Dear Freesurfer experts,
I am a medical student and am currently doing a fellowship at the JPK Stroke Research Center - MGH. My current research project involves measuring the area of a cortical hypointense brain MRI signal (cortical superficial siderosis) , a marker that lays along the subarachnoid space/pial surface, only visible in blood sensitive MRI (SWI in my case).
In summary: We are trying to do a parallel to fMRI studies (fMRI x T1w // SWI x T1w), analyzing SWI signal intensity on a registered inflated brain surface; Projecting SWI surface intensity would then allow manual area demarcation of hipointensities in a flat surface.
Here is our step-by-step plan (analogous to fMRIxT1w registration/BOLD signal intensity projection to surface):
1. Perform freesurfer recon-all of the subject in question to generate subject-surface models. 2. BET and register the image of interest (SWI) into the freesurfer-subject space (register both SWI and MEMPRAGE sequences) [bbregister] 3. Having SWI in subject space and a surface model (generated in 1); * Split registered SWI into LH and RH * Tkregister2 to get LTA to mri_vol2surf format * Mri_vol2surf each hemisphere to the recon output 4. Display the SWI hemi surface as an overlay 5. Inflate T1 surface and observe its SWI overlay; * Manual demarcation of characteristic SWI hypointense signals 6. Analyze measured signal We did try this approach, but yet with these steps we could only obtain an inflated cortical surface representation that has no correspondence to SWI`s intensity.
So, here comes the question: If BOLD signal intensity can be projected onto surface area; is there a way to project SWI intensity onto the cortical surface? Or Can we preserve the info of SWI surface voxel intensity while doing the surface inflation? If not Is it possible to use the positional information of t1w voxel (used in inflation process) as an index to retrieve its correspondent SWI intensity value?
Sorry for the long question. In advance I thank you already for being so attentive.
Best, Pedro
Pedro Augusto Assis Lopes Student Researcher J. Philip Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA 02114 Phone: (617) 643-3940