Hi Anjali,
At least the second error message makes it clear that you should
not transpose the ideal file.
Regarding the first error:
1. Is that -input really the correct file name? It almost looks
like 2 names together. Maybe.
2. Try running dos2unix on the files. Maybe they have non-unix
characters in them. You can use file_tool to check that.
I see your AFNI version is 1.5 years old. Upgrading might be a
good idea.
- rick