I am trying to process a T1-MPRAGE 7T scan with 0.5mm isotropic resolution with the recon-all -highres flag. FS is struggling to make a good mask even though I’ve tried various combinations in the recon-all command (e.g. different -skullstrip -wsthresh numbers, -wsmore, different -watershed atlases). I have tried with and without neck removal (using FSL’s robustfov) as well as bias field correction (via SPM and also FSL’s FAST), and feeding in with and without the scan already brain extracted (via robex). I am now trying to feed in my pre-made mask using the -expert flag.

 

* I have named my pre-made mask as brainmask.mgz and placed it in the directory where my t1.nii.gz is located

* I have made a text file (called expert.opts) that contains:

mri_mask brainmask.mgz

 

My recon-all command calls the file using -expert expert.opts

 

However, recon-all seems to ignore the calling of the expert.opts and so tries to make its own mask…

 

So my question is: am I correctly using the =expert flag and expert.opts to use my pre-made brainmask.mgz?

 

PS. I am using FS version 7.1 (as I am running Ubuntu 18.04 and can’t upgrade due to lots of other software running on the computer)

 

Thankyou!

 

Jerome