Re: [HCP-Users] -probtrackx-dot-convert volume label problem

As a guess, did you use "-crop" when you used -cifti-separate to get the amygdala ROI? If so, that changes the volume space (specifically the FOV), so indices don't correspond with the normal 2mm volume space. This would mean that you now need to make a label volume in this new FOV space.

Re: [HCP-Users] Myelin Map Summary Statistics

Use -cifti-weighted-stats, it reports the measures separately per hemisphere (and can integrate over surface area instead of a naive mean), and use the -roi option to report within an ROI. If you want to use a lot of ROIs that don't overlap, look at -cifti-parcellate. Tim On Wed, Nov 2, 2016

Re: [HCP-Users] Myelin Map Summary Statistics

Thanks Matt. Hmm I am still confused. So here is my command to extract myelin for the entire cortex: wb_command -cifti-stats 43387.MyelinMap.32k_fs_LR.dscalar.nii -reduce MEAN. Since -cifti-stats requires the -reduce flag the data I receive is only one number. What I am hoping to accomplish is to

[HCP-Users] redefining the trial

Hello, I am using the preprocessed data of resting state MEG signal, in the Matlab matrix the data is divided into 2 seconds, then for the work I am dealing with right now we need around 10 seconds of the data, 5 trials , thus the data is redefined to 10 seconds, and as we expect there is no

Re: [HCP-Users] correlation

Thank you Matt! Best, Nailin 2016-11-02 14:53 GMT-04:00 Glasser, Matthew : > The fMRI data are already in standard CIFTI space. > > Peace, > > Matt. > > From: nailin yao > Date: Wednesday, November 2, 2016 at 1:52 PM > To: Matt Glasser

Re: [HCP-Users] FNIRT for HCP diffusion data

You can use the nodif_brain_mask for this. As for questions about the FDT GUI, you will have to ask those on the FSL list as I am only familiar with the probtrackx command line. Peace, Matt. From: "Shadi, Kamal" > Date: Wednesday,

Re: [HCP-Users] FNIRT for HCP diffusion data

Many thanks Matt. I ran probtrackx with no XFM then. It seemed that probtrackx completed successfully, although I got this error at the very end: [cid:ADA2B284-976C-43DC-A8A3-0F49A79CD654] Any idea? From: "Glasser, Matthew" > Date: Wednesday,

Re: [HCP-Users] correlation

Thank you Tim and Matt, So when I extract hippocampus from Atlas_ROIs.2.nii.gz, and use it as roi to do -cifti-average-roi-correlation on one of the subject, does the ROI automatically overlay on the native subcortical space of that subject, or normalized space which is the same for everyone?

Re: [HCP-Users] FNIRT for HCP diffusion data

No need for XFMs. Peace, Matt. From: "Shadi, Kamal" > Date: Wednesday, November 2, 2016 at 1:19 PM To: Matt Glasser >, "hcp-users@humanconnectome.org"

Re: [HCP-Users] Myelin Map Summary Statistics

You should be able to do that with the commands Tim mentioned with the -roi sub option. Peace, Matt. From: > on behalf of Timothy Hendrickson > Date: Wednesday,

[HCP-Users] -probtrackx-dot-convert volume label problem

Hello, I'm trying to convert a .dot from probtrackx2 with -matrix3 option to a dconn.nii. The -lrtarget was a list containing all volumes and surfaces conforming to the HCP grayordinate file. The -target3 is the L (or R) amygdala from Atlas_ROI.2.nii.gz. The output from probtrackx2 looks