Re: [Freesurfer] Corresponding structures to an ROI
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> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wang, Lily <mailto:lwan...@partners.org> Sent: Thursday, August 29, 2019 11:17 AM To: Freesurfer support list <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> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <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> <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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Corresponding structures to an ROI
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 on behalf of Wang, Lily Sent: Thursday, August 29, 2019 11:17 AM To: Freesurfer support list 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 on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, August 29, 2019 10:55 AM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Corresponding structures to an ROI
External Email - Use Caution Hi Lily, I believe bbregister should work with T1 and FLAIR using the --t2 contrast (white darker than grey). Works for me! You could also use mri_mask with input your parcellation (wmparc) and mask your FLAIR ROI. Then you could run mri_binarize with "--count file.txt" option for each label with "--match label_id" and it will output the hits on the terminal, but also on your text file. You don't need to save that in a volume, but you would need to do this for each label because if you send many ids on the --match it would merge the count. Best! Viv On Thu, Aug 29, 2019 at 11:18 AM Wang, Lily wrote: > 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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Thursday, August 29, 2019 10:55 AM > *To:* 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 > ___ > 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
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 on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, August 29, 2019 10:55 AM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
