Re: [HCP-Users] Question: How to transform MNINonLinear-derived dscalar surface to T1w space?

Surface data is different - we don't actually put surface coordinates into dscalar, or any other cifti files (or metric files). In our data, the surface coordinates are only contained in .surf.gii files. Getting the surface data into "Native" volume space is as simple as using the surfaces in

Re: [HCP-Users] Question: How to transform MNINonLinear-derived dscalar surface to T1w space?

Hi Tim, Terrific! I hadn't appreciated how the spatial coordinates of surface vertices were distinct from data at those vertices until now. Many thanks for the quick and thorough reply! Best, Dave On Thu, Jan 24, 2019 at 2:10 PM Timothy Coalson wrote: > Surface data is different - we

[HCP-Users] Regress confounds out of CIFTIs

Dear Experts, I have a text file of confound regressors that I would like to regress out of a resting state .dtseries.nii file and save the residuals of this procedure as a new .dtseries.nii file. I was wondering if there is a computationally efficient way of doing this, possibly using the

Re: [HCP-Users] Regress confounds out of CIFTIs

We do this in matlab. It is not necessary to loop, just use proper matrix math. For example: newdtseries = dtseries - (demean(regressor) * (pinv(demean(regressor)) * dtseries'))’; Where demean(regressor) removes the mean of each regressor. Matt. From:

Re: [HCP-Users] NaN introduced in cifti

Does your FOV cover the whole brain? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date: Thursday, January 24, 2019 at 1:29 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Regress confounds out of CIFTIs

Dear Matt, Looks like I really need to improve my linear algebra. Thank you very much! Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu | (650) 5615738 From: "Glasser, Matthew" Date: Thursday,

[HCP-Users] Downloading Movement Regressor Data for 7T Scans

Hi, I am trying to download a group of movement regressor text files for 7T resting state scans via REST but there does not seem to be any relation between the subject number and the URL needed to download the file. For example the URL for the first 7T rest scan for subject 100610 is

[HCP-Users] Question: How to transform MNINonLinear-derived dscalar surface to T1w space?

Hi all, What is the procedure for transforming scalar surfaces in the MNINonLinear space back to a subject’s (processed) T1w space using wb_command tools? Briefly, I am working with an independently-collected, HCP-like dataset which has been processed with the HCP Pipelines tools.