Re: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?

Indeed we are unable to offer BIDS support, but are happy to support running the HCP Pipelines from our GitHub repository. Peace, Matt. From: > on behalf of "Harms, Michael"

[HCP-Users] Postdoc position in the CMRR at the University of Minnesota

Hello, We are seeking for a postdoc to conduct research funded by the NIH BRAIN Initiative U01 grant. Please see attached job ad for more details. Thanks, xiaoping Xiaoping Wu, Ph.D. Assistant Professor Center for Magnetic Resonance Research Radiology, Medical School University of Minnesota -

[HCP-Users] Three Postdoctoral or PhD positions in Stochastic Signal Processing/Computational Modelling fMRI/EEG

Three postdoctoral (or graduate) positions are available at the Mind, Brain Imaging & Neuroethics lab. The candidates should have strong background in brain imaging (fMRI, MRS, EEG/MEG, TMS) and preferably strong education in neuroscience/brain imaging, engineering, physics, and/or

Re: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?

Hi, We didn’t create the HCP Pipeline BIDS app, and have no experience using it. Users should be aware that the current BIDS App “hides” various choices that one would normally have to make when running the HCP Pipelines, and I’m not sure what particular choices it has implemented. In that

Re: [HCP-Users] gradient nonlinearity correction question

Some problems can arrise if the NIFTI files are unexpectedly manipulated prior gradient_unwarp. Two things to check: 1. dcm2nii and dcm2niix has options to perform additional processing like reorienting or cropping, some of which may be enabled by default. Make sure those are all DISABLED. (for

Re: [HCP-Users] gradient nonlinearity correction question

Hi, I would like to use gradunwarp for offline gradient nonlinearity correction of some data acquired on our local Siemens scanners. I used dcm2niix to convert the dicom data to nifti format. After applying gradunwarp to a T1 image in nifti format (the one that originally has the _ND

[HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?

I want to use the HCP Pipeline BIDS app to preprocess T1w, T2w, and BOLD data collected at the CMRR. The BOLD data were acquired to apply the "PEpolar" method, whereby one short (TR=1.5s, 10 reps) set of EPI data were collected with AP phase-encoding, and one long (TR=1.5s, 400 reps) set of EPI

Re: [HCP-Users] ICA-FIX

Also why do you need to do this to begin with? Peace, Matt. From: > on behalf of Stephen Smith > Date: Friday, April 6, 2018 at 4:45 AM To: Megan Ní Bhroin

Re: [HCP-Users] ICA-FIX

Hi - I would think the easiest and best thing to do would be just to apply more aggressive high-pass filtering to the already FIX-cleaned data. Was there a reason you didn't want to do that? It's not at all a problem that the less aggressive HP filter had already been applied before original

[HCP-Users] ICA-FIX

Hi there, I'm very new to Neuroimaging but wondering if you could help me with some issues I am having. I want to run the ICA FIX pipeline on HCP resting state data. I wish to do this as I would like to apply a more aggressive temporal filtering than is already in place. Do you have any