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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-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.
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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-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.
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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-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.
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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
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*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.
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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:
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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
<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-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.
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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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