[HCP-Users] probtrackx2 surface tracking in matrix2 mode

Hello experts, I am trying track from a seed surface roi to all WM surface vertices using matrix2 mode in probtackx2 using data from the HCP. I have followed the guide on how to convert surfaces using the surf2surf command where necessary. However I get this error when running probtrackx2 Done

Re: [HCP-Users] probtrackx2 surface tracking in matrix2 mode

That error suggests that that particular flag is not ready for surfaces yet and is looking for a NIFTI volume. Do you have the latest version of FSL? Perhaps Stam can comment on whether --target2 will be able to handle surfaces in the future. Peace, Matt. From:

Re: [HCP-Users] fat suppression and diffusion scans

Hi Mark, The locked sequences that we are using for HCP, and on which those protocol print-outs are based, are based on a fairly old (at this point) version of the CMRR sequences, for which Fatsat = none actually means that a gradient reversal based method of fat suppression is used rather

Re: [HCP-Users] fat suppression and diffusion scans

Hi Michael Thanks for that information, very helpful. I forgot to mention that we haven't requested the HCP sequences at this point since we have the Siemens MB sequences installed (we may end up requesting them at some point). In any case this first test protocol I created was using the stock

Re: [HCP-Users] fat suppression and diffusion scans

Siemens strong fat suppression” = fat sat pulse + gradient reversal On Jul 9, 2015, at 2:37 PM, Mark A. Pinsk mpi...@gmail.com wrote: Hi Michael Thanks for that information, very helpful. I forgot to mention that we haven't requested the HCP sequences at this point since we have the

Re: [HCP-Users] fat suppression and diffusion scans

Ah ha, many thanks for that information. On Thu, Jul 9, 2015 at 4:44 PM, Xu, Junqian junqian...@mssm.edu wrote: Siemens strong fat suppression” = fat sat pulse + gradient reversal On Jul 9, 2015, at 2:37 PM, Mark A. Pinsk mpi...@gmail.com wrote: Hi Michael Thanks for that

[HCP-Users] Easy way to have PreFreeSurferBatch.sh not process the T2w?

Hi all, Is there an easy way to set PreFreeSurferBatch.sh to perform full preprocessing on the T1w scan, but skip all preprocessing steps that involve the T2w? Thanks, Dan ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] Connectome Workbench v1.1 Released!

News from the Human Connectome Project (HCP) July 9, 2015 Connectome Workbench v1.1 Released The WU-Minn HCP Consortium is pleased to announce that version 1.1 of Connectome Workbench (WB) brain visualization and analysis software is now available at

Re: [HCP-Users] Easy way to have PreFreeSurferBatch.sh not process the T2w?

Sorry, but no -- not currently. The T2w is a fundamental component of HCP acquisitions and pipelines, so stuff related to it is embedded into the pipelines. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the