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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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

orig.mgz is not converted to Talairach. The computed Talairach xfm is used internally by some stages of recon-all, but none of the volumes are ever converted to Talairach/MNI space.

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 8:50 AM, "Ed Gronenschild" ed.gronenschild@maastrichtuniversity.nl wrote:

Hi Harm,

Thanks for the trick. Will this, however, give not rise to conversion to Talairach coordinates?

Cheers, Ed

On 6 Feb 2014, at 15:38, Harms, Michael wrote:

...

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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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.

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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.