If it happens with one, it will happen with all of them. We never got around to having our code look in the .img header to see if it is really nifti. Why not use the single-file nifti with nii extension? doug

Satrajit Ghosh wrote:

hi all,

when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type be detected from the header?

also it would be good to know if this behavior is consistent across all of freesurfer or restricted to certain binaries.

see below for mri_info output

cheers,

satra

$ mri_info con_0001.img Volume information for con_0001.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial

voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -8

ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000

$ mri_info con_0001.hdr Volume information for con_0001.hdr type: nifti1 dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial

voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -8

ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000

---

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer