In the end, the direction does not make a difference because the transform can just be inverted
On 8/30/2019 9:35 AM, Wang, Lily wrote: I think I'm confused about what the inputs and outputs of the bbregister command are. Should the input volume --mov be my FLAIR? I thought that would register the FLAIR to the T1--or is there no difference between registering FLAIR to T1 and T1 to FLAIR? Best, Lily ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wang, Lily <lwan...@partners.org><mailto:lwan...@partners.org> Sent: Thursday, August 29, 2019 11:17 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Corresponding structures to an ROI 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Thursday, August 29, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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