All,
I have some DICOM files from a pet scan and an MRI. I viewed the files in three different ways:
1. Opened the DICOM's directly in a viewer (Pmod) 2. Used mri_convert to change the DICOMs to a .nii, and opened them. 3. Used dcm2nii to change the DICOMS to a .nii and opened them.
It's my intuition that the raw intensity values are displayed when I directly open the DICOM images. However, both step (2) and (3) give images with intensity values scaled--(2) scales by different factors depending on the modality, anywhere from 16 to 50; (3) scales by a fixed amount (two orders of magnitude, possibly understandable).
The images are indistinguishable when the levels are set properly, so this scaling would appear to be a flat linear multiplier. I'd like to know where it comes from--is there some information in the DICOM headers that mri_convert is using to scale things?
I checked the archives of this mailing list and found the tag -ns 1, but this didn't change the output file at all.
Any help is appreciated.
-- Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003
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 facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 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.
Can you send the terminal output from when you run mri_convert?
On 11/09/2016 11:24 AM, Funk, Quentin wrote:
All,
I have some DICOM files from a pet scan and an MRI. I viewed the files in three different ways:
- Opened the DICOM's directly in a viewer (Pmod)
- Used mri_convert to change the DICOMs to a .nii, and opened them.
- Used dcm2nii to change the DICOMS to a .nii and opened them.
It's my intuition that the raw intensity values are displayed when I directly open the DICOM images. However, both step (2) and (3) give images with intensity values scaled--(2) scales by different factors depending on the modality, anywhere from 16 to 50; (3) scales by a fixed amount (two orders of magnitude, possibly understandable).
The images are indistinguishable when the levels are set properly, so this scaling would appear to be a flat linear multiplier. I'd like to know where it comes from--is there some information in the DICOM headers that mri_convert is using to scale things?
I checked the archives of this mailing list and found the tag -ns 1, but this didn't change the output file at all.
Any help is appreciated.
-- Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003
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 <houstonmethodist.org>. Follow us at twitter.com/MethodistHosp <twitter.com/MethodistHosp> and facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 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.
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