The ASLprep documentation mentions, “…the M0 scans in your dataset should preferably be scaled before running ASLPrep."
I’ve checked the NIfTI headers for both my M0 and ASL images, and both have:
scl_slope = 1
scl_inter = 0
I interpret this to mean the images are not scaled — is that correct? I’m trying to figure out if I need to add the --m0_scale option when running ASLprep.
Since both the M0 and ASL images have these same header values, I’m unsure if this means they’re already appropriately scaled. Any clarification would be appreciated!
The data in the NIfTI would be multiplied by scl_slope. Since scl_slope is 1, the data are not being scaled based on that field. However, the actual data arrays in the NIfTIs could be modified by whoever curated the dataset.
If you are the one who curated the data (i.e., did DICOM-to-NIfTI conversion and BIDSified the dataset) then you have control over whether the data have been scaled. However, if you’re working with pre-curated data, then I think you need to check the dataset documentation or ask the original curator whether the M0 scans were scaled appropriately.
I asked if ASL and M0 had some scaling, I got the answer below:
“There was no scaling difference in the HCP-ASL. All the images were acquired in the same series and should have been converted together and thus not resulting in differences in scl_slope.”
Therefore, my question is, should I or should I not use flag --m0_scale?
Documentation says:
“Relative scale between ASL and M0. M0 scans are multiplied by m0_scale before calculating CBF. It is important to note, however, that BIDS expects ASL and M0 data to scaled in the raw dataset, so this parameter should only be used if your dataset does not have pre-scaled data.”
I tried running it with that flag and got this error message: aslprep: error: argument --m0_scale: expected one argument
But I have no idea what type of number should I use here if the data is not scaled.