Computing & Initiatives
New Tools for NDA Submission
The MRI Computing Team has created a comprehensive set of tools for uploading MR data to the NDA database. Please email Juan.Sanchez@nyspi.columbia.edu if you’re interested in using these tools and indicate whether your data is already stored on our cluster.
The NDA tool will:
- Create a valid
image03file - Create an upload package without the need for local storage
- Submit the validated package to the corresponding collection
Projects on the Horizon
Standardized DTI Acquisition/Processing
Caitlin Lloyd and Xiaofu He are creating a standardized DTI acquisition protocol complemented by an open-source and validated processing pipeline, QSIprep. The acquisition protocol is identical to the multiband/single-shell protocol used by the ABCD project.
QSIprep is an automated diffusion MRI preprocessing pipeline that includes denoising, artifact removal, distortion and motion correction, co-registration, resampling, visual reports, and QC metrics. Let us know if you’d like to add this protocol to your next project.
Multi-echo fMRI
Zhishun Wang and Jack Grinband are testing a robust preprocessing pipeline for multi-echo fMRI on the cluster. Multi-echo fMRI can shorten acquisition times and improve reproducibility for resting-state studies. The MEfMRIPrep pipeline extends fMRIPrep by incorporating TE-dependent PCA/ICA from the tedana pipeline and pre-denoising multi-echo data.
Baby fMRI
Marilyn Cyr is implementing a standardized protocol for infant fMRI acquisition and processing. Based on fMRIPrep, the nibabies pipeline produces surface-mapped EPI CIFTI files suitable for surface-based analyses.
MRI Technical Meetings
We hold alternating technical and computing meetings every Monday afternoon, led by Dr. Gaurav Patel. Anyone is welcome to bring technical issues for help or troubleshooting.
Please email us to be added to the agenda:
All technical meetings are hybrid (Zoom + in-person in the NYSPI Boardroom). A Zoom link is sent to the mailing list.
C3N Seminars
🗓️ C3N Seminar Schedule
📍 NYSPI Pardes Building (Map)
✉️ Join the Mailing List
C3N Seminars stimulate discussion about translating cognitive and computational neuroscience to clinical psychiatry. Seminars occur Wednesdays at 3 pm in the 6th-floor Multipurpose Room of the Pardes Building and are streamed on Zoom.