Hi Pedro, what you are trying to do is certainly possible. It looks like 
you are doing the right thing as far as I can tell, but I got a little 
lost after step 4, particularly the "Analyze measured signal" step. One 
other thing that may be an issue is what projection fraction you used in 
the mri_vol2surf step.

On 12/30/19 2:21 PM, Assis Lopes, Pedro Augusto wrote:
>
> 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);
>      1. Split registered SWI into LH and RH
>      2. Tkregister2 to get LTA to mri_vol2surf format
>      3. 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;
>      1. 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
>
>
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