Skip to content

Support ushort for the mgh/mgz reader #1415

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
May 16, 2025
Merged

Support ushort for the mgh/mgz reader #1415

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d085556
adds ushort to the mgz reader
bthyreau May 14, 2025
dd17469
Update nibabel/freesurfer/mghformat.py
bthyreau May 15, 2025
e03cacc
add a comment regarding datatype support
bthyreau May 16, 2025
643f7a1
TEST: mgz should fail on f64, no more fail on u16
bthyreau May 16, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 6 additions & 1 deletion nibabel/freesurfer/mghformat.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,11 +57,16 @@

# caveat: Note that it's ambiguous to get the code given the bytespervoxel
# caveat 2: Note that the bytespervox you get is in str ( not an int)
# FreeSurfer historically defines codes 0-10 [1], but only a subset is well supported.
# Here we use FreeSurfer's MATLAB loader [2] as an indication of current support.
# [1] https://github.com/freesurfer/freesurfer/blob/v8.0.0/include/mri.h#L53-L63
# [2] https://github.com/freesurfer/freesurfer/blob/v8.0.0/matlab/load_mgh.m#L195-L207
_dtdefs = ( # code, conversion function, dtype, bytes per voxel
(0, 'uint8', '>u1', '1', 'MRI_UCHAR', np.uint8, np.dtype('u1'), np.dtype('>u1')),
(4, 'int16', '>i2', '2', 'MRI_SHORT', np.int16, np.dtype('i2'), np.dtype('>i2')),
(1, 'int32', '>i4', '4', 'MRI_INT', np.int32, np.dtype('i4'), np.dtype('>i4')),
(3, 'float', '>f4', '4', 'MRI_FLOAT', np.float32, np.dtype('f4'), np.dtype('>f4')),
(4, 'int16', '>i2', '2', 'MRI_SHORT', np.int16, np.dtype('i2'), np.dtype('>i2')),
(10, 'uint16', '>u2', '2', 'MRI_USHRT', np.uint16, np.dtype('u2'), np.dtype('>u2')),
)

# make full code alias bank, including dtype column
Expand Down
4 changes: 2 additions & 2 deletions nibabel/freesurfer/tests/test_mghformat.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -172,11 +172,11 @@ def test_set_zooms():

def bad_dtype_mgh():
"""This function raises an MGHError exception because
uint16 is not a valid MGH datatype.
float64 is not a valid MGH datatype.
"""
# try to write an unsigned short and make sure it
# raises MGHError
v = np.ones((7, 13, 3, 22), np.uint16)
v = np.ones((7, 13, 3, 22), np.float64)
# form a MGHImage object using data
# and the default affine matrix (Note the "None")
MGHImage(v, None)
Expand Down
Loading