I am writing regarding the post of Prof Paul Mullins on his blog.
I understand the need of taking into account tissue composition within the voxel. Indeed, LCModel has such an option of corrections both water concentration (wconc) and T2 relaxation (atth2o). Comparing the equations provided in LCModel’s manual with eg. J. Near et al. 2020, one can spot that S. Provencher does not consider tissue specific relaxation rates. I’ve got 2 questions then:
Does the correction for the tissue adjusted water concentration combined with the updated t2 water attenuation factor is the state-of-the-art (LCModel)? Or should the results be taken out to be corrected for all the possible relaxation/concentration terms?
Is it possible to include all the tissue specific corrections within LCModel pipeline? It seems to be more convenient to first run a segmentation and then quantify the spectra accordingly to the derived parameters.
Looking forward to Your comments and clarification
Bartosz Kossowski
LCModel has no direct way of incorporating results from segmentation, so the WCONC and ATTH2O parameters are always understood as average. My recommendation would always be to set these values (and ATTMET) to 1, and do the tissue-specific quantification outside of LCModel. But someone else might have found a way to, for example, pass on appropriate WCONC, ATTH2O and ATTMET through the control file. It just feels to me it would make life unnecessarily hard, and only for the sake of insisting that LCModel computes an exponential correction factor that you can much faster apply yourself.
Does that help? Let me know if you have further questions.
The problem with the options for LCModel (and the same is true for Tarquin) is that it assumes a homogeneous voxel of one tissue. Once you have different tissue components in the voxel then it is not possible to write the signal as the linear product of concentration and attenuation. My preference is to calculate the combined scaling factor as described in Near et al. 2020 and then pass it in as one of the two parameters (WCONC OR ATTH2O), setting the other to 1. This means that the results returned from LCModel will be in mM which is convenient (e.g. if you just want to share the output pdf etc.). This of course does not work if you wish to use metabolite specific T2 values in which case you have to make the corrections after the LCModel step as Georg suggests. However if applying a global value I find it easier to calculate it first and supply it to the quantification program.
Suspect has a function in its fitting module which will calculate the molar scaling factor you need to supply. It uses the form from the Near paper along with tissue parameters from Gussew 2012, although these can be selectively overridden if desired. If calling Tarquin from Suspect you can pass this parameter directly as aq_factor and it will set the WCONC and ATTH2O params for you, but this is not yet implemented for the LCModel integration.
Thanks, it’s great to see that it’s possible to feed the correction parameters directly into Tarquin.