What it does. Computes a quantitative T1 map (in ms) from a Siemens MP2RAGE
acquisition, corrected for transmit-field (B1⁺) inhomogeneity using either a SA2RAGE
scan or a separately acquired B1 map (e.g. a Siemens tfl B1 map). It can also compute a
standalone relative B1 map from SA2RAGE, and denoise the MP2RAGE UNI into a clean
UNI-DEN (O'Brien et al. robust combination, removes the salt-and-pepper background noise).
It is a Rust→WebAssembly port of the T1-mapping parts of
J. P. Marques' scripts,
validated to match the reference pipeline to machine precision.
Outputs. Depending on the task: a B1-corrected T1 map (ms) and the uncorrected T1,
a relative B1 map, a denoised UNI-DEN, the B1-corrected UNI, and a
parameters.json. The result panel overlays a pre/post (uncorrected vs corrected) T1
histogram; download each as NIfTI (plus a derived DICOM T1 series), or grab them all at once as a
single .zip.
Privacy. Everything you load and all image processing runs inside this browser tab via
WebAssembly. Your images, DICOM/NIfTI files and results are never uploaded to any server, and the
tool keeps working with the network disconnected. The page does load Google Analytics, which
reports anonymous usage (page views and interactions) to the NeuroDesk team so they can see how
many people use the tool. It never has access to your images or results, only that a visit
happened. (If you use the folder picker, Chrome shows an “upload… only continue if you trust this
site” prompt. That is Chrome’s wording for granting the page read access to a folder
on your disk, not a network upload. Drag & drop skips it.)
How to use. (1) Drop your NIfTI files or DICOM folders and tag their roles. (2) Confirm the
sequence parameters, from JSON sidecars, DICOM headers, or a 7T/3T preset. (3) Pick a task
(T1 map, SA2RAGE → B1 map, or UNI denoising) and Compute, then preview and
download. A T1 map needs the UNI, INV2 (brain mask) and a B1 source (2-volume
SA2RAGE or a B1 map); denoising needs UNI + INV1 + INV2.
Batch (BIDS). Switch the input toggle to BIDS directory and pick a dataset root. The app
lists every subject and session, matches the MP2RAGE and fmap files by their BIDS entities, and flags
anything missing or non-standard. Run each session with its Calculate button (parameters come from
that session's JSON sidecars), download the map from its row, then Download and unload to free the
memory before the next subject. Only one session is held in memory at a time.
Research software, provided as-is with no warranty. Sanity-check the maps and confirm the
parameters against your protocol. Cite Marques 2010 (NeuroImage), Marques & Gruetter 2013 (PLoS ONE),
Eggenschwiler 2012 (MRM).
