When I received the download for Infant FreeSurfer, it included not only the packages specific to Infant FreeSurfer, but the entire FreeSurfer download as well. I already had FreeSurfer downloaded on the computer, but to make things easier, I decided to remove the FreeSurfer version I had installed on my computer, and use the version that came with Infant FreeSurfer. This was a mistake.

From what I can tell, the version of FreeSurfer that came with the download of Infant FreeSurfer was a “daily build.” The FreeSurfer website allows you to download either “stable builds” or “daily builds.” The stable builds generally work without error, while the daily builds may have some errors that have not been resolved. This was exactly the case with the version of FreeSurfer that came included in the Infant FreeSurfer download.

The first error I noticed was a problem with mri_tessellate. This problem was mentioned in the FreeSurfer Help Forums, and was easily solved by replacing the mri_tessellate script with the one from a newer daily build of FreeSurfer.

My next problem was with Freeview. For some reason, Freeivew would not open normally. The errors that I got had to do with the qt libraries in FreeSurfer. No one else on the forums seemed to be experiencing these errors, so I had assumed it was a problem with my computer. I tried using the qt libraries from a newer daily build of FreeSurfer and from the stable build of FreeSurfer, and neither worked. I had nearly given up on using Freeview, when I decided to try installing the stable version of FreeSurfer (without Infant FreeSurfer) on the same computer, and trying to open Freeview from there. To my surprise, Freeview opened just fine on the same computer when I used the stable FreeSurfer version.

At this point, I decided to merge the Infant FreeSurfer download with the stable version of FreeSurfer. I copied over everything from the Infant FreeSurfer folder that did not exist in the stable FreeSurfer folder. Now, Infant FreeSurfer works just fine, and I have no errors from FreeSurfer.

I highly recommend that if you download Infant FreeSurfer, you copy the new files into a stable version of FreeSurfer, rather than using the daily build of FreeSurfer that comes as part of the Infant FreeSurfer download. It will hopefully save you a lot of headache and let you jump right into your analyses in Infant FreeSurfer.