Sorry, I meant the masks were made using FLAIR. Does bbregister work on registering T1 to FLAIR?
I was considering using mri_binarize but because I have 20+ subjects each with multiple ROI's that can span several brain structures, I would have to go through every single subject and manually find the corresponding segmentation code numbers?
Thank you,
Lily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Thursday, August 29, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corresponding structures to an ROI
Use bbregister instead of mri_robust_register You can then use mri_label2vol with the --seg option to map into either direction. Once they are in register, I would isolate each of your ROIs by creating a binary volume for each with mri_binarize --i yourrois.mgz --match SegId --o segid.mgz where SegId is your segmentation code number. Then run mri_segstats --seg wmparc.mgz --i segid.mgz --ctab-default --sum sum.segid.dat The values in the "Mean" field of sum.segid.dat (6th column I think) will be the fraction of the ROI in that wmparc segment.
On 8/29/19 10:25 AM, Wang, Lily wrote:
Hi All,
I have several white matter ROI masks unique to each subject that were made using the subjects' T2 scans and I would like to use wmparc to find out what brain structures those ROI's correspond to. I'm guessing that I will need to either register T1 to T2 or T2 to T1 at one point, which I have done by using mri_robust_register to register T1 to T2 (and it seemed to turn out ok, but how do I check other than by eye? And is there a better way to register?), and apply that transformation to wmparc. But other than figuring out the registration, what else do I do?
Thank you,
Lily
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