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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
