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Hi all,
In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline.
"ANTS denoise is used when creating the orig surface (but not thefinal surfaces)"
Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline.
Can you provide some further clarification.
Thx. Jim
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
It is only used to create the orig surface. It is not used in the volume segmentation or the final placement of the surfaces. Volume smoothing of any kind has the potential to bias the surface placement so we recommend against denoising the input.
On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Hi all,
In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all,
However, FS 7.1 now appears to use the denosing utility in parts of the pipeline.
“ANTS denoise is used when creating the orig surface (but not thefinal surfaces)”
Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline.
Can you provide some further clarification.
Thx.
Jim
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I'm looking through the pipeline table , looking to see where the orig surfaces are created, which appear to be in autorecon2 /tessellation step . What advantage is gained by denoising the image (which image is actually denosed?) at this stage if id does not contribute the final surfaces?
Sorry for asking for more detail, just want to make sure I understand the application of the utility. Many groups are now denoising their input images into many pipelines.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, August 25, 2020 4:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
* External Email - Caution * It is only used to create the orig surface. It is not used in the volume segmentation or the final placement of the surfaces. Volume smoothing of any kind has the potential to bias the surface placement so we recommend against denoising the input. On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Hi all,
In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline.
"ANTS denoise is used when creating the orig surface (but not thefinal surfaces)"
Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline.
Can you provide some further clarification.
Thx. Jim
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
brain.mgz is denoised to create antsdn.brain.mgz. This volume is then used to create the initial surface. The final surfaces are created from the unfiltered brain.mgz but using the orig surface created with the denoised brain.mgz. So the denoising helps to create the orig surface which is then used to initialize the final surfaces.
On 8/25/2020 5:37 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I’m looking through the pipeline table , looking to see where the orig surfaces are created, which appear to be in autorecon2 /tessellation step . What advantage is gained by denoising the image (which image is actually denosed?) at this stage if id does not contribute the final surfaces?
Sorry for asking for more detail, just want to make sure I understand the application of the utility. Many groups are now denoising their input images into many pipelines.
Jim
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, August 25, 2020 4:05 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] use of ANTs Denoising in FS 7.1
** External Email - Caution **
It is only used to create the orig surface. It is not used in the volume segmentation or the final placement of the surfaces. Volume smoothing of any kind has the potential to bias the surface placement so we recommend against denoising the input.
On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:
* External Email - Use Caution * Hi all, In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline. “ANTS denoise is used when creating the orig surface (but not thefinal surfaces)” Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline. Can you provide some further clarification. Thx. Jim ------------------------------------------------------------------------ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Thanks for clarifying.
Some initial results on a cohort of 1-2 yo subjects we have run through both the infant FS and 7.1.1 pipelines, seem to benefit from using a denoised T1 image as input. Specifically, denoising in images with motion generates better WM segmentations in complexly folded regions (i.e. occipital/calcarine). We are still evaluating.
Jim
Get Outlook for Androidhttps://aka.ms/ghei36 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, August 25, 2020 10:17:43 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
* External Email - Caution *
brain.mgz is denoised to create antsdn.brain.mgz. This volume is then used to create the initial surface. The final surfaces are created from the unfiltered brain.mgz but using the orig surface created with the denoised brain.mgz. So the denoising helps to create the orig surface which is then used to initialize the final surfaces.
On 8/25/2020 5:37 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I’m looking through the pipeline table , looking to see where the orig surfaces are created, which appear to be in autorecon2 /tessellation step . What advantage is gained by denoising the image (which image is actually denosed?) at this stage if id does not contribute the final surfaces?
Sorry for asking for more detail, just want to make sure I understand the application of the utility. Many groups are now denoising their input images into many pipelines.
Jim
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 Douglas N. Greve Sent: Tuesday, August 25, 2020 4:05 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
* External Email - Caution *
It is only used to create the orig surface. It is not used in the volume segmentation or the final placement of the surfaces. Volume smoothing of any kind has the potential to bias the surface placement so we recommend against denoising the input.
On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Hi all,
In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all,
However, FS 7.1 now appears to use the denosing utility in parts of the pipeline.
“ANTS denoise is used when creating the orig surface (but not thefinal surfaces)”
Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline.
Can you provide some further clarification.
Thx.
Jim
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Dear Jim,
I had been looking at the effect of denoising the data to improve processing speed in case of noisy data in an ISMRM abstract couple of years ago. However, I haven't had the time to follow up on this. Glad to see something similar now being implemented in recon-all.
As Doug and Matt pointed out, denoising the input data will bias your results potentially which is why it is not recommend to do at all. However, denoising the data just for the initialization will reduce defects and errors of the initial white matter surface, reducing processing time from many to a few hours in case of noisy data. As the actual surface is fitted using the unfiltered data this should not impair surface placement.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 26. August 2020 06:04 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
External Email - Use Caution Thanks for clarifying.
Some initial results on a cohort of 1-2 yo subjects we have run through both the infant FS and 7.1.1 pipelines, seem to benefit from using a denoised T1 image as input. Specifically, denoising in images with motion generates better WM segmentations in complexly folded regions (i.e. occipital/calcarine). We are still evaluating.
Jim
Get Outlook for Androidhttps://aka.ms/ghei36 ________________________________ 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 Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Tuesday, August 25, 2020 10:17:43 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
* External Email - Caution *
brain.mgz is denoised to create antsdn.brain.mgz. This volume is then used to create the initial surface. The final surfaces are created from the unfiltered brain.mgz but using the orig surface created with the denoised brain.mgz. So the denoising helps to create the orig surface which is then used to initialize the final surfaces. On 8/25/2020 5:37 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I'm looking through the pipeline table , looking to see where the orig surfaces are created, which appear to be in autorecon2 /tessellation step . What advantage is gained by denoising the image (which image is actually denosed?) at this stage if id does not contribute the final surfaces?
Sorry for asking for more detail, just want to make sure I understand the application of the utility. Many groups are now denoising their input images into many pipelines.
Jim
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 Douglas N. Greve Sent: Tuesday, August 25, 2020 4:05 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
* External Email - Caution *
It is only used to create the orig surface. It is not used in the volume segmentation or the final placement of the surfaces. Volume smoothing of any kind has the potential to bias the surface placement so we recommend against denoising the input.
On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Hi all,
In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all,
However, FS 7.1 now appears to use the denosing utility in parts of the pipeline.
"ANTS denoise is used when creating the orig surface (but not thefinal surfaces)"
Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline.
Can you provide some further clarification.
Thx.
Jim
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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