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Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
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________________________________ 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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Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 - which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires "This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility."
I don't think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven't had much time to test v7 intensively, though.
Hope this helps.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.
External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ 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.
Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires.
On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution
Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.”
I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though.
Hope this helps.
Best,
Falk
*Von:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Im Auftrag von *Alexopoulos, Dimitrios *Gesendet:* Mittwoch, 9. September 2020 05:27 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Use Caution *
Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook for Android https://aka.ms/ghei36
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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Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
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: Wednesday, September 9, 2020, 9:11 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires.
On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.”
I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though.
Hope this helps.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.
External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ 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.
In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm.
On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
Jim
Get Outlook for Android https://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:* Wednesday, September 9, 2020, 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
** External Email - Caution **
Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires.
On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution
Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.”
I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though.
Hope this helps.
Best,
Falk
*Von:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Im Auftrag von *Alexopoulos, Dimitrios *Gesendet:* Mittwoch, 9. September 2020 05:27 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Use Caution *
Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook for Android https://aka.ms/ghei36
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
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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Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)?
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020, 9:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm.
On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
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: Wednesday, September 9, 2020, 9:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires.
On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.”
I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though.
Hope this helps.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.
External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ 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.
honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with.
On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)?
Get Outlook for Android https://aka.ms/ghei36
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, September 9, 2020, 9:48 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
** External Email - Caution **
In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm.
On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
Jim
Get Outlook for Android https://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:* Wednesday, September 9, 2020, 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
** External Email - Caution **
Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires.
On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution
Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.”
I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though.
Hope this helps.
Best,
Falk
*Von:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Im Auftrag von *Alexopoulos, Dimitrios *Gesendet:* Mittwoch, 9. September 2020 05:27 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Use Caution *
Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
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Ok. So you prefer -hires since surface placement at hi res is similar to conf2hires?
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________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020, 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with.
On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote:
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Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)?
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________________________________ 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 Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020, 9:48 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm.
On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:
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Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
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: Wednesday, September 9, 2020, 9:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires.
On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.”
I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though.
Hope this helps.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.
External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ 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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Just a further clarification between the using conf2hires or -hires in FS7.1. Our data is acquired at 0.8mm isotropic.
In both cases are the surfaces placed on the hi-res images, correct? The subcortical structure volumes with con2hires are at 1mm, whereas they are at native resolution or 0.8 in our case, correct?
Probably not a big diff in subcortical volumes with either method , but which method will give the most accurate surfaces for GM/WM/aparc volumes?
Would running FS7 without the -hires flag be better (resampling to 1mm)?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Wednesday, September 09, 2020 10:11 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with. On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)?
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________________________________ 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 Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020, 9:48 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
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: Wednesday, September 9, 2020, 9:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires. On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 - which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires "This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility."
I don't think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven't had much time to test v7 intensively, though.
Hope this helps.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.
External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
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________________________________ 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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On 3/19/2021 12:03 PM, Alexopoulos, Dimitrios wrote:
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Just a further clarification between the using *conf2hires* or *–hires * in FS7.1. Our data is acquired at 0.8mm isotropic.
In both cases are the surfaces placed on the hi-res images, correct?
Yes
The subcortical structure volumes with con2hires are at 1mm, whereas they are at native resolution or 0.8 in our case, correct?
Yes
Probably not a big diff in subcortical volumes with either method , but which method will give the most accurate surfaces for GM/WM/aparc volumes?
I don't know. In the end, the differences in surface placement end up being 10s of microns which is hard to judge visually on 1mm data.
Would running FS7 without the –hires flag be better (resampling to 1mm)?
Again, hard to say.
Jim
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Wednesday, September 09, 2020 10:11 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
** External Email - Caution **
honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with.
On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote:
* External Email - Use Caution * Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)? Get Outlook for Android <https://aka.ms/ghei36> ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Wednesday, September 9, 2020, 9:48 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. ** External Email - Caution ** In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote: * External Email - Use Caution * Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc. So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures. Jim Get Outlook for Android <https://aka.ms/ghei36> ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Wednesday, September 9, 2020, 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. ** External Email - Caution ** Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires. On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.de <mailto:falk.luesebrink@med.ovgu.de> wrote: * External Email - Use Caution * Hi Jim, The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution. The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement. With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127 <https://doi.org/10.1016/j.neuroimage.2013.04.127>) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus. Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060 <https://doi.org/10.1016/j.neuroimage.2017.09.060>) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016 <https://doi.org/10.1016/j.neuroimage.2012.12.016>) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof. To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.” I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though. Hope this helps. Best, Falk *Von:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *Im Auftrag von *Alexopoulos, Dimitrios *Gesendet:* Mittwoch, 9. September 2020 05:27 *An:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Betreff:* [Freesurfer] -hires vs -conf2hires in 7.1.1. * External Email - Use Caution * Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android <https://aka.ms/ghei36> ------------------------------------------------------------------------ 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 <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.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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Thx Doug.
