Unix and Matlab MAJOR issue?

I am pulling my hair out over this problem.

I have just learned the unix shell scripting langs. I use bourne. I have spent weeks designing a program and refining it that converts a certain kind of file to a different kind of file via the rearranging of colums through matlab. the one problem i face is that i call upon unix to "ls" crd files and put them into a text file. Matlab reads this text file and stores the names of the CRD's as variables and works on them.

The one issue i face is that it wont work with subdirectories. matlab can only work with files in it's immediate directory. the logical resolution is to CD matlab. But, I need to let Matlab know where to CD to, while at the same time, my unix script knows that Matlab is changing directories, so unix can act appropriately. I cannot get past this. can anyone offer help?

Thanks, This is a lifesaver...

Unix and Matlab MAJOR issue?

Well, I'm an expert with shell scripts, but I know very little about Matlab. If you can provide a little more information about your shell script, I suspect lots of folks could answer your question. Maybe you could post the portion of the code that has to do with listing the current directory to pass on to Matlab?