# Errors when morphing source estimates for group analysis

**URL:** <https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923>\
**Category:** Support & Discussions\
**Tags:** source-localization\
**Created:** [November 6, 2021, 2:27pm UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923 "2021-11-06T14:27:48Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![masataka-wada](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/masataka-wada/32/901_2.png) [@masataka-wada](https://mne.discourse.group/u/masataka-wada)\
**Post date:** [November 6, 2021, 2:27pm UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/1 "2021-11-06T14:27:48Z")

</div>

Hi, all!

- MNE-Python version: 0.23.4
- operating system: Win10

I have a problem with morphing source estimates for group analysis.  
The dataset consists of 80 subjects out of which 7 subjects have this problem.  
I have checked the Freesurfer reconstruction of these subjects and they look OK.

What I am doing right now is as follows:

```python
fsave_vertices = [s['vertno'] for s in src]
morph = mne.compute_source_morph(stc, subject, 'fsaverage',spacing=fsave_vertices, subjects_dir=subjects_dir)

```

I get the following error:

```python
  File "C:\Users\masaw\Documents\Python Scripts\run\M_Source_group_analysis.py", line 95, in <module>
    morph = mne.compute_source_morph(stc, subject, 'fsaverage',

  File "<decorator-gen-327>", line 22, in compute_source_morph

  File "C:\Users\masaw\anaconda3\envs\mne\lib\site-packages\mne\morph.py", line 248, in compute_source_morph
    morph_mat = _compute_morph_matrix(

  File "C:\Users\masaw\anaconda3\envs\mne\lib\site-packages\mne\morph.py", line 1112, in _compute_morph_matrix
    morpher.append(_hemi_morph(

  File "C:\Users\masaw\anaconda3\envs\mne\lib\site-packages\mne\morph.py", line 1152, in _hemi_morph
    mm = maps[vertices_to] * mm

  File "C:\Users\masaw\anaconda3\envs\mne\lib\site-packages\scipy\sparse\_index.py", line 33, in __getitem__
    row, col = self._validate_indices(key)

  File "C:\Users\masaw\anaconda3\envs\mne\lib\site-packages\scipy\sparse\_index.py", line 138, in _validate_indices
    row = self._asindices(row, M)

  File "C:\Users\masaw\anaconda3\envs\mne\lib\site-packages\scipy\sparse\_index.py", line 170, in _asindices
    raise IndexError('index (%d) out of range' % max_indx)

IndexError: index (165866) out of range

```

Any help would be appreciated.

Thanks.

---

<div class="post-metadata">

**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [November 7, 2021, 5:13pm UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/2 "2021-11-07T17:13:10Z")

</div>

that’s weird. Are you sure the stc, src used are all from the subject processed here?

if so can you share with me a folder and a script to replicate the pb?

thx  
Alex

---

<div class="post-metadata">

**Author:** ![masataka-wada](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/masataka-wada/32/901_2.png) [@masataka-wada](https://mne.discourse.group/u/masataka-wada)\
**Post date:** [November 7, 2021, 10:36pm UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/3 "2021-11-07T22:36:19Z")

</div>

Hi, Alex!

Thanks for your comment!  
I pre-processed the data through EEGLAB, but it is not the cause of this problem because other data pre-processed through EEGLAB don’t have this problem.  
The other process was conducted through MNE using the following code.

```python
import os.path as op
import os
import glob
import mne
from mne.cov import compute_covariance
from mne.minimum_norm import make_inverse_operator, apply_inverse
from mne import make_forward_solution
import collections
import re

print( __doc__ )

# setting
snr = 1.0 # use smaller SNR for raw data
method = 'dSPM'
parc = 'aparc' # the parcellation to use, e.g., 'aparc' 'aparc.a2009s'
lambda2 = 1.0 / snr ** 2
n_subjects1 = 8
n_subjects2 = 5
datas_path = "E:\\MNE-forum\\"
EEG_path = os.path.join(datas_path,'EEG-datas')
EEG_file = glob.glob(os.path.join(EEG_path, '*.set'))
subjects_dir = os.path.join(datas_path, 'subjects_dir')

for sub_num in range(len(EEG_file)):
    #set montage
    epochs = mne.read_epochs_eeglab(EEG_file[sub_num])
    epochs2 = epochs.copy().rename_channels({'FP1':'Fp1', 'FPZ':'Fpz', 'FP2':'Fp2', 'FZ':'Fz', 'FCZ':'FCz','CZ':'Cz', 'CPZ':'CPz', 'PZ':'Pz', 'POZ':'POz','CB1':'O1w', 'O1':'Ozw','OZ': 'O2w','O2': 'BAD1','CB2': 'BAD2'})
    epochs3 = epochs2.copy().rename_channels({'O1w':'O1', 'Ozw':'Oz','O2w': 'O2'})
    epochs4 = epochs3.drop_channels(['BAD1', 'BAD2'])
    od = collections.OrderedDict()
    for chan_name in epochs4.ch_names:
        od[chan_name] = epochs4.get_montage()._get_ch_pos()[chan_name]/1000
    posit = mne.channels.make_dig_montage(od)
    epochs5 = epochs4.copy().set_montage(posit)
    epochs_1020 = epochs5.copy().set_montage('standard_1020')
    
    # read MRI
    subjects_dir_list2 = os.listdir(path=subjects_dir)
    subjects_dir_list3 = [s for s in subjects_dir_list2 if re.match('.*T1w_MPR.*nii', s)]
    subjects_dir_list4 = [s for s in subjects_dir_list2 if re.match('.*navigation.*nii', s)]
    subjects_dir_list = subjects_dir_list3 + subjects_dir_list4
    EEG_id = re.search(r'\d\d\d\d\d+', EEG_file[sub_num])
        
    for mri_num in range(len(subjects_dir_list)):
        mri_id = re.search(r'\d\d\d\d\d+', subjects_dir_list[mri_num])
        if EEG_id[0] == mri_id[0]:
            subject = subjects_dir_list[mri_num]
            break
            
    trans_fname = op.join(subjects_dir, subject, '%s-trans.fif' % subject) 
    trans = mne.read_trans(trans_fname)
    bem_dir = os.path.join(subjects_dir,subject, 'bem')
    src = mne.read_source_spaces(os.path.join(subjects_dir,subject, 'bem','%s-oct6-src.fif' % subject))
    fname_model = op.join(bem_dir, '%s-5120-5120-5120-bem.fif' % subject)
    fname_bem = op.join(bem_dir, '%s-5120-5120-5120-bem-sol.fif' % subject)
        
    # create noise_cov→forward_model→inverse_operator→apply_inverse_epochs
    noise_cov = compute_covariance(epochs_1020, tmax=0. ,method='auto')
    fwd = make_forward_solution(epochs_1020.info, trans=trans, src=src, bem=fname_bem, mindist=5.0)
    inverse_operator = make_inverse_operator(epochs_1020.info, fwd, noise_cov)
    evoked = epochs_1020.copy().set_eeg_reference(projection=True).average()
    stc = apply_inverse(evoked, inverse_operator=inverse_operator,lambda2=lambda2, method=method)
        
    # compute_source_morph
    fsave_vertices = [s['vertno'] for s in src]
    morph = mne.compute_source_morph(stc, subject, 'fsaverage',
                                     spacing=fsave_vertices, subjects_dir=subjects_dir)

