Jenessa,
Try the following steps:
1. In the $SUBJECTS_DIR create separate folders for each subject 2. in each subject's folder create a folders mri and mri/orig (e.g. mkdir -p $SUBJECTS_DIR/SUBJECT-NAME/mri/orig) 3. Convert data from nii (or nii.gz) to mgz and place it in the $SUBJECTS_DIR/SUBJECT-NAME/mri/orig folder:
$FREESURFER_HOME/bin/mri_convert /PATH/TO/YOUR-IMAGE.nii $SUBJECTS_DIR/SUBJECT-NAME/mri/orig/001.mgz
If mri_convert is having trouble converting try more elaborate version of the same syntax:
$FREESURFER_HOME/bin/mri_convert --in_type nii --out_type mgz --input_volume /PATH/TO/YOUR-IMAGE.nii --output_volume $SUBJECTS_DIR/SUBJECT-NAME/mri/orig/001.mgz
Cheers,
Jacek
-- Jacek Jonca-Jasinski
^..^<
Jacek Jonca-Jasinski Texas Tech University