Hi, The current HCP structural pipeline was developed well before the forthcoming FS version that will have improved support/processing of “hires” structurals.
In fact, parts of the HCP structural pipeline are there basically so that we could refine the positioning of the surfaces to take full advantage of the acquisition resolution. In principle, when “FS 6.0” comes out, some of this functionality will be incorporated into the standard ‘recon-all’ stream itself, so it may be possible to simplify the FS related stuff in the HCP Structural Pipeline. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: <[email protected]<mailto:[email protected]>> on behalf of Antonin Skoch <[email protected]<mailto:[email protected]>> Date: Monday, October 31, 2016 at 11:44 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option) Dear experts, I was wondering, why do you run in FreeSurferPipeline the recon-all with downsampled 1mm3 data? It is due to the fact that you do not want to rely on development version of FreeSurfer which only enables reconstruction of high resolution data (via -cm or -hires option)? Isn't it a bit step backward for subcortical analysis to do the subcortical recon with 1mm resolution? Since I really needed subcortical segmentation in high resolution (for Hippocampal subfields modelling) but wanted to capitalize on HCP pipeline added values, I tried to modify FreeSurferPipeline scripts to use FreeSurfer dev version. I used mris_make_surfaces from HCP verion of FreeSurfer, other binaries and scripts are from dev version. I had to make only several minor changes in FreeSurferHiResWhite and FreeSurferHiResPial: I only needed to slightly modify parameter format of mri_surf2surf to accomodate expectation of dev version of mri_surf2surf and acknowledge the fact that recon-all -white in dev version does not make ?h.white files, but ?h.white.preaparc and aseg.presurf instead of aseg. I ran my data by my modified "full-hires" pipeline and the results seem reasonable. Do you see any potential pitfalls with this approach? 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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
