As far as I can tell, mri_convert doesn't apply the scaling factor, and also doesn't copy over the slope scale header entry, when converting from dicom to nifti.
By contrast, dcm2nii does not apply the scale either, however, it copies over the slope scale header entry, enabling other software (eg Freeview..) to apply the scaling..
Hope this clarifies. Thanks for checking into this.
On 11/10/2016 12:18 PM, Douglas N Greve wrote:
Sorry, is it a scale in the dicom file or the nifti file that is not being applied properly?
On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
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-request@nmr.mgh.harvard.edu wrote:
Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID: 908818ac-156f-f6d2-1338-694626cde58f@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