# mne.bem.make\_watershed\_bem compatablity with freesurfer 7.3.2

**URL:** <https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794>\
**Category:** Support & Discussions\
**Tags:** visualization\
**Created:** [October 23, 2022, 9:51pm UTC](https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794 "2022-10-23T21:51:49Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![rethinking\_eeg](https://avatars.discourse-cdn.com/v4/letter/r/bbe5ce/32.png) [@rethinking\_eeg](https://mne.discourse.group/u/rethinking_eeg)\
**Post date:** [October 23, 2022, 9:51pm UTC](https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794/1 "2022-10-23T21:51:49Z")

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Hello  
MNE version 1.1.1

i tried to create bems via:

```python
import mne
mne.set_config("FREESURFER_HOME", '/usr/local/freesurfer/7.3.2')
mne.set_config("subjects_dir", '/usr/local/freesurfer/7.3.2/subjects')

#subjects_dir = '/home/theuser/mne_data/MNE-fsaverage-data/fsaverage'
subject = 'fsaverage'
mne.bem.make_watershed_bem(subject, subjects_dir=None, overwrite=False, volume='T1',
                           atlas=False, gcaatlas=False, preflood=None, show=False,
                           copy=True, T1=None, brainmask='ws.mgz', verbose=None)

```

but i get this error:

```python
FileNotFoundError: [Errno 2] No such file or directory: 'mri_watershed'

```

while searching for “mri\_watershed” i found it in $FREESURFER\_HOME/bin/mri\_watershed  
any help would be much appreciated.

i wanted to work with MRI template fsaverage  
so i tried `mne.datasets.fetch_fsaverage()` but i got this error `Downloading data from 'https://osf.io/3bxqt/download?version=2' to file '/tmp/tmpc6phsyf2/temp.zip'.`  
then i tried to open the [https://osf.io](https://osf.io) website in my browser and it wouldn’t open. is there another link to the template?

thanks so much in advance

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<div class="post-metadata">

**Author:** ![rethinking\_eeg](https://avatars.discourse-cdn.com/v4/letter/r/bbe5ce/32.png) [@rethinking\_eeg](https://mne.discourse.group/u/rethinking_eeg)\
**Post date:** [October 23, 2022, 10:28pm UTC](https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794/2 "2022-10-23T22:28:48Z")

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i tried this command in terminal:

```python
mri_watershed -useSRAS -surf /home/theuser/mne_data/MNE-fsaverage-data/fsaverage/bem/watershed/fsaverage /home/theuser/mne_data/MNE-fsaverage-data/fsaverage/mri/T1.mgz /home/theuser/mne_data/MNE-fsaverage-data/fsaverage/bem/watershed/ws.mgz

```

and it worked!

i guess maybe there are some problem with default path in MNE library for mri\_watershed and current path in Freesurfer 7.3.2

thanks for your attention

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**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [October 24, 2022, 9:54am UTC](https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794/3 "2022-10-24T09:54:02Z")

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mne.datasets.fetch\_fsaverage() should download and expand automatically the files.

you should not have to do anything manually

regarding freesurfer is you have it setup when starting mne then mne should be able  
work while you stay in python

Alex

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**Author:** ![tbonesung](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tbonesung/32/3365_2.png) [@tbonesung](https://mne.discourse.group/u/tbonesung)\
**Post date:** [April 12, 2024, 7:48pm UTC](https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794/4 "2024-04-12T19:48:09Z")

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Hello! I was running across the same problems myself. Have you found out how to run mne.bem.make\_watershed\_bem in Python rather than in the terminal?  
Thank you in advance!

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**Author:** ![ebharti01](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/ebharti01/32/3939_2.png) [@ebharti01](https://mne.discourse.group/u/ebharti01)\
**Post date:** [October 17, 2024, 6:03pm UTC](https://mne.discourse.group/t/mne-bem-make-watershed-bem-compatablity-with-freesurfer-7-3-2/5794/5 "2024-10-17T18:03:22Z")

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Hi! Running into the same problem and was wondering if you found out how to run it through python?