# forward model having only segmentation files **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [March 8, 2012, 1:31pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415 "2012-03-08T13:31:44Z")\ **Posts on this page:** 10\ **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:** [March 8, 2012, 1:31pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/1 "2012-03-08T13:31:44Z")
Dear all, I want to create forward model in MNE software. But I have only segmentation data (skull.mgz, skin. mgz, brain.ngz) got in FSL software + EEG electrodes coordinates. Is it possible to do at all? If yes, could anyone give me an advice how to do it or refer to some tutorial where I could read about. I've read how to do it having 'raw' data and using Freesurfer software + MNE. But in my case all I have only are segmentation files and file with electrodes positions. Regards, Anton ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 8, 2012, 4:58pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/2 "2012-03-08T16:58:25Z")
Hello Anton, it's doable but it's far from trivial as it requires you to understand the internal of the MNE anatomical pipeline (where MNE expects to find the files etc.). I would seriously consider running freesurfer on my subject and rely the automatic / standard pipeline. Freesurfer also gives you all the segmentations including the cortical surface for sources' locations. Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 9, 2012, 10:27am UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/3 "2012-03-09T10:27:09Z")
Hello Alex, Thank you very much for your reply. I completely understand that it is better to use Freesurfer first. But I deal with neonatal data. And Freesurfer, unfortunately, fails to analyse such kind of data (when I tried it even did not create all folders and files, those i could edit manually). As far as I got from literature, people (almost) always do segmentation of neonatal data manually and then launch Freesurfer. But it takes a lot of time to do and is not trivial task. But I have already segmentation files done in FSL. So, my idea was somehow to use them in MNE to get forward model. What would you recommend? What do you think the most optimal way to act in my case? Regards, Anton ??? "Alexandre Gramfort" \: ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 9, 2012, 4:59pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/4 "2012-03-09T16:59:47Z")
Hi Anton, The only thing I can think of would be to use mne\_volume\_source\_space. You would still need to generate a couple of surfaces for your BEM, but this should not be very difficult. If you need more advice about that, please let me know. D tokariev at [mappi.helsinki.fi](http://mappi.helsinki.fi) wrote: ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 9, 2012, 9:09pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/5 "2012-03-09T21:09:21Z")
Hi Anton, I agree with Dan. You should work with a volume source space. It's not going to be trivial but the way to go is: - extract the BEM surfaces and write them a folder matching ${SUBJECTS\_DIR}/${SUBJECT}/bem see the mne-sample-data for an example of database layout you'll probably need to have surface in the ${SUBJECTS\_DIR}/${SUBJECT}/mri folder to mne\_analyze to be able to do the coregistration. - then you can run the forward computation see: [https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run\_meg\_volume\_tutorial.sh](https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_volume_tutorial.sh) - then with python you can run an inverse computation. See: [http://www.martinos.org/mne/auto\_examples/inverse/plot\_compute\_mne\_inverse\_volume.html](http://www.martinos.org/mne/auto_examples/inverse/plot_compute_mne_inverse_volume.html) you should then be able to write a nifty or .mgh file to overlay the activations on the volume e.g. with freeview shipped with freesurfer may the force be with you ! Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 13, 2012, 2:31pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/6 "2012-03-13T14:31:47Z")
The easiest thing to do would be to play around with the FreeSurfer command mri\_watershed use -surf For each volume you give it the created outer skin surface will be the outermost surface you can use for your bem. Use it serially, re-naming the files for use in your BEM. If this is. You may have to play a while to get it to work. I suspect you will need to apply the mask to your original volume, as it expects non-binary data. D tokariev at [mappi.helsinki.fi](http://mappi.helsinki.fi) wrote: ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 28, 2012, 11:15am UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/7 "2012-05-28T11:15:29Z")
