if I can find the time!
On Tue, 7 Feb 2017, Antonin Skoch wrote:
Dear Bruce,
Would you recommend to use -first_wm_peak with -hires option? My tests with
-first_wm_peak on v6.0 ( with search for peak in second derivative) indicate
that the white surface is placed too much internally with respect to actual
gm/wm interface. See the screenshots (with -first_wm_peak and without
-first_wm_peak).
I think that before update to second derivative (december 2016) the
placement of white surface with -first_wm_peak was more anatomically
relevant. Do you plan also to optimize this for v6.1?
Regards,
Antonin
Dear experts,
I am reposting here my mail to FreeSurfer experts (so far
without response) concerning my results of testing of
mris_make_surfaces in V6 freeSurfer version with modified HCP
pipeline (tested on dev version from 3rd January, which is
practically the same as now released 6.0.0 version, since no
additional commits regarding mris_make_surfaces have been done).
My inquiry was concerning the change of behavior of
-first_wm_peak option of mris_make_surfaces in 6.0.0 version.
Apart from previous version the -first_wm_peak option now tries
to search also for peak in second derivative.
It seems to me that this modification of -first_wm_peak behavior
leads now to the white surface placement too internally in gray
matter which is not very anatomically relevant. See the
screenshots where I compared the results:
1. standard recon-all -hires version 6.0.0 adding -first_wm_peak
to mris_make_surfaces (trying to search for peak in second
derivative)
2. FreeSurferHiResWhite.sh with 6.0.0 version and
-first_wm_peak (trying to search for peak in second derivative)
3. FreeSurferHiResWhite.sh with V6 beta version (from december
2016, before change) and -first_wm_peak (without trying to
search for peak in second derivative)
4. standard recon-all -hires version 6.0.0 default setting, i.e.
without adding -first_wm_peak to mris_make_surfaces - quite
similar but not identical results to the 3 - some regions are
more internally, some more externally wrt to 3 - the difference
can be also caused by better gm/wm contrast in brain.finalsurfs
wrt T1w_hires_norm used in FreeSurferHiResWhite.sh.
Could you please get time to look at the results and comment on
which option you assess as most anatomically relevant?
Regards,
Antonin Skoch
Subject: Re: posts about recent updates of freesurfer V6beta
Dear experts,
I also investigated further the second issue -
change of the behavior of -first_wm_peak of
mris_make_surfaces.
I am using modified HCP pipeline where the
mris_make_surfaces -first_wm_peak is used. I worked
to adapt this pipeline to work with V6beta version
of FreeSurfer with using -cm flag to impose
high-resolution reconstruction.
With the change of behavior of -first_wm_peak option
(to look for first peak in 2nd derivative) by commit
in 20th December 2016 the results with up-to-date
versions are no longer compatible with previous
versions (where first peak in 1st derivative was
used I suppose).
My testing using -first_wm_peak with the version
after 20th December 2016 shows that the white
surface is placed much more internally towards white
matter. I am not sure the placement of white surface
so internally is anatomically relevant.
See the screenshots of examples where
1. -first_wm_peak with version from 3rd January 2017
using brain.finalsurfs
2. -first_wm_peak with version from 3rd January
2017 using normalized T1w image (i.e. image without
which did not underwent full previous steps of
recon-all - this is default implementation of
FreeSurferHiResWhite.sh in HCP pipeline).
3. -first_wm_peak with version from November 2016
using normalized T1w image
All versions use -orig -orig_white options with
white surface generated by recon-all -white (i.e.
mris_make_surfaces run without -first_wm_peak using
brain.finalsurfs). This white surface generated by
recon-all -white in 3rd January version is shown in
screenshot 4.
Here are my specific questions / suggestions:
Do you think the -first_wm_peak results with the 3rd
January 2017 version are anatomically relevant?
To assure backward compatibility, I would vote for
keeping option to look for first peak in 1st
derivative in mris_make_surfaces (aside from the new
option with looking to the first peak in the 2nd
derivative).
Could you please comment on?
Regards,
Antonin Skoch
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