Re: [HCP-Users] run-level (level 1） functional MRI data

Hi Michael, I am sorry I didn't put it clearly. I want "level 1 " results processed through the task model (GLM)? Are they in file ${subj}/MNINonLinear/Results/${fMRIName}_{LR,RL}/${fMRIName}_{LR,RL}__{L,R}.native.func.gii? Thanks, Jiang Jian At 2017-05-23 22:31:34, "Harms, Michael"

[HCP-Users] BOLD signal

Hi, Is there a functional brain region atlas? How can I visualize the BOLD signal of every brain region? Take a step back, is there any way to visualize the signal? Thanks. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] BOLD signal

The HCP has released a cortical areas atlas, but it is unfortunately unaccessible due to some IT problems. Hopefully it will be back up soon. Peace, Matt. From: > on behalf of wtj

[HCP-Users] FIX: setting up environment variables

Dear HCP experts:I’m trying to install FSL FIX on my Mac in order for applying ICA+FIX on rfMRI data. I have installed R packages and MATLAB Runtime Componentas indicated in README text file of FSL FIX folder. And I have edited the "settings.sh" script to reflect my system setup as

Re: [HCP-Users] run-level (level 1） functional MRI data

By level 1 do you mean subject wise? Peace, Matt. From: > on behalf of Jiang Jian > Date: Tuesday, May 23, 2017 at 9:11 PM To: "Harms, Michael"

[HCP-Users] (no subject)

Hello, I was wondering if subject 130619 has been flagged in any way previously. Thanks, -- *Ariana Cahn* *BSc (Hons), *Neuroscience *ac...@ualberta.ca * ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] (no subject)

I do not have any flags for this subject from structural scan or surface QC measures. What are you referring to specifically? Erin On May 24, 2017, at 11:44 AM, Ariana Cahn > wrote: Hello, I was wondering if subject 130619 has been flagged in any

[HCP-Users] create 2k space

HI HCP MEG dataset provides surfaces with 4k vertices, I would like to resample it to 2k. I have tried wd_command -cifti-resample, but it requires a cifti-template, but i don't have any cifti of 2k. What commands should I use to get a 2k surface for every subject? Thanks

Re: [HCP-Users] create 2k space

For resampling just the surface (just the coordinates, no functional data), the command is -surface-resample. There is also -metric-resample and -label-resample for single-hemisphere format data files (for functional data, myelin maps, etc), which are likely to be more useful for creating a

Re: [HCP-Users] create 2k space

Probably also would need wb_command -surface-create-sphere to actually make the 2K space. Peace, Matt. From: > on behalf of Timothy Coalson > Date: Wednesday, May 24,

Re: [HCP-Users] (no subject)

I see asymmetries in the ventricles. Is this what you are referring to? Our Radiologist looked at all of our subjects’ scans and didn’t note any issue. Erin On May 24, 2017, at 12:46 PM, Ariana Cahn > wrote: The brain is very asymmetric, so I was

Re: [HCP-Users] 答复: GIFTI surface data

You might need to use the command line version of the latest FSL. The latest version of melodic does natively work with CIFTI. Peace, Matt. From: wtj <1257735...@qq.com> Date: Wednesday, May 24, 2017 at 7:21 PM To: Matt Glasser

Re: [HCP-Users] create 2k space

You could take a look at this code and adapt as needed: https://github.com/alexlicohen/script-toolbox/blob/master/CreateNewTemplateSpace.sh -Alex > On May 24, 2017, at 2:49 PM, Glasser, Matthew wrote: > > Probably also would need wb_command -surface-create-sphere to

Re: [HCP-Users] create 2k space

Indeed, for some reason that script isn’t in the main HCP repo. Peace, Matt. From: Alexander Li Cohen > Date: Wednesday, May 24, 2017 at 9:29 PM To: Matt Glasser > Cc: Timothy Coalson

Re: [HCP-Users] create 2k space

And now yours is much nicer and would probably be the better starting point for Tim… Matt. From: Alexander Li Cohen > Date: Wednesday, May 24, 2017 at 9:57 PM To: Matt Glasser > Cc: Timothy Coalson

Re: [HCP-Users] create 2k space

Oh interesting. Now I can't remember if I found that version and used it as a starting point. This was a couple of years ago. Regardless, either one should be able to make new templates to downscale or upscale as needed... -Alex > On May 24, 2017, at 10:47 PM, Glasser, Matthew

Re: [HCP-Users] run-level (level 1） functional MRI data

I’m not sure if that is a great idea as one run is RL and the other LR and I don’t think they were really intended to be used that way from a task design perspective either. Perhaps instead you could make use of the test-retest dataset which has 45 subjects completely rescanned through the

Re: [HCP-Users] create 2k space

Well, this script I made from scratch with some experimentation, but I presume there's an in house version that does something similar... -Alex > On May 24, 2017, at 10:35 PM, Glasser, Matthew wrote: > > Indeed, for some reason that script isn’t in the main HCP repo. > >