Re: [HCP-Users] -cifti-reduce -exclude-outliers

It is not iterative, it calculates the stdev on the full data and uses that. Tim On Mon, Jun 4, 2018 at 4:19 PM, Harms, Michael wrote: > > > Hi Tim, > > I was wondering about the details of the -cifti-reduce -exclude-outliers > operation. In particular, is it “iterative”? i.e., does it

[HCP-Users] -cifti-reduce -exclude-outliers

Hi Tim, I was wondering about the details of the -cifti-reduce -exclude-outliers operation. In particular, is it “iterative”? i.e., does it recompute the std without the outliers from the previous pass(es) and iterate until no further new outliers are identified? Thanks, -MH -- Michael

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

What isn’t available is individual subject parcellations which you didn’t need anyway given your initial question> ;) Matt. From: Thomas Nichols mailto:thomas.nich...@bdi.ox.ac.uk>> Date: Monday, June 4, 2018 at 11:45 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: HCP Users

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

Hi Matt, Ah! Sorry, I didn't realise a 32k_fs_LR version was ready (I thought it was only available for the 449 subjects). Will check it out. -Tom On Mon, Jun 4, 2018 at 5:41 PM, Glasser, Matthew wrote: > Hi Tom, > > Why not use the multi-modal parcellation? https://balsa. >

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

Hi Tom, Why not use the multi-modal parcellation? https://balsa.wustl.edu/file/show/3VLx Matt. From: Thomas Nichols mailto:thomas.nich...@bdi.ox.ac.uk>> Date: Monday, June 4, 2018 at 11:37 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: HCP Users mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

Thanks Matt! We're using it to just coarsely chop up the surface to build phenotypes. What atlas would you suggest that we can easily apply with wb_command -cifti-parcellate? -Tom On Mon, Jun 4, 2018 at 4:29 PM, Glasser, Matthew wrote: > Hi Tom, > > This is because FreeSurfer “fits” the aparc

Re: [HCP-Users] FSL version in the HCP pipelines

Yes, you should be able to use the latest FSL release. In fact, due to code consolidation in the newest release, FSL 5.0.6 is no longer allowed for the task-fMRI processing. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of

[HCP-Users] FSL version in the HCP pipelines

Hi, The README.md on Github points to release notes for 3.0.4, which specifically requires FSL 5.0.6. With pipelines v 3.27.0, is it still necessary to use 5.0.6 at all? Is it possible to use the latest release (5.0.11)? Thanks ___ HCP-Users

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

Hi Tom, This is because FreeSurfer “fits” the aparc to each subject. There is probably an atlas aparc somewhere inside FreeSurfer that wouldn’t have this property. That does raise the question of why you are using aparc instead of one of the more functionally relevant parcellations available

Re: [HCP-Users] Additional smoothing of FIX extended resting state data?

Thanks, Matthew & Timothy, that gave me some valuable insight, I appreciate that! All the best, David 2018-05-31 1:37 GMT+02:00 Timothy Coalson : > A bit more explanation: smoothing only spreads signal out, diluting it > with non-signal or unrelated signal, it can't concentrate it "towards"