For more detail, to import a parcels by parcels connectivity matrix into cifti, you will need to make a parcel by parcel .pconn.nii file first - the simplest approach is probably to take any dense cifti file (.dscalar.nii or .dtseries.nii), run it through -cifti-parcellate to make a .pscalar.nii or .ptseries.nii, then the result of that through -cifti-correlate to make a .pconn.nii.
Also note that -cifti-convert -to-text should be able to produce a .csv by specifying "-col-delim ,". However, -cifti-convert only converts the data values, it does not put any names or labels in the file (also, it expects only data values in the input to -from-text). The order of parcels is set during -cifti-parcellate, determined by the key values of each label (which in turn is set during -cifti-label-import). Tim On Thu, Feb 7, 2019 at 5:11 PM Timothy Coalson <tsc...@mst.edu> wrote: > BALSA does not require that files be "queryable". It is scene-centric, so > most of the files that get uploaded happen to be files that we know what to > expect inside them, but it is designed such that this is an added > convenience on top of storing the files, not as a requirement. > > Tim > > > On Thu, Feb 7, 2019 at 4:58 PM Harms, Michael <mha...@wustl.edu> wrote: > >> >> >> Supporting “arbitrary” formats requires putting a whole system in place >> for describing the format, and making it queryable. The good thing is >> that if the pconn’s are available, users could use those inputs to their >> own derived graph-theoretic measures. >> >> >> >> Cheers, >> >> -MH >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave. Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> >> >> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Caio Seguin >> <caioseg...@gmail.com> >> *Date: *Thursday, February 7, 2019 at 4:52 PM >> *To: *NEUROSCIENCE tim <tsc...@mst.edu> >> *Cc: *hcp-users <hcp-users@humanconnectome.org> >> *Subject: *Re: [HCP-Users] Sharing HCP-derived brain networks and >> graph-theoric measures >> >> >> >> 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 >> >> >> ------------------------------ >> >> 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
