Hi Antonella,
- I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the
structural data in this case called C01?
Given that you are preparing your fa data for the analysis, indicated below, you will need to use the dti directories, eg.: C01_dti.
- When I concatenate fa from individuals into one file using: mri_concat */fa-tal.nii --o group-fa-tal.nii
how I can check if the order agrees with my fsgd?
You can list the files using "ls -l */fa-tal.nii" and the order that you see is the order in which they get concatenated in your output file. You need to make sure that that order agrees with the contents of your fsgd file.
- When I concatenate fa from individuals into one file do I need to move all the fa-tal.nii into one directory or I can have each of the fa-tal files under different subject's directory?
Aas example: C01_dti will contain the corresponding fa-tal.nii for the control 1, C02_dti will contain his corresponding fa-tal.nii, etc and all the subjects C01_dti, C02_dti,...P01_dti, P02_dti... are located into one directory called dtrecon.
You can have them under different subdirectories, but then your mri_concat command needs to reflect that, for example, mri_concat */dtrecon/fa-tal.nii --o group-fa-tal.nii
--Lilla