I as clarifying because I thought I read earlier that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. Is this not different from conf2hires?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, March 19, 2021 11:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
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On 3/19/2021 12:03 PM, Alexopoulos, Dimitrios wrote:
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External Email - Use Caution Just a further clarification between the using conf2hires or -hires in FS7.1. Our data is acquired at 0.8mm isotropic.
In both cases are the surfaces placed on the hi-res images, correct? Yes
The subcortical structure volumes with con2hires are at 1mm, whereas they are at native resolution or 0.8 in our case, correct? Yes
Probably not a big diff in subcortical volumes with either method , but which method will give the most accurate surfaces for GM/WM/aparc volumes? I don't know. In the end, the differences in surface placement end up being 10s of microns which is hard to judge visually on 1mm data.
Would running FS7 without the -hires flag be better (resampling to 1mm)? Again, hard to say.
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: Wednesday, September 09, 2020 10:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with. On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)?
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________________________________ 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 Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020, 9:48 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc.
So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures.
Jim
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________________________________ 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: Wednesday, September 9, 2020, 9:11 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
* External Email - Caution * Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires. On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de wrote:
External Email - Use Caution Hi Jim,
The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 - which is not really recommended. The segmentation and surface placement will take place at that resolution.
The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement.
With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus.
Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof.
To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires "This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility."
I don't think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven't had much time to test v7 intensively, though.
Hope this helps.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1.
External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images?
Which option is recommended and why?
Jim
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No, with conf2hires, the initial surface is created on the 1mm so it does not need to be downsampled.
On 3/19/2021 5:11 PM, Alexopoulos, Dimitrios wrote:
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External Email - Use Caution
Thx Doug.
I as clarifying because I thought I read earlier that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. Is this not different from conf2hires?
Jim
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, March 19, 2021 11:09 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.
** External Email - Caution **
On 3/19/2021 12:03 PM, Alexopoulos, Dimitrios wrote:
* External Email - Use Caution * * External Email - Use Caution * Just a further clarification between the using *conf2hires* or *–hires * in FS7.1. Our data is acquired at 0.8mm isotropic. In both cases are the surfaces placed on the hi-res images, correct?Yes
The subcortical structure volumes with con2hires are at 1mm, whereas they are at native resolution or 0.8 in our case, correct?Yes
Probably not a big diff in subcortical volumes with either method , but which method will give the most accurate surfaces for GM/WM/aparc volumes?I don't know. In the end, the differences in surface placement end up being 10s of microns which is hard to judge visually on 1mm data.
Would running FS7 without the –hires flag be better (resampling to 1mm)?Again, hard to say.
Jim *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Wednesday, September 09, 2020 10:11 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. ** External Email - Caution ** honestly, I have not really looked at it. I spent most of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with. On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote: * External Email - Use Caution * Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)? Get Outlook for Android <https://aka.ms/ghei36> ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Wednesday, September 9, 2020, 9:48 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. ** External Email - Caution ** In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote: * External Email - Use Caution * Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc. So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures. Jim Get Outlook for Android <https://aka.ms/ghei36> ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Wednesday, September 9, 2020, 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. ** External Email - Caution ** Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires. On 9/9/2020 3:13 AM, falk.luesebrink@med.ovgu.de <mailto:falk.luesebrink@med.ovgu.de> wrote: * External Email - Use Caution * Hi Jim, The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution. The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement. With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127 <https://doi.org/10.1016/j.neuroimage.2013.04.127>) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus. Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060 <https://doi.org/10.1016/j.neuroimage.2017.09.060>) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016 <https://doi.org/10.1016/j.neuroimage.2012.12.016>) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof. To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.” I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though. Hope this helps. Best, Falk *Von:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *Im Auftrag von *Alexopoulos, Dimitrios *Gesendet:* Mittwoch, 9. September 2020 05:27 *An:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Betreff:* [Freesurfer] -hires vs -conf2hires in 7.1.1. * External Email - Use Caution * Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android <https://aka.ms/ghei36> ------------------------------------------------------------------------ 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 <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.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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