Dear FS experts,
1) From dt_recon --help I found that:
Registration of lowb to same-subject anatomical using FSLs flirt creates mask.nii and register.dat
I would appreciate if you can let me know if mask.nii is theresampled image of any of my diffusion related files in the structural space. If not what is the name of this resampled image after I ran dt_recon? Do I need to have the resampled image of my diffusion data to the structural space before I run the GLM group analysis in TAL space?
2) How can I get the TAL_to_avg35 template?
3) How can I analyze my GLM group analysis, or how can I find if there are clusters that survived after multiple comparison. What I see on the dt_recon webpage is: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii
mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir groupanadir
What is the meaning of the 0.99n value? Can you please advise me how to do my data analysis for this GLM group study of my DTI data?
THANK YOU!
Antonella