Prepare T1 files

FSL does not read all nifti files properly, so we convert them. There was some issue with reading rotations/shears, so these are removed with reslicing. Additionally, testing on 0.65 x 0.65 x 0.0.65 mm voxel size files also needed a conversion to int16 from float 32 data format.

Create a folder for running the analysis

Create a folder in Linux for running the analysis. If using a VM, place the folder under LinuxShare. Note that FIRST expects all files to be in the same folder, so the T1's and segmentations for all subjects will be in one location. This can make for thousands of files in that folder, but that is normal.

Browser not supported