Dear experts, can also be the difference between v5.3 and v6.0 behavior in HCP pipeline and possible sub-optimal behavior of v6.0 with HCP pipeline given by different in image input to mris_make_surfaces in HCP pipeline (FreeSurferHiResWhite.sh) ?
For white surface estimation the recon-all input is brain.finalsurfs, which is very aggressively filtered so that the white matter voxels have typically values 110 and the SNR in deep white matter areas approach infinity. In contrast, for HCP pipeline the input T1w_hires_masked_norm image is filtered no to such an extent. Therefore there is much lower contrast-to-noise ratio in the region of GM-WM interface for mris_make_surfaces in FreSurferHiResWhite.sh. This maybe renders mris_make_surface more vulnerable to local deviations in intensity in GM-WM interface. My observation (without any thorougful tests) is that with v6.0 in HCP pipeline I had very often to edit wm.mgz in the region of GM-WM interface in the areas of (physiological) perivascular subcortical T1 hypointensities due to the ?h.white "leak" to these areas. And also, as I wrote in some of my previous (unanswered) posts: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51414.html the change of -first_wm_peak behaviour in v6.0 in fact worsened white surface estimation in my data I tested with HCP pipelines. I could upload some example subjects if you are interested and have time to dig in. In any case, it is probably hard to compare performance between standard recon-all and HCP pipeline and different versions of FreeSurfer due to different input to mris_make_surfaces and different flags used. The HCP pipeline, as it currently stands, would probably need different optimization of code or different command line options due to the different input used. Regards, Antonin Skoch Hi Bruce, I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the HCP 0.7mm data that I have looked at (and as I recall at least one other user had some similar issues, as did one of my collaborators), but that was all I meant to refer to. Sorry if my reply came across more general than that, as of course we want to move to using FreeSurfer V6+ in the future. It is the highres T1w and T2w stuff that my pipelines are designed to exploit, however. Also there are some changes I have to make to the HCP Pipelines for FreeSurfer V6+ because of differing file names, etc.Best, Matt. On 3/13/17, 9:40 PM, "Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: >Hi Matt > >To state without qualification that "6.0 has some regressions as far as >surface placement" is incorrect. We quantified its test-retest >reliability, >accuracy and power to detect disease effects and all were improved >relative >to 5.3. We tested V6 on hundreds of datasets across an array of >pathologies >and different MR sequences, field strengths and scanners. We visually >inspected dozens of brains multiple times in the process of improving >accuracy and robustness. I can believe that on Wash U HCP data there >could >be some specific issues, but to imply that V6 is generally less accurate >is >simply incorrect. > >cheers >Bruce > > >On Mon, 13 Mar 2017, Matt Glasser wrote: > >> Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP >> Pipelines. For now version 6.0 has some regressions as far as surface >> placement goes and there are also some adaptations we need to make to >>the >> pipelines. >> >> Peace, >> >> Matt. >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of CAGNA >>Bastien >> <bastien.ca...@univ-amu.fr> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Date: Monday, March 13, 2017 at 7:21 AM >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome >> project's pipeline ? >> >> Dear freesurfer experts, >> >> >> I'm wondering if it's possible to run the human connetome project's >>minimal >> processing pipeline using freesurfer 6 ? >> >> >> Does it require some update of the pipeline or is there anybody that >>have >> already enjoyed the new freesurfer version with this pipeline ? >> >> >> Thank you for your attention and your help, >> >> Bastien Cagna >>
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