as reviewers are also possibly working on it, I took a general look at the code and have the following point-outs for now:

• on line

  hMRI-toolbox/hmri_create_MTProt.m

  Line 1837 in cd72fc8

  mpm_params.output(coutput).descrip{end+1} = '- ESTATICS model (R2* map calculation)';

  
  I think we should have "Milotta" (please see the second minor point below) instead of "ESTATICS " if the linear is chosen instead of none as fit method
• I believe there is a typo in author's name (Melotti --> Milotta)
  

  hMRI-toolbox/examples/hmri_local_defaults_linear_fa_dependent_R2star.m

  Line 48 in cd72fc8

  % - 'linear': method from Melotti, et al. (MRM 2023). Note that this model

I don't know if it is being reviewed; I didn't hear from Martina or Giorgia.

Please feel free to fix the typo in Giorgia's name; sorry about that.

While you're right that the image description saying just "ESTATICS" could be misleading, I don't think using "Milotta" as a label would be best as a replacement, as it isn't very descriptive. How about something like "ESTATICS with linear flip angle modelling"?

Perhaps you can send them a reminder then.

no problem I will fix it.

an even better and more descriptive one is pehaps ""ESTATICS (Weiskopf et al. 2014) with linear flip angle modelling (Milotta et al. 2023)" but then please feel free to choose the one you like. as far as I looked into mtprot code now, any change will require adding and reading off the field famethod within the mtprot to set up the proper conditional on this line

in order to write the correct message depending on the fit method

I don't know if it is being reviewed; I didn't hear from Martina or Giorgia.

Please feel free to fix the typo in Giorgia's name; sorry about that.

While you're right that the image description saying just "ESTATICS" could be misleading, I don't think using "Milotta" as a label would be best as a replacement, as it isn't very descriptive. How about something like "ESTATICS with linear flip angle modelling"?

aah the field is already there, disregard my comment below : mpm_params.R2s_fit_method

Perhaps you can send them a reminder then.

no problem I will fix it.

an even better and more descriptive one is pehaps ""ESTATICS (Weiskopf et al. 2014) with linear flip angle modelling (Milotta et al. 2023)" but then please feel free to choose the one you like. as far as I looked into mtprot code now, any change will require adding and reading off the field famethod within the mtprot to set up the proper conditional on this line

hMRI-toolbox/hmri_create_MTProt.m

Line 1837 in cd72fc8

mpm_params.output(coutput).descrip{end+1} = '- ESTATICS model (R2* map calculation)';

in order to write the correct message depending on the fit method

I don't know if it is being reviewed; I didn't hear from Martina or Giorgia.
Please feel free to fix the typo in Giorgia's name; sorry about that.
While you're right that the image description saying just "ESTATICS" could be misleading, I don't think using "Milotta" as a label would be best as a replacement, as it isn't very descriptive. How about something like "ESTATICS with linear flip angle modelling"?

I think this is a bug, you are feeding mpm_params.R2s_fit_method in place of the argument famethod on this line

but value of mpm_params.R2s_fit_method is really OLS but famethod can only accept none or linear.

aah the field is already there, disregard my comment below : mpm_params.R2s_fit_method

Perhaps you can send them a reminder then.
no problem I will fix it.
an even better and more descriptive one is pehaps ""ESTATICS (Weiskopf et al. 2014) with linear flip angle modelling (Milotta et al. 2023)" but then please feel free to choose the one you like. as far as I looked into mtprot code now, any change will require adding and reading off the field famethod within the mtprot to set up the proper conditional on this line

hMRI-toolbox/hmri_create_MTProt.m

Line 1837 in cd72fc8

mpm_params.output(coutput).descrip{end+1} = '- ESTATICS model (R2* map calculation)';

in order to write the correct message depending on the fit method

I don't know if it is being reviewed; I didn't hear from Martina or Giorgia.
Please feel free to fix the typo in Giorgia's name; sorry about that.
While you're right that the image description saying just "ESTATICS" could be misleading, I don't think using "Milotta" as a label would be best as a replacement, as it isn't very descriptive. How about something like "ESTATICS with linear flip angle modelling"?

I think my confusion was due to calling of the function with fitmethod versus famethod as last argument, the below point is probably fine, it is not a bug, I will look closer.

I think this is a bug, you are feeding mpm_params.R2s_fit_method in place of the argument famethod on this line

hMRI-toolbox/hmri_create_MTProt.m

Line 185 in ca7eec8

R2s = hmri_calc_R2s(struct('data',data,'TE',TE_pdw),mpm_params.R2s_fit_method);

but value of mpm_params.R2s_fit_method is really OLS but famethod can only accept none or linear.

aah the field is already there, disregard my comment below : mpm_params.R2s_fit_method

Perhaps you can send them a reminder then.
no problem I will fix it.
an even better and more descriptive one is pehaps ""ESTATICS (Weiskopf et al. 2014) with linear flip angle modelling (Milotta et al. 2023)" but then please feel free to choose the one you like. as far as I looked into mtprot code now, any change will require adding and reading off the field famethod within the mtprot to set up the proper conditional on this line

hMRI-toolbox/hmri_create_MTProt.m

Line 1837 in cd72fc8

mpm_params.output(coutput).descrip{end+1} = '- ESTATICS model (R2* map calculation)';

in order to write the correct message depending on the fit method

I don't know if it is being reviewed; I didn't hear from Martina or Giorgia.
Please feel free to fix the typo in Giorgia's name; sorry about that.
While you're right that the image description saying just "ESTATICS" could be misleading, I don't think using "Milotta" as a label would be best as a replacement, as it isn't very descriptive. How about something like "ESTATICS with linear flip angle modelling"?

@lukeje as I was reviewing your last commit, it caught my eye that the only piece of code that fDeltaR2s substantially appears outside of the OLS code:

is this code block:

if ~isempty(fDeltaR2s)
fDeltaR2s_final = fullfile(respath, spm_file(fDeltaR2s,'filename'));
copyfile(fDeltaR2s,fDeltaR2s_final);
try copyfile([spm_str_manip(fDeltaR2s,'r') '.json'],[spm_str_manip(fDeltaR2s_final,'r') '.json']); end
fDeltaR2s = fDeltaR2s_final;
end

@line1134.

Would it make sense to remove the ~isempty(fDeltaR2s) and move it to the end of the conditional of the ols code finishing at:

because the above code block executes whenever fDeltaR2s is not empty but this is in turn only possible if the ols code block is executed (R2s_ols is True), otherwise it is set to empty anyways as you also commented out here:

so I thought it might make sense to move it into the ols code without the conditional in order to keep the related code together.

That last code block is copying the files from MPMcalc to the Results and Supplementary directories. If you check the code, you can see that this happens at the end of the script for all of the maps. I think it's a good idea to keep all of this copying together rather than doing some of it earlier and some of it later.

Edit: I also just remembered that fDeltaR2s is a returned value, so it always needs to be defined.