Hi, I wanted to perform source localization of my result and for that I would need to work with free surfer. I performed the MRI reconstruction with Free surfer on my virtual box, the process completed in 3 hrs, however I have BEM folder missing. The terminal result shows that the process was completed without any errors, yet I am unable to see the BEM subfolder? Why is it so? The MNE tutorial says and I quote:
`The first processing stage is the creation of various surface reconstructions. Usually a full FreeSurfer reconstruction is obtained by the following commands:
my_subject=sample
my_NIfTI=/path/to/NIfTI.nii.gz
recon-all -i $my_NIfTI -s $my_subject -all
where i stands for “input” and s for “subject”. Executing this will create the folder $SUBJECTS_DIR/sample and populate it with several subfolders ( bem , label , mri , etc).`
However I don’t get a folder called BEM after the reconstruction is over? Is this a problem? Are there further steps to this that I am missing?
What should I do to fix this?
Hi Barry, Thank you for the response. Could you help me with the documentation to compute forward model with MNE in a sequential order? I went through the available tutorials and they are really confusing as to which step I need to approach when.
what is trans.fif, how do I generate it? These are all confusing.
Just after the recon-all , you can run these commands on the fly to produce the BEM surfaces and more:
# for bem surface computation (or generating the full bem directory as you asked), use
mne watershed_bem --subject=$my_subject --overwrite
# for generating a dense scalp surface, better for MEG/EEG - MRI coregistration, use
mne_make_scalp_surfaces --subject=$my_subject --overwrite