I have been using FreeSurfer for a while now, but am working in a new lab and their goals fall outside of my realm of experience. 

We are using both MRI imaging as well as FNIRs. We have multiple vitamin E capsules placed during both and would like to be able to view them in FreeSurfer so that we can better estimate the projected cortical localization of these capsules. 

Using the generic recon-all -s -i -all we are unable to see our capsules, as they are most likely eliminated during the skull strip step. I see that I can change the threshold with "-wsmore", but am wondering if this is really the best way to accomplish what we are trying to do.

Is there any way to include our capsules without excluding the skull strip? If not could how would you recommend adjusting the threshold.

I tried excluding the skulls trip step with

recon-all -s -i -autorecon1 -noskullstrip

but then when I tried to view it using free view it was unable to open due to the lack of the brain mask.mgz.

Thank you so much for your time and consideration,

Seth H