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
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
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
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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 LWANG49@partners.org 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-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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Lily LWANG49@partners.org Sent: Thursday, August 29, 2019 11:17 AM To: Freesurfer support list 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-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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Lily LWANG49@partners.orgmailto:LWANG49@partners.org Sent: Thursday, August 29, 2019 11:17 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, August 29, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Viviana Siless -
Wang, Lily