# Missing BEM sub folder freesurfer **URL:** \ **Category:** Support & Discussions\ **Created:** [January 27, 2022, 11:40pm UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327 "2022-01-27T23:40:12Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Subrat\_Bastola](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/subrat_bastola/32/1190_2.png) [@Subrat\_Bastola](https://mne.discourse.group/u/Subrat_Bastola)\ **Post date:** [January 27, 2022, 11:40pm UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/1 "2022-01-27T23:40:12Z")
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? ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/5/5398a00ee05f7a2b280f61efca5779d49b4f2122.jpeg) ![20220127_165219](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/4/40e413c9bca93ca3534d8772d9d900ee0d010611.jpeg) ---
**Author:** ![BarryLiu97](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/barryliu97/32/33_2.png) [@BarryLiu97](https://mne.discourse.group/u/BarryLiu97)\ **Post date:** [January 28, 2022, 12:22am UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/2 "2022-01-28T00:22:48Z")
Hi, You could use MNE to generate that. Look at [mne.bem.make\_watershed\_bem — MNE 0.24.1 documentation](https://mne.tools/stable/generated/mne.bem.make_watershed_bem.html#mne.bem.make_watershed_bem) ---
**Author:** ![Subrat\_Bastola](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/subrat_bastola/32/1190_2.png) [@Subrat\_Bastola](https://mne.discourse.group/u/Subrat_Bastola)\ **Post date:** [January 28, 2022, 12:38am UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/3 "2022-01-28T00:38:32Z")
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. Any sequential documentation would help ---
**Author:** ![BarryLiu97](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/barryliu97/32/33_2.png) [@BarryLiu97](https://mne.discourse.group/u/BarryLiu97)\ **Post date:** [January 28, 2022, 1:37am UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/4 "2022-01-28T01:37:13Z")
Sorry, I have no experience with source localization. I just no you could use to generate BEM segmentation using ```python mne.bem.make_watershed_bem ``` ---
**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\ **Post date:** [January 28, 2022, 7:35am UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/5 "2022-01-28T07:35:47Z")
yes just now use mne.bem.make\_watershed\_bem however you should not call your subjects sample. Use the name that is meaningful for you (name or code of your subject) Alex ---
**Author:** ![neurosignal](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/neurosignal/32/200_2.png) [@neurosignal](https://mne.discourse.group/u/neurosignal)\ **Post date:** [January 5, 2023, 9:59am UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/6 "2023-01-05T09:59:30Z")
Just after the **recon-all** , you can run these commands on the fly to produce the BEM surfaces and more: ```python # 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 ``` Please make sure you have installed MNE-C ([Installing MNE-C — MNE 1.3.0 documentation](https://mne.tools/stable/install/mne_c.html)) Cheers. ---
**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\ **Post date:** [January 5, 2023, 6:19pm UTC](https://mne.discourse.group/t/missing-bem-sub-folder-freesurfer/4327/7 "2023-01-05T18:19:07Z")
> [@neurosignal](#): > > Please make sure you have installed MNE-C ([Installing MNE-C — MNE 1.3.0 documentation](https://mne.tools/stable/install/mne_c.html)) Using MNE-C is not strictly necessary; this step: > [@neurosignal](#): > > ```python > mne_make_scalp_surfaces --subject=$my_subject --overwrite > > ``` can be done with MNE-Python; the command is `mne make_scalp_surfaces`. [https://mne.tools/stable/generated/commands.html#mne-make-scalp-surfaces](https://mne.tools/stable/generated/commands.html#mne-make-scalp-surfaces) And you can even do that from within Python via `mne.bem.make_scalp_surfaces()`: [https://mne.tools/stable/generated/mne.bem.make\_scalp\_surfaces.html](https://mne.tools/stable/generated/mne.bem.make_scalp_surfaces.html) Best wishes, Richard