```

You can download the data which brings about the problem.  
[https://drive.google.com/drive/folders/1ti8D4b5rxyEbVZ5xVx6t4yY6MGu5ocgw?usp=sharing](https://drive.google.com/drive/folders/1ti8D4b5rxyEbVZ5xVx6t4yY6MGu5ocgw?usp=sharing)

Thanks!!

---

<div class="post-metadata">

**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [November 8, 2021, 3:47pm UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/4 "2021-11-08T15:47:02Z")

</div>

what do you get with:

mne.viz.plot\_alignment([epochs.info](http://epochs.info), trans=trans, subject=subject, subjects\_dir=subjects\_dir, src=src, eeg=True)

just to make sure your head model looks good.

Alex

---

<div class="post-metadata">

**Author:** ![masataka-wada](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/masataka-wada/32/901_2.png) [@masataka-wada](https://mne.discourse.group/u/masataka-wada)\
**Post date:** [November 9, 2021, 2:11am UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/5 "2021-11-09T02:11:05Z")

</div>

Thanks for the important advice.

This is the results of the following code,  
`mne.viz.plot_alignment(evoked.info, trans=trans, subject=subject, subjects_dir=subjects_dir, src=src, eeg=['projected', 'original'])`

 ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/087a28df73f5f8136a5ad82a1325172ced31056f.jpeg)  
 ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/e7c91890b4ee193f0286aafe1086d0bc2ba95ed0.jpeg)  
 ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/6841983f69a0eb17a36bc6a5a39ec0aedc00367d.jpeg)

And this is the results of the following code,

```python
mne.viz.plot_bem(subject=subject, subjects_dir=subjects_dir, 
                 brain_surfaces=[],
                 orientation='coronal')

```

 ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/6b33a895dd024b60ba5975918aaab849b2080f1b.jpeg)

Finally, I have tried to check the 3D bem surfaces using freesufer with the following code,  
`mne freeview_bem_surfaces -s subject`  
And the results are these.

 ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/0ed8df896fb1f75803278b512bca184af90e3e3a.jpeg)  
 ![image](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/f9401cb715ef6d1ffc303e8854d8ad33c390a703.jpeg)

But, they look good.

Masataka

---

<div class="post-metadata">

**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [November 11, 2021, 8:37pm UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/6 "2021-11-11T20:37:36Z")

</div>

Ok I think i got it.

You wrote:

fsave\_vertices = [s[“vertno”] for s in src]

and you passed this to spacing parameter in compute\_source\_morph.

the spacing param in compute\_source\_morph is relative to the target brain ie fsaverage.  
So you should pass vertices defined on fsaverage or just set spacing=5 (ie the default)  
to end up with an ico5 spacing in fsaverage space

hope this helps  
Alex

---

<div class="post-metadata">

**Author:** ![masataka-wada](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/masataka-wada/32/901_2.png) [@masataka-wada](https://mne.discourse.group/u/masataka-wada)\
**Post date:** [November 12, 2021, 12:42am UTC](https://mne.discourse.group/t/errors-when-morphing-source-estimates-for-group-analysis/3923/7 "2021-11-12T00:42:34Z")

</div>

Hi Alex,

Your excellent advice helped me to solve my problem.  
Thank you very much for your kindness.

Best regards,  
Masataka