Hello, I am trying to create surfaces for BEM. I have done next steps: 1. I have raw MRI images (DICOM). I did segmentation of inner/outer skull and outer skin manually. After this, I changed the original MRI images to segmented volumes (to keep all DICOM headers). In other words, I got MRI images, where instead of original MRI I put inner skull segmentation (also I have saved files like that to outer skull and outer skin). Each value of the segmented volume were set to 110. 2. I used mri\_convert to get from 3 sets of images in DICOM format, those contain segmentations, volumes in .mgz format. So I got inner\_skull.mgz, outer\_skull.mgz and outer\_skin.mgz. I put these files to the folder: .../freesurfer/subjects/subject/mri/orig Now I am trying to get surfaces with a help of the command 'mri\_watershed -surf'. I am using it like this: mri\_watershed -surf inner\_skull.mgz inner\_skull\_surf... But the program fails to create surfaces. What I am doing wrong on this stage? Could anyone give an advise? Best wishes, Anton Lainaus dgw \: ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 29, 2012, 1:47pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/8 "2012-05-29T13:47:26Z")
Hi Anton, Well mri\_watershed is not designed to deal with segmented data. You need to trick it. tokariev at mappi.helsinki.fi wrote: > Hello, > > I am trying to create surfaces for BEM. I have done next steps: > > 1. I have raw MRI images (DICOM). I did segmentation of inner/outer > skull and outer skin manually. After this, I changed the original MRI > images to segmented volumes (to keep all DICOM headers). In other words, > I got MRI images, where instead of original MRI I put inner skull > segmentation (also I have saved files like that to outer skull and outer > skin). Each value of the segmented volume were set to 110. > > 2. I used mri\_convert to get from 3 sets of images in DICOM format, > those contain segmentations, volumes in .mgz format. So I got > inner\_skull.mgz, outer\_skull.mgz and outer\_skin.mgz. I put these files > to the folder: .../freesurfer/subjects/subject/mri/orig Are these binarized masks? Are they masked at all? Regardless, you need to put a raw MRI volume saved as 001.mgz in /subjects/subject/mri/orig/001.mgz and run autorecon1 (check freesurfer wiki for details). > Now I am trying to get surfaces with a help of the command > 'mri\_watershed -surf'. I am using it like this: mri\_watershed -surf > inner\_skull.mgz inner\_skull\_surf... But the program fails to create > surfaces. What I am doing wrong on this stage? Could anyone give an advise? First run the above, and let me know what the files are then we can look into the subsequent steps (this is a non-standard hack I developed), so it will take some time to work through. D ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 29, 2012, 4:11pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/9 "2012-05-29T16:11:42Z")
Hi Dan, Thanx for your reply. Re masks: Yes, they are binary masks. But I set '1' values to suitable for Freesurfer data (to 110). As far as I know Freesurfer does not work with binary data. 'Skin mask' is a contour of skin: on the black background is a 1 pixel width countour that repeats skin countour (each pixel = 110). 'Skull mask' has the same principle but with other width. Re -autorecon1: I have done like you wrote. I used 'skin' volume for test. I got in folder 'mri' next files: error.log mri\_nu\_correct.mni.log nu.mgz orig orig.mgz rawavg.mgz T1.mgz transforms Folder 'transforms' contains files: bak talairach.auto.xfm talairach\_avi.log talairach\_avi\_QA.log talairach.xfm talsrcimg\_to\_711-2C\_as\_mni\_average\_305\_t4\_vox2vox.txt BW, Anton Lainaus dgw \: ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 29, 2012, 4:21pm UTC](https://mne.discourse.group/t/forward-model-having-only-segmentation-files/415/10 "2012-05-29T16:21:56Z")
Ok, The first thing you could try is to use mne\_watershed\_bem now. If you are happy with those results, you can stop there. If not the next step would involve using the FreeSurfer MATLAB tools to multiply your binary masks to the T1 volume and run mri\_watershed step by step on each shell. Unfortunately, this requires you to setup fake FreeSurfer directories for each shell. Eventually, you will be able to get there though. See if the initial run helps. D tokariev at [mappi.helsinki.fi](http://mappi.helsinki.fi) wrote: