Handle topup=reversed automatically

[maedoc]

using bash redirection may solve this one at least where there are only two runs to choose from:

~/vibrations mrinfo dti/ol-p03 <<EOF 2> choices.txt
q
EOF
~/vibrations head -n4 choices.txt | tail -n +3
   0 -  200 MR images 12:05:46 cmrr_mbep2d_diff_ap_b1800 (ep_b5#1) [6]
   1 -  200 MR images 12:17:25 cmrr_mbep2d_diff_pa_b1800 (ep_b5#1) [12]

Calling mrconvert with a choice is then

mrconvert dti/ol-p03 -o foo.nii <<EOF
0
EOF

[maedoc]

or for a general utility function consider

function mrchoose () {
    choice=$1
    shift # $2 becomes $1, $3 becomes $2 etc
    $@ <<EOF
$choice
EOF
}

and use like

mrchoose 0 mrconvert dti/ol-p03 -o dwi_1.nii
mrchoose 1 mrconvert dti/ol-p03 -o dwi_2.nii

[timpx]

I was looking in the direction of expect scripts, but this is nice as well, I will update

[maedoc]

Probably we can send a PR to mrtrix so that these aren't necessary. I would avoid expect unless you need extended interactivity with process. Here it works because there's a single block of stdin and then stdout.

[timpx]

I don't know if it very useful for MRtrix guys, because you want to know what is in you data before doing this, and this is done by doing mrinfo. Our case is very specific, what if the data are organized differently in the DICOM? That's why their script ask directly for dwi1.mif and dwi2.mif, and I think it makes sense

[maedoc]

ah I see then at least we have a workaround..

[timpx]

done