Hello everyone, Thanks for all the ideas, this has been very helpful. I will try to follow your suggestions to upload the data to BALSA. I will let you know if I have any further questions.
Best, Caio Em sáb, 9 de fev de 2019 às 04:09, Elam, Jennifer <e...@wustl.edu> escreveu: > Hi Caio, > > Ideally you would share the data both ways, as your original arbitrary > files and converted and visually displayed as parcel x parcel pconn CIFTI > files on the cortex and/or in matrices in Workbench scene files. > Alternatively (or additionally), you could just create scenes of your > figure images from your paper, by loading image files into Workbench and > display them -- I can give you further instructions on how to do this. > > > Either way you would then have a scene file that you can upload to BALSA > along with your arbitrary files. BALSA could then display one of your > scenes and have your study dataset be searchable on the BALSA homepage. > > > If you have any questions on how to put together your dataset for BALSA, > please let me know. > > > 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:* John Smith <jackdaw...@gmail.com> > *Sent:* Friday, February 8, 2019 10:29:45 AM > *To:* NEUROSCIENCE tim > *Cc:* Caio Seguin; Elam, Jennifer; hcp-users > *Subject:* Re: [HCP-Users] Sharing HCP-derived brain networks and > graph-theoric measures > > The "Upload Files" button on the Files modal should take you to a page > with a widget that allows you to upload arbitrary files to your BALSA > study. It is assumed that extra files are there to serve as documentation > or additional figures, so currently the uploader accepts files with the > following extensions: zip, txt, rtf, pdf, odt, odp, wpd, doc, docx, ppt, > pptx, jpg, png, fig, m, gif, csv. A file of any type can be uploaded so > long as it is in a directory contained in a zip file. Within that base > directory, such files can be nested into other directories, and that is > where they will appear when the dataset as a whole is downloaded. Any files > uploaded outside of a zip will be assumed to exist at the base directory > for the study. As a final note, files that are not directly used by a scene > will not be downloaded unless the user has selected to download the entire > study or has specifically selected those files for download. > > -John > > On Thu, Feb 7, 2019 at 5:08 PM Timothy Coalson <tsc...@mst.edu> wrote: > > As I recall, BALSA also allows arbitrary additional files to be uploaded > to studies. I'm not sure about the details of how to do this, though > (there is an "upload files" button in the "files" modal for a study you > own, but I'm not sure where those files end up). > > Tim > > > On Thu, Feb 7, 2019 at 4:52 PM Caio Seguin <caioseg...@gmail.com> wrote: > > Thanks Tim and Matt for the quick reply. > > Most of the files are NxN connectivity matrices, where N could denote, for > instance, ROIs from different parcellation schemes or resting-state > functional networks. > > Ok, so one option is to transform these matrices into cifti files and > share them through BALSA. On the one hand, this is a nice solution for it > solves the user term uses. On the other, it is a bit of a roundabout way to > store these files in the context of my manuscript. The matrices are used to > derive graph-theoretic measures about brain organization (rather than for > visualization purposes), so researchers interested in that would need to > convert the cifti files back to CSV. > > More generally, do you suggest any methods to share HCP-derived files in > an arbitrary format? > > Thanks in advance for the help. > > Best, > Caio > > > Em sex, 8 de fev de 2019 às 06:19, Timothy Coalson <tsc...@mst.edu> > escreveu: > > If your data is organized as a value per parcel/network, you should be > able to turn it into parcellated cifti files, which can be displayed in > wb_view (and therefore in scenes) as a matrix and/or as colored regions on > the surfaces and in the volume. > > See wb_command -cifti-parcellate (to make a template parcellated cifti > file you can use to import data into), -cifti-label-import (to get your > network ROIs into the format -cifti-parcellate wants), and -cifti-convert > (and its -from-text option, to read csv or other text data and output > cifti). > > Tim > > > On Thu, Feb 7, 2019 at 7:05 AM Caio Seguin <caioseg...@gmail.com> wrote: > > Dear experts, > > I have used diffusion and resting-state functional MRI data from the HCP > to derive whole brain connectomes for individual participants. I used the > connectomes to computed graph-theoretic measures that are part of a > manuscript I am working on. > > My question concerns the sharing of these connectomes and graph-theoretic > measures. My current understanding is that sharing this data is ok as long > as I make sure users abide to the HCP data usage terms. What are your > suggestions on how to do this? > > I've seen BALSA proposed to this end, since it provides a built-in > mechanism of user terms, but my files are CSV or .mat files rather than WB > scenes. > > Thanks in advance for your help. > > Best regards, > Caio Seguin > > _______________________________________________ > 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
