Problems with MRI segmentation and electrodes coregistration

1

Hello
i just started brain storm but i have several problems:

  • i cannot Register electrodes: the step " Refine registration using head points says not enough digitized head point to perform. even though i upload successfully the polhemus file. (but no coordinates are registered...)
    How to pass that?

  • other question
    i upload the MRI thank to dico systeme and images
    but i cannot generate any 3D except face, brain suite seems to stop at the second step...

thanks

2

Before trying to process your own data, I recommend you start by following all the introduction tutorials (section "Get started") using the example dataset provided, and then the EEG/Epilepsy tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials
This forum is not designed to handle questions that are already addressed in the tutorials

i cannot Register electrodes: the step " Refine registration using head points says not enough digitized head point to perform. even though i upload successfully the polhemus file.

Please post screen captures showing:

  • the database explorer with the channel file visible
  • the head surface + the electrodes positions (simply double-click on the channel file)
  • the contents of the "polhemus file" you imported
  • the full error message
    Add the exact sequence of buttons clicks you are doing to get to the error (from the import of the anatomy to the error you report)

i cannot generate any 3D except face, brain suite seems to stop at the second step...

Try using SPM12 or FreeSurfer.
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer

If you have errors with BrainSuite:

  • Try running BrainSuite in a stand-alone way (not from Brainstorm) - you would get more details on the process
  • Please report the error: either here (but in a different thread) or on the BrainSuite forum (Forums Archive - BrainSuite)
  • In both cases, please include the MRI you are trying to process (upload it somewhere and post the download link in the forum post)
3

Thank you François.

I followed your ideas/steps and try with several other data.

load the mri is ok
MNI normalization is ok
generate head is ok

some polhemus files seems corrupted but it works with other

bu as soon as i want to generate 3D tissues or BEM/MESH is stops.

i tried several time to reinstall spm12, it seems ok
the problem seems to be from cat 12

i try to install it my self and put it in SPM12 but no change.

could you help me ?

this is the message that i get when i install cat 12

image
image863×962 126 KB

4

some polhemus files seems corrupted but it works with other

More details are needed. Please see my previous message.

bu as soon as i want to generate 3D tissues or BEM/MESH is stops.

What stops? How?
Please give more details and screen captures

this is the message that i get when i install cat 12

Please refer to the instructions in the tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12#Install_CAT12

5

thank you françois

with your help i succeded:

  • i had to uninstall, delete all file an then reinstall matlab (i had different versions of matlab and different file of brain storm)
    and brain storm in a different file
  • i had to put brain storm file outside of program file
  • run matlab as an adminstrator (right click move)

an no i passed many problems, cat12 is running

but it is openMEEG that has a problem

image
image2560×1440 369 KB

6

You can find help here:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem

If you can't make it work:

  • Look for all the existing OpenMEEG bug reports on the forum, you might find one that has exactly the same error code and context as yours.
  • Otherwise, please start a new topic to discuss this problem. Include screen captures, and the files that are requested for debugging in all the other OpenMEEG bug reports
7

thank you for you amazing work

everything is now functionning.

Respectfully.