[HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

Hi, I was trying to relate the taste intensity score from the unrestricted data to the scale used for its measurement (the general Labelled Magnitude Scale). In the HCP reference manual (Q3), it shows that the values for the taste intensity range from 60 to 130. I was wondering whether the range

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. Alterna

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 at

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 disco

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 > Cc: Timothy Coalson , "hcp-users-request@ > humanconnect

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" mailto:kamal.shad...@gatech.edu>> Date: Wednesday, November 2, 2016 at 1:58 PM To

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" mailto:glass...@wustl.edu>> Date: Wednesday, November 2, 2016 at 2:30 P

Re: [HCP-Users] correlation

The fMRI data are already in standard CIFTI space. Peace, Matt. From: nailin yao mailto:ynai...@gmail.com>> Date: Wednesday, November 2, 2016 at 1:52 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, "hcp-users-requ...@humanconnectome.org

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? Than

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

No need for XFMs. Peace, Matt. From: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>> Date: Wednesday, November 2, 2016 at 1:19 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>> Subject:

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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Wednesday, November 2, 2016 at 11:42 AM To: Timothy Coalson mailto:tsc...@

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

So just to see if I understood your point, If I use surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k for probtrackx, then there is no need to provide –xfm and —inxfm transform arguments? Or do I still need to run FNIRT between diffusion space and T1w and use the results in —xfm and —xfm

Re: [HCP-Users] Myelin Map Summary Statistics

Hmm, I have a follow up question. I can extract average myelin for the entire cortex rather easily however I am having more trouble extracting hemispheric and ROI information. Suggestions? Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) On Mo

[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 sensible.