Re: [HCP-Users] Moving manual ROIs between subjects

The FSL MNI152 nonlinear template. Peace, Matt. From: Dorian Pustina > Date: Monday, December 5, 2016 at 1:45 PM To: Matt Glasser > Subject: Re: [HCP-Users] Moving manual ROIs between subjects Great, thank

Re: [HCP-Users] MNI mask in minimally processed fMRI data

That's right. Matt. From: > on behalf of "Elam, Jennifer" > Date: Monday, December 5, 2016 at 2:40 PM To: Nina de Lacy

Re: [HCP-Users] Transformation matrix (bti2spm)

The variable names you are using appear to suggest that you are applying a nonlinear warp to a set of coordinate triples - the resulting coordinates are unlikely to ever be regularly spaced. If you need the output to be regularly spaced like a volume file, you need to do a resampling, not a

Re: [HCP-Users] MNI mask in minimally processed fMRI data

Hi Nina, I believe the answer to your question is in Glasser et al. 2013 in the HCP pipelines: fMRIVolume section. If I'm reading it correctly, the brain mask is the final brain mask from the PostFreeSurfer pipeline for that

[HCP-Users] 3T / 7T in same subjects

Hello all, Thank you for this great and open source dataset! I was reading the Appendix III to the manual: 'The 3T/ subdirectory signifies that these data were acquired on the 3T Connectome Skyra at Wash U. For the subjects that are later scanned at 7T (200 of the 1200), the 7T data will

[HCP-Users] MNI mask in minimally processed fMRI data

Hi there:I am interested in using the minimally processed rest and task fMRI data. The details on the website mention:"One step spline resampling from the original EPI frames to atlas space including all transforms (motion, EPI distortion, EPI to T1w from FLIRT BBR, fine tuning of EPI to T1w

Re: [HCP-Users] thresholding the data to p-value

Hi Donna, Could you please re-attach the screen capture that you took for Vasudev? I cannot find it... I also am looking into how to observe significance levels with a threshold of p<0.05. Respectfully, -Tim You need to adjust your overlay settings; see attached capture. Make sure Threshold

[HCP-Users] (files) listing for file bundles

Dear HCP gurus, db.humanconnectome.org/ provides convenient bundles of subjects/data. Is it possible to obtain the lists of files (I guess as a subset of files within hcp-openaccess/HCP or hcp-openaccess/HCP_900 s3 buckets) which comes within each bundle? (without downloading all those bundles

[HCP-Users] 3T / 7T in same subjects

Hello all, Thank you for this great and open source dataset! I was reading the Appendix III to the manual: 'The 3T/ subdirectory signifies that these data were acquired on the 3T Connectome Skyra at Wash U. For the subjects that are later scanned at 7T (200 of the 1200), the 7T data will

[HCP-Users] Transformation matrix (bti2spm)

Dear all, I understood that in order to warp volumetric source locations (provided by the MEG pipeline) to MNI space, one needs to apply the transformation matrix transform.bti2spm. However, when I do this (pos_mni = ft_warp_apply(transform.bti2spm,sourcemodel3d.pos)) the resulting source

[HCP-Users] Moving manual ROIs between subjects

Hi all, Thank you all for providing the data and supporting user's needs. I am using volumetric ROIs (.nii.gz) to extract a specific white matter tract from HCP. Given the nature of the tract I have to manually draw them, which worked pretty well on a single subject. However, this is not optimal