Under the MTR section, the spinal cord segmentation for MT1 data says that the MT1 image is the image that has RF off-resonance pulse applied. Then a few steps later under the
“Computing MTR using co-registration MT0 and MT1 data” it says that mt0 is the image without the magnetization transfer pulse and mt1 the image with the magnetization transfer pulse, except for the first deepseg command where off pulse = mt1.
I think I must be misinterpreting the above so I was wondering if you could please clarify so I can name my files appropriately: is the following true for all commands: mt1 = on, mt0 = off. Thanks for your time!
is the following true for all commands: mt1 = on, mt0 = off.
yes, mt1 means that the off-resonance pulse is on. Could you please point us to the exact location where the documentation is wrong/confusing so we can update it? Thank you
Here are some links with the relevant quotes that @Lily has mentioned:
- MTR section of the tutorials
- First quote: “Before starting this tutorial”
Make sure that you have the following files in your working directory:
- single_subject/data/mt/mt0.nii.gz: The image without the magnetization transfer pulse.
- single_subject/data/mt/mt1.nii.gz: The image with the magnetization transfer pulse.
- Second quote: “Spinal cord segmentation”:
First, we will run the
sct_deepseg_sc command to segment the spinal cord from the MT1 image (i.e. the image that has the RF off-resonance pulse applied).
- Third quote: “Coregistering MT0 with MT1”
(Here, “MT0” refers to the image without the magnetization transfer pulse, and “MT1” refers to the image with the pulse.)
- Fourth quote: “Computing MTR using coregistered MT data”
- -mt0 : The input image without the magnetization transfer pulse.
- -mt1 : The input image with the magnetization transfer pulse.
I think that all of these quotes are consistent? (MT1 = on, MT0 = off)
My guess is that the confusion may stem from the name “off-resonance” (“off is on” is kind of confusing):
The second page is the only place where we use the term “RF off-resonance pulse” – all other pages use “magnetization transfer pulse” instead. So, it might be clearer to standardize on “magnetization transfer pulse” to avoid confusion.
Thank you very much, that was helpful and answered my question!