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When I heat set fabric markers, it said to run the iron over the marker as if you are ironing (back and forth motion) for four minutes at high (cotton) setting.
Good luck! That's very nice of you to do that. I'm sure she'll love it.
Everyone has given you great advice. Whatever you plan to use, I suggest you test it out on the fabric you plan to use. I recently purchased a set of colored Bic and Sharpie permanent marker pens. Each set had about 6 or 8 colors. I was planning to use them on fabric for my quilt labels. As I wrote on the test fabric, I found they bled into the fabric. That is not bad if you like the affect, just make sure it is what you want.
I agree that the micron pens are hard to write with. You might want to have your son try writing his name on fabric once you decide what you want to use. Hope it all goes well. It will mean so much to your son's teacher.
As a retired teacher myself, I can tell you your son's teacher will treasure that quilt forever.
I am sorry I have no idea on the markers to use, but what a wonderful, loving gift!
You can use a medium weight double sided fusible attaching the same color to the front and back of leaf shapes and have kids sign them (the pointy oval types work really well). Then stitch down the center from one point to the other. Another nice shape for leaves on something like this are hearts. Then your leaves will have dimension and you can then appliqué a really cool trunk of the tree. Perhaps even having additional leaves on the ground of other staff members or even the kids parents that may have helped in the classroom. (My parents are both retired teachers and I've made my share of retirement quilts.....I like pigma pens but sometimes they are hard for kids to write with and I end up using a sharpie.)