If the stipends are given to you and you are not taxed on them, that means you are not paying for these expenses. In that case, no- you cannot deduct them.
Is there a notation in Box 12 of your W2- such as Code L? That means you weren't taxed, and the stipends were not included in your income. You couldn't deduct that portion of your expenses.
In some cases, the actual costs may be greater than the stipend. In that event, you may get a benefit from the additional costs. However, if your income is reasonably high, this benefit may be small. The higher your income, the less likely you will benefit from these expenses.
As an example, lets say the total allowable expenses are $20,000 and your nontaxed stipend was $17,000. Lets say your Adjusted Gross Income is $80,000.
Expenses you paid: $3000 ($20,000 less $17,000 stipend)
Non deductible portion: $1600 ($80,000 AGI * 2%)
Deduction: $1400 ($3000-$1600)
Possible savings: $350 ($1400 *. 25 tax rate)
Before you do anything, ensure that you were not taxed on the reimbursement. If you were not, think about whether your actual out-of-pocket was greater than the stipend.