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New tools for NDA Submission

The MRI COMPUTING team has created comprehensive set of tools for uploading MR data to the NDA database! Please email if you have any interest in using these tools and indicate if your data is already stored on our cluster. The NDA-tool will:

  • Create a valid image03 file
  • 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
Cailtlin Llyoyd and Xiaofu He have been working on 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 preprocessing pipeline for diffusion MRI data that combines denoising, artifact removal, distortion correction, and motion correction steps, with image co-registration and resampling. It also produces easily inspected visual reports and QC metrics. Let us know if you are interested in adding this protocol to your next project!

Multi-echo fMRI
Zhishun Wang and Jack Grinband have been working on a robust preprocessing pipeline for multi-echo fMRI data which is being tested on the cluster. Multi-echo fMRI promises to shorten acquisition times and improve stability and reproducibility of resting state fMRI data. The MEfMRIPrep pipeline extends fMRIPrep’s functionality by including TE-dependent PCA and ICA from tedana pipeline and pre-denoising multi-echo fMRI data.

Baby fMRI
Marilyn Cyr has been working on implementing a standardized protocol for fMRI data acquisition and processing for baby fMRI data. Based on fMRIPrep, the nibabies pipeline will produce surface-mapped EPI cifti files that can then be used for surface-based analyses.

MRI Technical Meetings 

We continue to have alternating technical/computing meetings every Monday afternoon, led by Dr. Gaurav Patel. Anyone is welcome to bring their technical issues to these meetings for help and troubleshooting. Please email Joe and we will put you on the agenda for the meeting (

Until further notice, all tech meetings will be held via Zoom. Link will be provided to all of those on the mailing list. 

C3N Seminars

C3N Seminar Schedule

C3N Seminars aim to stimulate discussion about the translation of cognitive and computational neuroscience to clinical psychiatry.  The seminars take place on Wednesdays at 3pm in the 6th floor Multipurpose Room of the NYSPI Pardes Building and are streamed live on Zoom* 

Please email to be added to the mailing list.

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