Hello FreeSurfer Developers and experts,

I am trying to run our FSPGR sequences using the -mri_watershed script, but I am not able to set and vary the -t threshold. The aim of my work is to calculate the BPF in order to quantify parenchymal atrophy in patients with Multiple Sclerosis.

Instead of using the whole "-recon-all" command, I have tried to reduce the amount of datas (and the very long time needed to calculate them) performing this script:

"-mri_watershed -atlas"

The result of the extraction of the brain is good and fast, but I still could need to adjust the cut limits. I have tried to modify it into this new script:

"-mri_watershed -atlas -t X"

(where "X" stands for a variable between 0 and 50) but in this case, no matter what "X" I choose the results are all identical.

Is it possible to set a -t threshold using -atlas? If not, can you suggest us how to change our approach? Is it possibile to use freesurfer with FLAIR sequences with the same aim (extract the BPF to evaluate brain atrophy)?

Best regards, Mario Rossi

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Linux Mint 1 Debian MATE 64-bit