# interactive gui **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [April 12, 2016, 11:48pm UTC](https://mne.discourse.group/t/interactive-gui/998 "2016-04-12T23:48:39Z")\ **Posts on this page:** 19\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 12, 2016, 11:48pm UTC](https://mne.discourse.group/t/interactive-gui/998/1 "2016-04-12T23:48:39Z")
Hello, Sorry to bother you with this probably very stupid question. I have been working with mne software for about a year now. Until now I have always done data inspection via EEGLab in matlab and run all analysis via mne based python scripts. However, I would like to switch my entire pipeline to mne/python, but I seem to be unable to launch the user interface of me\_browse\_raw. Could anyone please tell me what I need to do to launch this interface. Thank you very much, Dirk ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 5:34am UTC](https://mne.discourse.group/t/interactive-gui/998/2 "2016-04-13T05:34:03Z")
Hi Dirk, To get started with mne using the python tools, you can follow along with this example \<[http://martinos.org/mne/stable/auto\_examples/io/plot\_read\_and\_write\_raw\_data.html#sphx-glr-auto-examples-io-plot-read-and-write-raw-data-py](http://martinos.org/mne/stable/auto_examples/io/plot_read_and_write_raw_data.html#sphx-glr-auto-examples-io-plot-read-and-write-raw-data-py)\> and our intro \<[http://martinos.org/mne/stable/auto\_tutorials/plot\_introduction.html](http://martinos.org/mne/stable/auto_tutorials/plot_introduction.html)\>. We have a python implementation of mne\_browse\_raw with core overlapping features. To browse your data, you need to read it in using the appropriate function here \<[http://martinos.org/mne/stable/manual/io.html](http://martinos.org/mne/stable/manual/io.html)\> given your data type (raw = mne.io.read\_raw\_xxx). Then you can plot and inspect your data using raw.plot(). Feel free to browse our website \<[http://martinos.org/mne/](http://martinos.org/mne/)\>. Let us know if you have any questions or if you find a particular section confusing. HTH, teon ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 3:34pm UTC](https://mne.discourse.group/t/interactive-gui/998/3 "2016-04-13T15:34:25Z")
Hey Teon, Thanks for your quick reply. The plotting of mne\_browse\_raw works fine. However, I should have been more clear in my question. I am looking for a way to quickly browse through my epoched data to check whether there are any remaining artifacts after automatic artifact rejection. In Matlab I was able to scroll to plots of EEG data to visually inspect the data and select epochs for rejection. Is this also possible in python via mne? I can now only think of the very inefficient work around to loop over all epochs with mne\_browse\_raw Thank you, Dirk ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 4:24pm UTC](https://mne.discourse.group/t/interactive-gui/998/4 "2016-04-13T16:24:16Z")
Hi Dirk, We have a new (as of v0.10) interactive plotting for epochs that is a method of the Epochs object. If you have made your epochs: epochs = mne.Epochs(raw), then you can just say epochs.plot and it will provide browser for looking at the epochs for artifact rejection. HTH, teon ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 4:36pm UTC](https://mne.discourse.group/t/interactive-gui/998/5 "2016-04-13T16:36:03Z")
Dear All   There are plenty of examples for MEG analysis. I was wondering, if anyone had a script for EEG source localization for volume source spaces? Maybe, there is one lying around somewhere. That would be big help to me. many thanks best regards parham hashemzadeh ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 5:38pm UTC](https://mne.discourse.group/t/interactive-gui/998/6 "2016-04-13T17:38:01Z")
with epochs.plot(block=True) you can click on epochs to mark them as bad HTH A ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 6:36pm UTC](https://mne.discourse.group/t/interactive-gui/998/7 "2016-04-13T18:36:24Z")
Parham, In general there is nothing different from MEG and EEG analysis, so the tutorial would look identical except the initial raw file would only have EEG data. The only real additional consideration you have is that your BEM has a much greater influence on EEG data than on MEG, so you may want to think about including special MRI sequences like the multi-echo FLASH for generating your BEM. hth d ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 7:48pm UTC](https://mne.discourse.group/t/interactive-gui/998/8 "2016-04-13T19:48:09Z")
Dear all I got an error when running a beamforming tutorial script. I modified the beamformer such that only the EEG leadfield is used and I just wanted to do EEG analysis. So I made the following changes: (a) meg=False in fwd (b) in epochs reject=dict(eog=150e-6) When it gets to the function lcm\_inverse, it throws an error: ""Only volume source estimates can be saved as volumes"" can be saved   I was wondering, if you would be able to point me in the right direction. Many thanks best regards parham hashemzadeh fwd = mne.make\_forward\_solution(raw\_fname, trans, src, bem,                                  fname=None, meg=False, eeg=True, mindist=5.0,                                  n\_jobs=2, overwrite=True) epochs = mne.Epochs(raw, events, event\_id, tmin, tmax, proj=True,                      picks=picks, baseline=(None, 0), preload=True,                      reject=dict(eog=150e-6)) evoked = epochs.average() leadfield = fwd['sol']['data'] ## Read regularized noise covariance and compute regularized data covariance noise\_cov = mne.read\_cov(fname\_cov) data\_cov = mne.compute\_covariance(epochs, tmin=0.04, tmax=0.15,method='shrunk') ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 8:41pm UTC](https://mne.discourse.group/t/interactive-gui/998/9 "2016-04-13T20:41:55Z")
