Hi Rene
You just need to provide a mask file after the -m option in the dtifit call. Currently you call -m -r ${BVEC} and the program tries to find a mask file named "-r”.
Cheers
Stam
> On 27 Apr 2016, at 18:34, René Labounek <[log in to unmask]> wrote:
>
> Dear fsl users,
> I have a problem with bvec file in dtifit library. Could somebody help, please?
>
> I have tried to normalize vectors directly at length 1 and not use 0.99999999999873. I have tried to change the 0 -0 -0 vectors at 1 0 0 because corresponding bval value is 0. But anything did not help.
>
> Here is the error output:
>
> labounek@PC-SE4158-455:~$ ./dtifit_script.sh
> terminate called after throwing an instance of 'Utilities::X_OptionError'
> what(): /media/labounek/Hologram/Data/Cspine/mod/755A/Diffusion/755A_03d_ep2d_diff_tra_4mm_ZOOMit_RL_63d_2sh_GN_DFC_MIX.bvec: is an unrecognised token!
> Aborted (core dumped)
> labounek@PC-SE4158-455:~$
>
> The dtifit command inside the script look like this:
> dtifit -k ${DTI_INPUT} -o ${DTI_OUTPUT} -m -r ${BVEC} -b ${BVAL} -V -w
>
> The data in the file 755A_03d_ep2d_diff_tra_4mm_ZOOMit_RL_63d_2sh_GN_DFC_MIX.bvec look like this (I has 3 rows and numbers in row are separated by ' '):
>
> 0 0 0.146104 0.972015 -0.193212 -0.908216 0.0235466 -0.841999 -0.578926 0.220549 0.497585 0.234838 -0.680732 0 -0.792105 -0.725572 0.363011 -0.601642 0.371998 -0.539266 0.0461296 -0.509688 0.706092 0.972851 -0.266904 0 -0.051835 0.509042 0.0523792 0.700121 -0.306541 0.857044 -0.233158 -0.572842 -0.658564 0.557754 0.408808 0 -0.0196473 0.916319 0.234007 0.978199 0.721136 -0.825578 -0.140947 0.368227 -0.54161 0.279889 0.130783 0 0.674262 -0.895038 -0.600493 -0.332925 0.758857 -0.776882 0.118499 -0.858488 0.200537 0.603717 -0.363813 0 0.941753 -0.781299 -0.253045 0.268844 0.221084 0.491597 0.188494 0.976168
> -0 -0 -0.249847 0.215077 0.942398 -0.414585 -0.491167 0.485878 0.180897 -0.847319 0.557969 0.841823 0.0895958 -0 0.0124785 0.569309 0.924828 -0.429027 -0.81877 -0.170074 -0.594278 -0.854041 -0.678829 -0.0723749 -0.168214 -0 0.388743 -0.477289 0.99532 0.536823 -0.163684 0.375264 0.875605 0.81907 -0.677885 0.683084 -0.617523 -0 -0.62346 -0.337383 0.845437 -0.083134 -0.29299 -0.0666818 0.225969 0.228696 0.0780748 -0.948632 -0.988875 -0 0.669327 0.427575 0.574044 -0.561271 -0.383024 -0.628559 -0.8181 -0.353495 -0.0766201 0.285964 -0.912849 -0 -0.191716 0.301885 0.681871 0.763775 0.474458 -0.798368 0.710486 0.183577
> -0 -0 0.957199 -0.0944968 0.273048 0.0571247 -0.870747 -0.234435 0.79506 0.483124 0.664138 -0.485989 -0.727033 -0 -0.610258 0.386564 0.113647 0.673768 0.437303 0.824783 -0.802935 -0.10408 -0.201558 -0.219825 -0.948929 -0 -0.919887 0.71629 -0.0812101 0.470799 0.937678 0.353062 0.423028 0.0312414 0.326749 -0.471495 -0.671968 -0 0.781608 0.215712 0.480081 0.190302 -0.62779 0.560334 0.963884 0.90117 -0.836997 0.147511 0.0708678 -0 0.312046 0.126832 -0.55667 0.757718 0.526715 0.036991 -0.562735 0.371536 -0.976685 0.744144 0.185328 -0 -0.276307 0.546294 -0.686309 0.586831 0.852063 -0.347767 -0.677997 0.115738
>
> Yours faithfuly,
> Rene Labounek
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