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 -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
