You can get the help info of commands by running them with no arguments, or from here:
http://www.humanconnectome.org/software/workbench-command.php?function=-label-to-volume-mapping Note that the ribbon mapping method (which is generally recommended when you have pial and white surfaces) of surface to volume mapping is "generous" in that it assigns values to voxels that are only partially inside the cortical ribbon - this can be dealt with if it is a problem for your use. Tim On Tue, Oct 11, 2016 at 2:11 AM, Peter McColgan <pmccolga...@qub.ac.uk> wrote: > > Thanks Matt, I am keen to generate a single-subject-specific version using > -cifti-separate and -label-to-volume-mapping, using the subject's own > surfaces. > > > Could you advise how I go about doing this? > > > Thanks again for your help. > > > bw > > > Peter > ------------------------------ > *From:* Glasser, Matthew <glass...@wustl.edu> > *Sent:* 11 October 2016 00:09:24 > *To:* Peter McColgan; NEUROSCIENCE tim; Elam, Jennifer > *Cc:* hcp-users@humanconnectome.org > > *Subject:* Re: [HCP-Users] Glasser nature atlas > > A number of people have been using this file: HCP_PhaseTwo/Q1-Q6_ > RelatedValidation210/MNINonLinear/fsaverage_LR32k/ > Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_ > Areas_Group_Colors.32k_fs_LR.dlabel.nii > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Peter McColgan > <pmccolga...@qub.ac.uk> > Date: Monday, October 10, 2016 at 3:22 PM > To: Timothy Coalson <tsc...@mst.edu>, "Elam, Jennifer" <e...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Glasser nature atlas > > Thanks Tim, I have found a number of files at https://balsa.wustl.edu/ > sceneFile/show/L731 can I ask which is the best one to use for the nature > paper parcellation? > > Thanks > > Peter > > ------------------------------ > *From:* Timothy Coalson <tsc...@mst.edu> > *Sent:* 04 October 2016 22:45:46 > *To:* Elam, Jennifer > *Cc:* Peter McColgan; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Glasser nature atlas > > Making a "nifti version" isn't a simple conversion, as some lengthy > conversations on this list have elaborated on. > > The good news: if you want a single-subject-specific version, that is > possible, using -cifti-separate and -label-to-volume-mapping, using the > subject's own surfaces. > > The bad news: if you want it to be a group atlas, the currently popular > volume registration methods aren't good enough at cortical area alignment > to make our parcellation meaningful in a group-average volume space, and > thus we do not recommend making a volumetric version in such a space. In > the meantime, surface registration avoids several difficulties inherent to > volume registration, and was instrumental in being able to create the > parcellation at all (via alignment of areal features). > > For more detailed discussion: > > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03078.html > > Tim > > > On Tue, Oct 4, 2016 at 9:47 AM, Elam, Jennifer <e...@wustl.edu> wrote: > >> Hi Peter, >> >> The data for the new parcellation are available in the BALSA database, >> see this thread: http://www.mail-archive.com/hc >> p-us...@humanconnectome.org/msg02876.html >> >> >> We recommend using the included Connectome Workbench scene file to >> conveniently view the data in the wb_view part of the software platform. >> Get Connectome Workbench here: https://www.humanconnectome.or >> g/software/get-connectome-workbench.html >> >> >> Many of the files are in the CIFTI data format >> <http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-help>, >> which has a lot of advantages, but if you need NIFTI versions, you can use >> wb_command >> <http://www.humanconnectome.org/software/workbench-command.php> >> (distributed as part of Connectome Workbench) to do the conversion. >> >> >> There's lots of help for using wb_command in the HCP-Users mail archive, >> and/or you could post more questions to the list. >> >> >> Best, >> >> Jenn >> >> >> Jennifer Elam, Ph.D. >> Scientific Outreach, Human Connectome Project >> Washington University School of Medicine >> Department of Neuroscience, Box 8108 >> 660 South Euclid Avenue >> St. Louis, MO 63110 >> 314-362-9387 >> e...@wustl.edu >> www.humanconnectome.org >> >> ------------------------------ >> *From:*hcp-users-boun...@humanconnectome.org < >> hcp-users-boun...@humanconnectome.org> on behalf of Peter McColgan < >> pmccolga...@qub.ac.uk> >> *Sent:* Tuesday, October 4, 2016 9:29:30 AM >> *To:* hcp-users@humanconnectome.org >> *Subject:* [HCP-Users] Glasser nature atlas >> >> >> >> Dear HCP team, >> >> >> Is it possible to download a nifti version of the Glasser atlas featured >> recently in nature? >> >> >> Thanks >> >> >> bw >> >> >> Peter >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
