks like you have --index=index, but that your index file is in fact
> called ‘index.txt'. It looks like eddy is looking for ‘index’, but cannot
> find it.
>
> Jesper
>
>
> As far as I can tell it is creating the file in the right place and seems
> to have 105 ones in it. Any other ideas?
>
> Thanks again,
>
> Nicole
>
>
> On Tue, Nov 15, 2016 at 11:30 PM, Jesper Andersson <
> [log in to unmask]> wrote:
>
>> Dear Nicole,
>>
>> > Could not open matrix file index
>> > eddy: msg=--index must be an 1xN or Nx1 matrix where N is the number of
>> volumes in --imain
>> > terminate called after throwing an instance of 'EDDY::EddyException'
>> > what(): eddy: msg=--index must be an 1xN or Nx1 matrix where N is the
>> number of volumes in --imain
>> > ./preprocessDTI.bash: line 7: 11805 Aborted (core
>> dumped) fsl5.0-eddy --imain=${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
>>
>
>
>
