mne coreg issues

dasdiptyajit · April 12, 2022, 1:14pm

Hi guys!

I recently updated to mne 1.0. After the update, the mne coreg is not working. I am getting this error text:

cmd: mne coreg

output:

Using pyvistaqt 3d backend.

    Triangle neighbors and vertex normals...
Using high resolution head model in /media/dip_linux/Transcend/Visual_p3_data/3847/surf/lh.seghead
Traceback (most recent call last):
  File "/home/dip_linux/anaconda3/envs/mne/bin/mne", line 8, in <module>
    sys.exit(main())
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne/commands/utils.py", line 107, in main
    cmd.run()
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne/commands/mne_coreg.py", line 85, in run
    mne.gui.coregistration(
  File "<decorator-gen-558>", line 12, in coregistration
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne/gui/__init__.py", line 193, in coregistration
    return CoregistrationUI(
  File "<decorator-gen-570>", line 12, in __init__
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne/gui/_coreg.py", line 238, in __init__
    self.coreg = Coregistration(
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne/coreg.py", line 1371, in __init__
    self._setup_bem()
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne/coreg.py", line 1426, in _setup_bem
    'mesh (%d vertices): %s' % (len(self._bem_high_res.surf.rr),
AttributeError: 'dict' object has no attribute 'surf'

system info:

Platform:         Linux-5.13.0-39-generic-x86_64-with-glibc2.31
Python:           3.10.4 | packaged by conda-forge | (main, Mar 24 2022, 17:38:57) [GCC 10.3.0]
Executable:       /home/dip_linux/anaconda3/envs/mne/bin/python
CPU:              x86_64: 8 cores
Memory:           15.3 GB

mne:              1.0.0
numpy:            1.21.5 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy:            1.8.0
matplotlib:       3.5.1 {backend=QtAgg}

sklearn:          1.0.2
numba:            0.55.1
nibabel:          3.2.2
nilearn:          0.9.0
dipy:             1.5.0
cupy:             Not found
pandas:           1.4.2
pyvista:          0.33.3 {OpenGL 3.3 (Core Profile) Mesa 21.2.6 via Mesa Intel(R) UHD Graphics (CML GT2)}
pyvistaqt:        0.8.0
ipyvtklink:       0.2.2
vtk:              9.1.0
PyQt5:            5.12.3
ipympl:           0.8.8
pooch:            v1.6.0

mne_bids:         Not found
mne_nirs:         Not found
mne_features:     0.2
mne_qt_browser:   0.2.6
mne_connectivity: 0.3

any help would be appreciated.

best,
Dip

agramfort · April 12, 2022, 1:39pm

how did you update mne?

Alex

dasdiptyajit · April 12, 2022, 1:43pm

just: pip install mne==1.0

dasdiptyajit · April 12, 2022, 1:46pm

sorry, I set the mne environment from scratch using the instructions given in mne website. So technically I didn’t update if that answer your question

agramfort · April 12, 2022, 2:53pm

I want to make sure that you installed with conda on a fresh env.

otherwise consider using the fully packaged installer

Alex

richard · April 12, 2022, 3:48pm

Hello @dasdiptyajit, I think this might be a bug in MNE-Python.

It should not occur if you have a low-resolution head surface available. I assume that if you look inside the FreeSurfer subjects folder for that particular subject, and then navigate to the bem sub-folder (i.e., /media/dip_linux/Transcend/Visual_p3_data/3847/bem in this particular case), there’s no outer_skin.surf file, right?

Running make_scalp_surfaces() should fix this for you. Importantly, leave no_decimate at its default (False) so it will generate the low-resolution surface.

Please let me know how it goes,
Richard

dasdiptyajit · April 13, 2022, 7:14am

@richard it works! cool

richard · April 13, 2022, 7:42am

Thank you, I’ve reported the bug upstream: Coreg GUI doesn't start if only high-resolution, but no low-resolution skin surface is not available · Issue #10520 · mne-tools/mne-python · GitHub

mschendel · May 18, 2022, 3:47pm

Hi all,
I’m having this issue, too.

When I try mne.bem.make_scalp_surfaces I get an error for FREESURFER_HOME not being set up. I have a working freesurfer distribution. What should the FREESUREFER_HOME be and how do I set this variable for this module to work? Just making FREESURFER_HOME= ‘/path_to_freesurfer/’ didn’t do anything.

