Misaligned BrainSuite Cortex and MRI

Discussions
1

Hi there!

I have processed T1 anatomies using BrainSuite separately from BrainStorm so that I could manually alter the edge and diffusion constants to capture the entire cortex following the BrainSuite tutorial (Cortical Surface Extraction Tutorial · BrainSuite).

I used the "Import anatomy folder (auto)" option to import the MRIs and surfaces for all participants into BrainStorm. There are no importation errors, however, for some, the cortex and MRI are misaligned (please see attached image).

The manual alteration of edge and diffusion constants does not appear to an issue as the registration worked for other volumes that were manually altered.
Any help into resolving the registration would be greatly appreciated!

brainsuite misalignment
brainsuite misalignment609×670 35.7 KB

2

@tmedani, @Anand_Joshi @chinmay.chinara
Can you provide some insights about this issue?

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3

Would it be possible to share one example image for which this issue arises?

4

Hi Anand,

Sure thing. Attached is the misalignment displayed in MRI viewer and 3D MRI.

brainsuite misalignment 1
brainsuite misalignment 11221×1316 146 KB

brainsuite misalignment 2
brainsuite misalignment 2881×1033 324 KB

5

Sorry, I meant if you can share the NIFTI images (.nii.gz), that will allow me to reproduce it at my end.

6

Hi Anand,

Apologies for the overdue response! I ended up finding the issue. I'd made the mistake of exporting the T1 from BrainStorm and running BrainSuite on that. When performed on the original, there were no issues with alignment.

Best wishes,
Ellie

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