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TO: freesurfer@nmr.mgh.harvard.edu FROM: zlseu2109@163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers,
I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal)
| | zlseu2109 | | zlseu2109@163.com |
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Dear zlseu, We currently do not have an “official” release of the probabilistic atlas in a reference space. It is try that some of the smallest nuclei may not appear in the hard (discrete) segmentation, but you can always use the option to write down the posteriors. Then you can open the file corresponding to eg the Pt and see the soft probability map. The instructions can be found in the FAQ section of the wiki: https://secure-web.cisco.com/1WLdU6eWp0r0oi5ZtLH-suvhQZo4bilAef24xA5DF8-Fi-v... Cheers, /E
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1mOqS3QIf3uAWOF8-fWWdyr8xCbchx5YP3crK_PrmzkU8bQb...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zlseu2109 zlseu2109@163.com Date: Monday, July 10, 2023 at 9:11 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: chmxie@163.com chmxie@163.com Subject: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
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TO: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
FROM: zlseu2109@163.commailto:zlseu2109@163.com
SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
Hello FreeSurfer Developers,
I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one?
1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2
2) Platform: Ubuntu Release 20.04.6 (focal)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10UJioIagz0Wb9TxkEGENkRKFPUs6Hmk98CJpO8LTMIGPBGrbOeES4rKHrSHo1bmDt5d7nzGawhcGrXRRrvcBPchog43DBoAjbx5YmZCmQHzM0eU64B1dbaVgPR2V3XNdKXsM5cOFv0d0K_xAMqWL5rOt_ZN2S3rUQ3GdMIFHioYWf7cO_euq6moGl2HTFtx7dgTmRnmyNq5sgRRJ45W3ldMrnRXCMkdzQXR9d1r-99HSBNjnOLEDUdwgym1M7WZ1kKe3mvdFzn9iY5xXmdGMPh40mUZ5LO9DfQqafjTH1XMAXuRwP5u6ezTAEbr9gDz-EGzd0NvRC97EcoZThI8b_g/https%3A%2F%2Fmaas.mail.163.com%2Fdashi-web-extend%2Fhtml%2FproSignature.html%3FftlId%3D1%26name%3Dzlseu2109%26uid%3Dzlseu2109%2540163.com%26iconUrl%3Dhttps%253A%252F%252Fmail-online.nosdn.127.net%252Fqiyelogo%252FdefaultAvatar.png%26items%3D%255B%2522zlseu2109%2540163.com%2522%255D [Image removed by sender.] zlseu2109 zlseu2109@163.com
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The Pt is one of a few nuclei that can sometimes not make it into the final visualisation (others being the Pc and Vm). For these very small nuclei, their posterior probabilities (soft segmentation) generated by the Bayesian segmentation algorithm sometimes don't "win" any voxels so they don't show up in the "hard" segmentation (ThalamicNuclei.v13.T1.mgz) where we display the labels with the voxelwise maximum posterior. However, we generate the volume measurements from the posteriors rather than the hard segmentation so we can give volume estimates for these nuclei.
If you would like to visualise the likely locations of these nuclei you can output the posterior probabilities to get a heat map by running the segmentation after setting the WRITE_POSTERIORS environmental variable. (eg. in bash > export WRITE_POSTERIORS=1)
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zlseu2109 zlseu2109@163.com Sent: 10 July 2023 14:11 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: chmxie@163.com chmxie@163.com Subject: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
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TO: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu FROM: zlseu2109@163.commailto:zlseu2109@163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
Hello FreeSurfer Developers,
I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10UJioIagz0Wb9TxkEGENkRKFPUs6Hmk98CJpO8LTMIGPBGrbOeES4rKHrSHo1bmDt5d7nzGawhcGrXRRrvcBPchog43DBoAjbx5YmZCmQHzM0eU64B1dbaVgPR2V3XNdKXsM5cOFv0d0K_xAMqWL5rOt_ZN2S3rUQ3GdMIFHioYWf7cO_euq6moGl2HTFtx7dgTmRnmyNq5sgRRJ45W3ldMrnRXCMkdzQXR9d1r-99HSBNjnOLEDUdwgym1M7WZ1kKe3mvdFzn9iY5xXmdGMPh40mUZ5LO9DfQqafjTH1XMAXuRwP5u6ezTAEbr9gDz-EGzd0NvRC97EcoZThI8b_g/https%3A%2F%2Fmaas.mail.163.com%2Fdashi-web-extend%2Fhtml%2FproSignature.html%3FftlId%3D1%26name%3Dzlseu2109%26uid%3Dzlseu2109%2540163.com%26iconUrl%3Dhttps%253A%252F%252Fmail-online.nosdn.127.net%252Fqiyelogo%252FdefaultAvatar.png%26items%3D%255B%2522zlseu2109%2540163.com%2522%255D [https://secure-web.cisco.com/12dk8WGu6dtG3euNKCjofzh6Q0xNegXffDqiATEghzr_FdG...] zlseu2109 zlseu2109@163.com
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Thanks for your answer! I’ve output posterior probabilities and got 25 heat maps (.mgz files) for thalamic nuclei. However, I do not know the standard you use to generate the volume measurements of individual thalamic nuclei. Could you explain it? Can I apply this standard to heat maps I’ve got and output .mgz/.nii file of each nuclei for further analysis?
