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., 2., 2.
> 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., y_r = 0., z_r = 0., c_r
> =-1.
> : x_a = 0., y_a = 1., z_a = 0., c_a
> = -17.
> : x_s = 0., y_s = 0., z_s = 1., c_s
> =18.
> Orientation : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2. 0. 0.78.
> 0. 2. 0. -112.
> 0. 0. 2. -50.
> 0. 0. 0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>-0.5000 0. 0.39.
>-0. 0.5000 -0.56.
>-0. -0. 0.500025.
> 0. 0. 0. 1.
>
> $ mri_info con_0001.hdr
> Volume information for con_0001.hdr
> type: nifti1
> dimensions: 79 x 95 x 68
>voxel sizes: 2., 2., 2.
> 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., y_r = 0., z_r = 0., c_r
> =-1.
> : x_a = 0., y_a = 1., z_a = 0., c_a
> = -17.
> : x_s = 0., y_s = 0., z_s = 1., c_s
> =18.
> Orientation : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2. 0. 0.78.
> 0. 2. 0. -112.
> 0. 0. 2. -50.
> 0. 0. 0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>-0.5000 0. 0.39.
>-0. 0.5000 -0.56.
>-0. -0. 0.500025.
> 0. 0. 0. 1.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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