Hi Alfonso,

Thank you very much for the meaningful advices before and your excellent work on updating the toolbox and its manual.

I've trying to use the toolbox for some time. I did some tests to see whether I could manage it properly, I used ADNI data to run some ROI-to-ROI resting state functional connectivity analysis with 90 AAL atlas, DMN, Salience and memory networks to see the group difference between HC and AD. I don't think I got results that make sense, either it was hard to get any significant result or the significant connections were much more in AD patients than in healthy controls.

So, I am wondering if I could trouble you to have a look at the .mat file I attached to check if I did something wrong for setting up the toolbox. The data were already preprocessed without the toolbox: corrected for head motion dependent image distortions, normalised to MNI space,  smoothed with 5mm FWHM, detrended, filtered(0.08-0.01) and removed white matter, CSF and head motion covariates (without removing global signal).

In addition, I would like to run the regression like this: Performance~functional connectivity+age+gender, here FC is the predictor. Do I properly define the contrasts as follows:
1) to compare between the two groups (HC and AD) the association between FC and performance, select the covariates of performance_HC(values for HC, 0s for AD), performance_AD(values for AD, 0s for HC), HC, AD, age, gender and define the contrast of [0 0 1 -1 0 0].
2) to compare the association between FC and performance within one group(e.g. HC group), but control for age and gender, select the covariates of performance_HC, HC, age_HC, gender_HC (using 0 and 1 to stand for male and female, values for HC and 0s for AD) and define the contrast of [0 1 0 0]. Is there a mistake to define the covariate of gender_HC because both male and AD subjects are defined by 0?

Thank you in advance for any suggestion!

Best regards,
Yifei