[Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

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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Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[falk.luesebr...@med.ovgu.de]

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-boun...@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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Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Douglas N. Greve]

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.luesebr...@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-boun...@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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Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@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

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Douglas Greve]

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*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.luesebr...@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-boun...@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

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Douglas N. Greve]

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*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-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. 
Greve 

*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.luesebr...@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. Pers

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

External Email - Use Caution

Ok. So you prefer -hires since surface placement at hi res is similar to 
conf2hires?



Get Outlook for Android<https://aka.ms/ghei36>


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

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:

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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<mailto:dgr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@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 tr

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

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?
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-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<mailto:dgr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@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.neu

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Douglas N. Greve]

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-boun...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas Greve  <mailto:dgr...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@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.luesebr...@med.ovgu.de
<mailto:falk.luesebr...@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

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

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-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<mailto:dgr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@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 re

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

[Douglas N. Greve]

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:


External Email - Use Caution

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-boun...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas Greve 
<mailto:dgr...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf
of Douglas N. Greve 
<mailto:dgr...@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.




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