Doug, Can you verify? The dicom and mri_covnert .nii are identical (integer values, as per dicom convention) when we inspect the matrix in MATLAB.
The img matrices for mri_convert and dcm2nii are also identical, the difference appears to be that dcm2nii retains the slope scale in the header, allowing the viewer (freeview, pmod, etc..) to apply it. We have been trying to nail down this issue for the last couple days, any insight would be appreciated. Eli On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve > <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert > slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID: > <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed I think we > actually apply the scaling, so including it in the output would be > inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote: >> >Hello, >> > >> >We have been using mri_convert to convert our dicoms into .nii niftis. >> >There is an entry in the .nii header for the slope scale, but >> >mri_convert appears to discard this value instead of copying it into the >> >header (whereas mricron retains this value) We prefer to use mri_convert. >> > >> >Is there a way to have mri_convert carry this value over? Why is it >> >being discarded? >> > >> >Thanks, >> >Eli >> > -- Elijah Rockers Research Data Analyst Houston Methodist Research Institute O: 713-363-7729 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. _______________________________________________ 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.
