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
<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>
<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>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas Greve
<dgr...@mgh.harvard.edu><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>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><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-boun...@nmr.mgh.harvard.edu>
<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 information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
