Hi, experts,

 

I am interested in only the positive sulc  and would like to make group analysis of the postive sulc values. Hence I would like to mask off the negative values (as the lh.sulc file has both positive and negative value). Before making group analysis, I have to resample and smooth the sulc value. How do I smooth the positive sulc in a way that the negative sulc values will not have an effect on the smoothing process? Example if I smooth the positive sulc directly with the negative values, it will have some effect on the positive values since gyri and sulci are alternating.

 

you suggest me using mri_binarize and mri_fwhm to make a mask and smooth it with a mask.

As suggested, I have done so.

 

However, there is a problem I can not tackle.

 

Using mri_binarize --i lh.sulc --min 0 --o lh.such.mask.mgh
When I read the lh.such.mask.mgh into matlab so that I can see the data inside.
To my surprise, I saw a vector which contains nearly all 0's except some very small numbers like 1.401298464324817e-45, not binary file which contains only 0's and 1's.

I further tried:
mri_binarize --i lh.sulc --min 0 --o lh.such.mask.mgh --binval 1

It has the same problem as above.
After launching:
mris_fwhm --i  sulc --subject Ad001 --surf white --mask lh.such.mask.mgh --hemi lh --fwhm 20 --o lh.sulc.mgh
I read lh.sulc.mgh into matlab, it contains all 0's.

 

I read the mgh file using Keith worsley's SurfStatReadData function.

I do not know where it is wrong.

 

Thank doug for your helpful suggestions!

 

Thank you very much!

 

yuanchao