Hi Ed, If you want to avoid the rotation (e.g., to avoid an interpolation at the conform step) then you need to manually alter the input so as to remove the off-diagonal elements. That is in fact what we do as part of our DICOM2NIFTI conversion in the HCP.
cheers, -MH
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
On 2/6/14 7:43 AM, "Ed Gronenschild" ed.gronenschild@maastrichtuniversity.nl wrote:
Hi Bruce,
Yes, I do understand that is coronal, but there is an actual rotation apart from an orientation to coronal. You can read it from the off-diagonal matrix elements.
Cheers, Ed
On 6 Feb 2014, at 14:36, Bruce Fischl wrote:
yes, we reorient it to be coronal as part of the "conform" process
cheers Bruce On Thu, 6 Feb 2014, Ed Gronenschild wrote:
Hi,
Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation of the T1 data early in the pipeline, i.e., converting rawavg.mgz to orig.mgz., see excerpt of output of mri_info below
rawavg.mgz:
xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = 14.8386 : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = 13.1335
orig.mgz:
xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 0.0813 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 14.8386 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 13.1335
Is that the default way of processing the data?
Cheers, Ed
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