Thanks for the help,
Megan

mschendel · May 18, 2022, 4:19pm

Hi again,
I figured out to use mne.set_config(‘FREESURFER_HOME’,FREESURFER_HOME, set_env=True), so I was able to use mne.bem.make_scalp_surfaces. I see a head-dense.fif, head-medium.fif, and a head-sparse.fif in the subject/bem/ directory.

However, when I try mne coreg, I still see output that it’s trying to use the high resolution head model and I see the same errors listed above in this topic.

I did a fresh mne install in a conda environment, and I’m using mne1.0 on Ubuntu 18.04.5 LTS.

I don’t know where it’s getting the subject from when I do mne coreg, but the output lists
Using high resolution head model in /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87102616/bem/M87102616-head-dense.fif

Thanks for any help,
Megan

mschendel · May 18, 2022, 4:30pm

One more update…

I tried adding the -s -d and -f tags to the mne coreg command to explicitly set those variables, and then I use --low-res-head. But it is STILL trying to open the dense head surface and still throwing the no attribute ‘surf’ error!

Megan

richard · May 18, 2022, 4:41pm

Please post the complete command you’re using and the full error message, thank you.

mschendel · May 18, 2022, 4:53pm

Exactly as dasdiptyajit said…

Trial 1:

(mne1.0_ubuntu) mschendel@mars:/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/mne_source/python-scripts$ mne coreg
Using pyvistaqt 3d backend.

Using high resolution head model in /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87102616/bem/M87102616-head-dense.fif
Traceback (most recent call last):
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/bin/mne", line 10, in <module>
    sys.exit(main())
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/commands/utils.py", line 107, in main
    cmd.run()
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/commands/mne_coreg.py", line 85, in run
    mne.gui.coregistration(
  File "<decorator-gen-558>", line 12, in coregistration
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/gui/__init__.py", line 193, in coregistration
    return CoregistrationUI(
  File "<decorator-gen-570>", line 12, in __init__
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/gui/_coreg.py", line 238, in __init__
    self.coreg = Coregistration(
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/coreg.py", line 1371, in __init__
    self._setup_bem()
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/coreg.py", line 1426, in _setup_bem
    'mesh (%d vertices): %s' % (len(self._bem_high_res.surf.rr),
AttributeError: 'dict' object has no attribute 'surf'

Trial 2 with tags:

(mne1.0_ubuntu) mschendel@mars:/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/mne_source/python-scripts$ mne coreg -d '/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/' -s 'M87102616' -f '/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_AUTO_ANALYSIS/subjects/M87102616/M87102616_prosaccade_visit1_tsss_mc.fif' --low-res-head
Using pyvistaqt 3d backend.

Using high resolution head model in /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87102616/bem/M87102616-head-dense.fif
Traceback (most recent call last):
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/bin/mne", line 10, in <module>
    sys.exit(main())
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/commands/utils.py", line 107, in main
    cmd.run()
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/commands/mne_coreg.py", line 85, in run
    mne.gui.coregistration(
  File "<decorator-gen-558>", line 12, in coregistration
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/gui/__init__.py", line 193, in coregistration
    return CoregistrationUI(
  File "<decorator-gen-570>", line 12, in __init__
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/gui/_coreg.py", line 238, in __init__
    self.coreg = Coregistration(
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/coreg.py", line 1371, in __init__
    self._setup_bem()
  File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.0_ubuntu/lib/python3.10/site-packages/mne/coreg.py", line 1426, in _setup_bem
    'mesh (%d vertices): %s' % (len(self._bem_high_res.surf.rr),
AttributeError: 'dict' object has no attribute 'surf'

Thanks for taking a look,
Megan

richard · May 18, 2022, 4:54pm

Are you sure you’re running the latest release of MNE-Python (1.0.3)? The problem should not occur there.

richard · May 18, 2022, 4:56pm

I’m sorry, I was mistaken, this fix is only in the development version and was not backported to 1.0.x.

richard · May 18, 2022, 4:57pm

Can you please share the contents (list of files and directories) inside the

/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87102616/bem

folder?

mschendel · May 18, 2022, 5:01pm

Ok, I’m using 1.0.0
I’ll have to decide if I want to try the dev version or just use old tools.

I reread your instructions for the other user - should I have .surf files in the bem folder after using make_scalp_surfaces ? I only see the 3 head-*.fif files and no .surf ones.

Thanks,
Megan

richard · May 18, 2022, 5:02pm

Yes, exactly, you should see those .surf files.

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system info:

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