Do you not think it would be valuable to visualize these parcel results on cortical surfaces? CIFTI would be good for that, and can easily be read into matlab as a matrix.
Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Coalson <[email protected]<mailto:[email protected]>> Date: Thursday, February 7, 2019 at 5:24 PM To: "Harms, Michael" <[email protected]<mailto:[email protected]>> Cc: Caio Seguin <[email protected]<mailto:[email protected]>>, hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Sharing HCP-derived brain networks and graph-theoric measures 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Caio Seguin <[email protected]<mailto:[email protected]>> Date: Thursday, February 7, 2019 at 4:52 PM To: NEUROSCIENCE tim <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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. 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