I think the problem is that you apply the registration twice instead of once. the first time is on the volume output of bbregister, but then you do it again when you run mri_vol2surf. I would just use SWI-bet.nii.gz (input to bbregister) as input to mri_vol2surf. Also, it is unnecessary to do bet or mri_binarize or mri_mask for this process (though you may need it for other things). Also, I would use --projfrac 0.5 when running mri_vol2surf
On 1/6/2020 10:03 PM, Assis Lopes, Pedro Augusto wrote: > Dear Freesurfer experts, > > Thank you for the quick response Dr. Greve! It`s an attempt to measure > siderosis area, a thin (pathologically), small and blooming cortical signal > seen through SWI (due to B0 inhomogeneity). We did: > Recon-all > > SWI BET and registration to T1 > #BET > bet $SUBJECTS_DIR/$subject/SWI_Surface/original/$subject\_SWI.nii.gz > $SUBJECTS_DIR/$subject/SWI_Surface/bet/$subject\_SWI-bet.nii.gz -R > > > #bbregister (SWI to T1 skull stripped output from recon all) > bbregister --s $subject --mov > $SUBJECTS_DIR/$subject/SWI_Surface/bet/$subject\_SWI-bet.nii.gz --reg > $SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.dat --o > $SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.nii.gz --t1 > > #Divided hemispheres > #LH and RH > mri_binarize --i > $SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_filled.nii.gz --match 255 > --o $SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_filled_LH.nii.gz > mri_mask $SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.nii.gz > $SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_filled_LH.nii.gz > $SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_SWI-LH.nii.gz > > #Transform the volume into a surface file with mri_vol2surf > #Left Hemi > mri_vol2surf --mov > $SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_SWI-LH.nii.gz --srcreg > $SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.lta --hemi lh > --o > $SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-LH_surface.nii.gz > --regheader $subject > #and right > mri_vol2surf --mov > $SUBJECTS_DIR/$subject/SWI_Surface/hemi/$subject\_SWI-RH.nii.gz --srcreg > $SUBJECTS_DIR/$subject/SWI_Surface/bbreg/$subject\_SWI_bbreg.lta --hemi rh > --o > $SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-RH_surface.nii.gz > --regheader $subject > > #Freeview and project SWI as an overlay onto the inflated surface > freeview -f > $SUBJECTS_DIR/$subject/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=$SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-LH_surface.nii.gz > -f > $SUBJECTS_DIR/$subject/surf/rh.inflated:annot=aparc.annot:annot_outline=1:overlay=$SUBJECTS_DIR/$subject/SWI_Surface/vol2surf/$subject\_SWI-RH_surface.nii.gz > > We did not specify any projection fraction in our mri_vol2surf. Sorry for not > being clearer in the step of analyze measured signal. We aim to make a brain > mask of such hypointense signal and obtain its proportional area to total > brain pial surface. > > Thank you so much for the attention Dr. Greve, I look forward in receiving > your response! > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Greve, Douglas N.,Ph.D. > Sent: Monday, January 06, 2020 12:33 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Cortical inflation and maintenance of surface voxel > intensity > > 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 > > _______________________________________________ > 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