| | zlseu2109 | | zlseu2109@163.com |
---- Replied Message ---- | From | Tregidgo, Henryh.tregidgo@ucl.ac.uk | | Date | 07/10/2023 21:41 | | To | freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu | | Subject | Re: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz |
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The Pt is one of a few nuclei that can sometimes not make it into the final visualisation (others being the Pc and Vm). For these very small nuclei, their posterior probabilities (soft segmentation) generated by the Bayesian segmentation algorithm sometimes don't "win" any voxels so they don't show up in the "hard" segmentation (ThalamicNuclei.v13.T1.mgz) where we display the labels with the voxelwise maximum posterior. However, we generate the volume measurements from the posteriors rather than the hard segmentation so we can give volume estimates for these nuclei.
If you would like to visualise the likely locations of these nuclei you can output the posterior probabilities to get a heat map by running the segmentation after setting the WRITE_POSTERIORS environmental variable. (eg. in bash > export WRITE_POSTERIORS=1)
From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zlseu2109 zlseu2109@163.com Sent: 10 July 2023 14:11 To:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc:chmxie@163.com chmxie@163.com Subject: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
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TO: freesurfer@nmr.mgh.harvard.edu FROM: zlseu2109@163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers,
I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to beMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to beMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to beMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be | | zlseu2109 | | zlseu2109@163.com |
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The final posteriors are used in two ways. To get the "hard" segmentation we simply assign each voxel the label corresponding to the maximum posteriors in that location.
To get our volume estimates we divide the volume of each voxel between the labels proportionately to the posteriors. Essentially this is just multiplying the posteriors by the volume of a voxel and summing across voxels.
If you are doing this with the output posteriors you may need check that the posteriors sum to 1 in each voxel. i.e. they haven't been renormalised for visualisation and you have the posteriors for labels outside of the thalamus which are also modelled during the segmentation.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zlseu2109 zlseu2109@163.com Sent: 15 July 2023 13:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
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Thanks for your answer! I’ve output posterior probabilities and got 25 heat maps (.mgz files) for thalamic nuclei. However, I do not know the standard you use to generate the volume measurements of individual thalamic nuclei. Could you explain it? Can I apply this standard to heat maps I’ve got and output .mgz/.nii file of each nuclei for further analysis?
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---- Replied Message ---- From Tregidgo, Henryh.tregidgo@ucl.ac.uk mailto:h.tregidgo@ucl.ac.uk Date 07/10/2023 21:41 To freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
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The Pt is one of a few nuclei that can sometimes not make it into the final visualisation (others being the Pc and Vm). For these very small nuclei, their posterior probabilities (soft segmentation) generated by the Bayesian segmentation algorithm sometimes don't "win" any voxels so they don't show up in the "hard" segmentation (ThalamicNuclei.v13.T1.mgz) where we display the labels with the voxelwise maximum posterior. However, we generate the volume measurements from the posteriors rather than the hard segmentation so we can give volume estimates for these nuclei.
If you would like to visualise the likely locations of these nuclei you can output the posterior probabilities to get a heat map by running the segmentation after setting the WRITE_POSTERIORS environmental variable. (eg. in bash > export WRITE_POSTERIORS=1)
________________________________ 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 zlseu2109 <zlseu2109@163.commailto:zlseu2109@163.com> Sent: 10 July 2023 14:11 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: chmxie@163.commailto:chmxie@163.com <chmxie@163.commailto:chmxie@163.com> Subject: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
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TO: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu FROM: zlseu2109@163.commailto:zlseu2109@163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
Hello FreeSurfer Developers,
I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal)
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freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E. -
Tregidgo, Henry -
zlseu2109