Hi Antonin, The conclusion that Bruce, Doug, and I have come to is that we need to do more work on FreeSurfer and the HCP Pipelines to make FreeSurfer v6+ work as well or better than 5.3 for highres surface placement and the T2w stream. The current recommendation would be to stick with version 5.3 for the HCP Pipelines. Hopefully over the next few months we will be able to make the improvements though.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Antonin Skoch <[email protected]<mailto:[email protected]>> Date: Wednesday, January 25, 2017 at 8:49 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] mris_make_surfaces -first_wm_peak - change behavior in FreeSurfer 6.0.0 version -> placement of white surface too internally to white matter? 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 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ 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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