Hi,
In case anyone runs into the same issue this seems to be a solution (thanks
to John Harlap from the BIC at the MNI):
-The TIX error message occurs because the program can't find the
C:\cygwin\usr\local\fsl\bin\remove_ext file (which is quite right because
the remove_ext file it doesn't exist with my download of cygwin/fsl for some
reason).
-This file removes extensions (such as .nii.gz) from image filenames.
-Fslview saves the mask you create in it as .nii.gz
-It seems then that one solution is when inputting the seed mask file with
the probtrack GUI, simply manually remove/delete the ".nii.gz" extension
from the file's name - i.e. scroll to find your mask.nii.gz. file, choose
it, and then backspace out the nii.gz part.
-When I tried running probtrack on a mask created in fslview, the error
message still appeared because the remove_ext file still doesn't exits, but
having removed the mask's filename nii.gz extension in the probtrack GUI, I
could ignore the error message, press go, and the output was successfully
created as far as I could tell.
I am running FSL on a windows xp machine, in the cygwin version that is
recommended on the FSL website.
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