Hi Parham, It sounds like you are using this tutorial: [http://martinos.org/mne/dev/auto\_examples/inverse/plot\_lcmv\_beamformer.html?highlight=beamformer](http://martinos.org/mne/dev/auto_examples/inverse/plot_lcmv_beamformer.html?highlight=beamformer) If that is the case, it uses the cortical surface as the source space and not a volume, so it doesn't really make sense to save as a nifti. hth d ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2016, 10:01pm UTC](https://mne.discourse.group/t/interactive-gui/998/10 "2016-04-13T22:01:02Z")
Dear   Thank you for your email. But actually no I am not using that tutorial. I am using this tutorial which is focused on the Volume Source Space. [http://martinos.org/mne/dev/auto\_examples/inverse/plot\_lcmv\_beamformer\_volume.html#sphx-glr-auto-examples-inverse-plot-lcmv-beamformer-volume-py](http://martinos.org/mne/dev/auto_examples/inverse/plot_lcmv_beamformer_volume.html#sphx-glr-auto-examples-inverse-plot-lcmv-beamformer-volume-py) All I am doing is that I am turning off the MEG and just want to use the EEG. In theory it should work even with this reduced leadfield matrix. Before it was 366 rows but now only 60 rows (Just EEG). So my volume (source space) does not change. It is exactly the same thing. My number of sensors are reduced. The error happens at the line below: mne.save\_stc\_as\_volume('lcmv\_inverse.nii.gz', stc, fwd['src'], mri\_resolution=False) ""Only volume source estimates can be saved as volumes"" can be saved Any help will be appreciated. besst regards parham ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 14, 2016, 1:58am UTC](https://mne.discourse.group/t/interactive-gui/998/11 "2016-04-14T01:58:19Z")
Thank you very much, it works great. As I understand the marked epochs are directly dropped from the epochs object. Is there also a way to not drop the epochs but store their indices (such that you know which trials to exclude from the behavioral file?) Anyway this is great. Really appreciate it. Dirk ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 14, 2016, 3:33am UTC](https://mne.discourse.group/t/interactive-gui/998/12 "2016-04-14T03:33:59Z")
Hi Parham, Where are you getting src from? It doesn't seem to be a volume source space. hth d ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 14, 2016, 8:54am UTC](https://mne.discourse.group/t/interactive-gui/998/13 "2016-04-14T08:54:34Z")
Dear   I simply ran the tutorial below, which uses the file name fname\_fwd = data\_path + '/MEG/sample/sample\_audvis-meg-vol-7-fwd.fif' So, it is a volume. I simply set Meg=False. It appears to me that it is volume. At least it says that it is volume "vol-7-fwd.fif". I wanted to only do the beamformer with EEG. best regards parham hashemzadeh ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 14, 2016, 3:17pm UTC](https://mne.discourse.group/t/interactive-gui/998/14 "2016-04-14T15:17:56Z")
Hi Parham, There are a couple of problems you are running into here: 1. That forward solution only contains MEG sensors, you would need to generate your own with EEG only sensors if you want to. 2. You didn't mention changing the picks call which would also need to be done. Next time if you copy and paste all and exactly what you ran, I can probably help you quicker. hth d ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 15, 2016, 12:56pm UTC](https://mne.discourse.group/t/interactive-gui/998/15 "2016-04-15T12:56:28Z")
Dear Dan   Thank you very much for spending so much time guiding me. In this email, I have pasted the complete code from line 1 to last line of the code. It is pasted after the first bit of code where I get the error and includes the bit of code that gives the error.   I implemented your advice, which by the way was very beneficial for me for pedagogical reasons. Everything went gone smoothly until, I get the following error: ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 15, 2016, 4:34pm UTC](https://mne.discourse.group/t/interactive-gui/998/16 "2016-04-15T16:34:02Z")
please don't paste code in email but use dedicated services like: [https://gist.github.com/](https://gist.github.com/) almost if you want someone to test and replicate use an MNE dataset or make your data available A ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 22, 2016, 4:45am UTC](https://mne.discourse.group/t/interactive-gui/998/17 "2016-04-22T04:45:16Z")
Hi Dirk, The Epochs \<[http://martinos.org/mne/stable/generated/mne.Epochs.html#mne.Epochs](http://martinos.org/mne/stable/generated/mne.Epochs.html#mne.Epochs)\> object has an attribute, `epochs.selection` that maintains the indices of the remaining epochs from the original epochs object. You can then use those indices to select the same trials/events in your behavioral file (granted that the original epochs and behavioral file are allowed in length from the beginning). HTH, teon ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 22, 2016, 11:26am UTC](https://mne.discourse.group/t/interactive-gui/998/18 "2016-04-22T11:26:14Z")
Dear All   I was hoping to do a source reconstruction with fieldtrip. My question involves MNE-sample data set. under the mri directory, there are a number of files. Can you kindly tell, which is the original mri file (main one), that one can use the free surfer to generate the meshes and basically if I wanted to follow the steps in [http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate](http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate) but applied to MNE-sample data set, which mri image, do I need to load and how to determine the coordinate system?,... many thanks best regards parham ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 22, 2016, 12:20pm UTC](https://mne.discourse.group/t/interactive-gui/998/19 "2016-04-22T12:20:15Z")
use mri/T1.mgz HTH Alex