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getting_started:bioimage [2018/10/21 15:07]
42.49.180.224 [FieldTrip (elec structures) → BioImage Suite (*.mgrid files)]
getting_started:bioimage [2018/07/11 13:23] (current)
robert [Getting started with BioImage Suite]
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 It is also possible to localize electrodes in FieldTrip, using **[[reference:​ft_electrodeplacement]]**,​ and subsequently view and/or edit their positions in BioImage Suite. To accomplish this, the elec structure must be saved as a BioImage Suite compatible *.mgrid file using FieldTrip’s **[[reference:​fieldtrip2bis]]** function. The first input to **[[reference:​fieldtrip2bis]]** specifies the path to the *.mgrid file. The second input is the elec structure generated by **[[reference:​ft_electrodeplacement]]**. And the third input is the path to the brain volume file that was used to localize the electrodes. It is also possible to localize electrodes in FieldTrip, using **[[reference:​ft_electrodeplacement]]**,​ and subsequently view and/or edit their positions in BioImage Suite. To accomplish this, the elec structure must be saved as a BioImage Suite compatible *.mgrid file using FieldTrip’s **[[reference:​fieldtrip2bis]]** function. The first input to **[[reference:​fieldtrip2bis]]** specifies the path to the *.mgrid file. The second input is the elec structure generated by **[[reference:​ft_electrodeplacement]]**. And the third input is the path to the brain volume file that was used to localize the electrodes.
  
-  fieldtrip2bis(&lt;path to *.mgrid file&gt;, elec, &lt;path to corresponding brain volume file&gt;)+  fieldtrip2bis(<path to *.mgrid file>, elec, <path to corresponding brain volume file>)
  
 === Load the *.mgrid File and corresponding brain volume into BioImage Suite === === Load the *.mgrid File and corresponding brain volume into BioImage Suite ===
  
 Once the *.mgrid file is created, it can be loaded into the BioImage Suite Electrode Editor along with the corresponding brain volume file. If the electrodes appear severely misaligned in BioImage Suite, it is likely because the orientation of the brain volume in BioImage Suite does not match the orientation of the brain volume in FieldTrip, which may happen for a variety of reasons. To solve this problem, simply reorient the brain volume in BioImage Suite (in the brain volume window: Relabel → ReOrient Image → select from drop down) to match the orientation of the brain volume in FieldTrip, which can be determined from the [[/​faq/​how_are_the_different_head_and_mri_coordinate_systems_defined|coordinate system]] of the brain volume. Once the *.mgrid file is created, it can be loaded into the BioImage Suite Electrode Editor along with the corresponding brain volume file. If the electrodes appear severely misaligned in BioImage Suite, it is likely because the orientation of the brain volume in BioImage Suite does not match the orientation of the brain volume in FieldTrip, which may happen for a variety of reasons. To solve this problem, simply reorient the brain volume in BioImage Suite (in the brain volume window: Relabel → ReOrient Image → select from drop down) to match the orientation of the brain volume in FieldTrip, which can be determined from the [[/​faq/​how_are_the_different_head_and_mri_coordinate_systems_defined|coordinate system]] of the brain volume.
 +
 ===== Suggested further reading ===== ===== Suggested further reading =====
 {{topic>​tutorial +ieeg &list}} {{topic>​tutorial +ieeg &list}}