Failure to load freesurfer MRI data

Discussions
2

There are maybe issues in the ways links are being handled here.
FreeSurfer 7.x creates links between certain files, typically lh.pial is not a real file, but a symbolic link to lh.pial.T1.
Because symbolic links are not handled in all the programs or OS in the same way, there are sometimes conversions that are done, e.g. when copying the FreeSurfer subject folder to a Windows computer, or when zipping and unzipping.

Different states can result from these successive symbolic link conversions:

  • the full copy of all the links as hard files => a new file lh.pial is created with the same contents as lh.pial.T1 - This causes an increase of storage size of the folder, but guarantees its readability from all the programs
  • the link lh.pial can be replaced with a text file containing the path to the target file lh.pial.T1 => the link somewhat exists but is not usable in most applications
  • the link lh.pial can be replaced with an empty file => the link is broken.

Or it could be a problem that occurs during the transfer of the folder, if not all the files where copied correctly.

This problem was already reported here: