FreeSurfer now supports import and export of NIfTI-1 volumes.  While many FreeSurfer programs will read and write NIfTI-1 volumes, the preferred usage is to convert data to .mgh/.mgz format once when importing data, working with .mgh/.mgz during analysis, and converting to NIfTI-1 when exporting data.   .mgh/.mgz volumes preserve information not present in NIfTI-1 volumes, and FreeSurfer does not currently support any NIfTI-1 extensions.

mri_convert may be used to convert between formats.  mri_convert will automatically determine the format of the input data and will determine the output format by the filename extension or by a command-line flag, if given.  Output volumes with the extension .img are written as ANALYZE volumes, so to write a two-file NIfTI-1 volume, it is necessary to explicitly specify the output format on the mri_convert command line.  Other FreeSurfer programs that support writing arbitrary formats only look at the output filename extension, so writing two-file NIfTI-1 volumes is only possible using mri_convert.

Running "mri_convert --help" will give usage information for mri_convert.

FreeSurfer will accept the following data types when voxel values are unscaled (scl_slope = 0):

• DT_UNSIGNED_CHAR
• DT_SIGNED_SHORT
• DT_SIGNED_INT
• DT_FLOAT
  

and represent the data internally in the type given.  For scaled data, FreeSurfer accepts:

• DT_UNSIGNED_CHAR
• DT_SIGNED_SHORT
• DT_SIGNED_INT
• DT_FLOAT
• DT_DOUBLE
• DT_INT8
• DT_UINT16
• DT_UINT32

and represents the data internally as floating point numbers.  FreeSurfer will always write volumes in the data type used internally and will never write scaled voxel values (so scl_slope = 0 always).

FreeSurfer only supports single-valued 3D volumes and 3D volumes with multiple time points.  Vector-valued datasets are unsupported and may be handled incorrectly.  Intent codes are ignored on read and intent_code is always set to NIFTI_INTENT_NONE on write.

NIfTI-1 extensions are unsupported; any extensions are ignored on read and none are written.

FreeSurfer volumes internally support a single voxel to world transformation.  This transformation is always written to both qform and sform.  When reading, the source of the orientation is checked as follows:

• if qform = 0, the origin is taken as the center of the volume, and orientation is taken as i: L -> R, j: P -> A, k: I -> S;
• if sform <= 0, qform is used,
• otherwise sform is used.
  

Non-trivial slice timing patterns are unsupported.

Two-file NIfTI-1 volumes are written uncompressed, and are expected to be uncompressed when reading.  Single-file volumes are similarly uncompressed when the extension .nii is used, and compressed when the extension .nii.gz is used.