Papers wanted
Legal copies retrieved 2026-08-22 and reviewed in the ledger: Todd 2010
(author manuscript), Valošek 2024, Cohen-Adad 2021 spine-generic data,
Lévy 2015, De Leener 2018 PAM50, De Leener 2017 SCT, Fonov 2014
MNI-Poly-AMU, Rexed 1952, Cohen-Adad 2021 spine-generic protocol. The
items below still need a legal copy. Use the Stanford OpenURL when a
DOI exists.
OpenURL base: https://libkey.io/libraries/1462/openurl
Le Troter et al., 2023 — AMU7T (ISMRM abstract)
ISMRM abstract, not a journal article
- Citation
- Le Troter A, Laines Medina NJ, Mchinda S, Cohen-Adad J, Callot V. AMU7T: a 3D qT1 and T2*w high-resolution in vivo template with refined white and gray matter parcellation dedicated to 7T spinal cord MR analyses. ISMRM 2023, abstract 0569.
- DOI
- 10.58530/2023/0569
- PMID
- none found
- PMCID
- none
- Proposed filename
- letroter2023-amu7t-spinal-cord-template.pdf
- Relevance
- Source of the MIT AMU7T NIfTI used for Phase 1 meshes. Review as abstract-reviewed, not as a journal full text.
- Date added
- 2026-08-22
- Retrieval
- Europe PMC no hit. User-supplied PDFs in this pass did not include this abstract.
- Stanford OpenURL
- libkey.io doi=10.58530/2023/0569
Hausman, 1962 — Atlases of the Spinal Cord and Brainstem
Book; no DOI
- Citation
- Hausman L. Atlases of the Spinal Cord and Brainstem and the Forebrain. Charles C. Thomas, Springfield, 1962.
- DOI
- none
- PMID
- none
- Proposed filename
- hausman1962-spinal-cord-brainstem-atlas.pdf
- Relevance
- AMU7T gray-matter parcels are derived from this atlas (AMU7T README). Not the PAM50 GM source.
- Date added
- 2026-08-22
- Retrieval
- Not an OA journal article. Methods-reviewed only if a legal copy is read. No DOI so no OpenURL.
Nieuwenhuys, Voogd and van Huijzen, 2008 — spinal cord topography chapter
Book chapter; PAM50 GM source
- Citation
- Nieuwenhuys R, Voogd J, van Huijzen C. Topography of spinal cord, brain stem and cerebellum. In: The Human Central Nervous System: a Synopsis and Atlas. Springer, 2008, pp. 177–245.
- DOI
- none recorded in De Leener 2018
- PMID
- none
- Proposed filename
- nieuwenhuys2008-spinal-cord-brainstem-topography.pdf
- Relevance
- De Leener 2018 built PAM50 gray-matter subregions from this atlas, not from Hausman 1962. Needed before any PAM50 GM mesh pass.
- Date added
- 2026-08-22
- Retrieval
- Book chapter. No DOI was given in the citing paper, so no OpenURL was built. Methods-reviewed only if a legal copy is read.
PAM50 NIfTI data licence (not a journal article)
Template exists; GitHub tree has no LICENSE file; not used
- Citation
- De Leener B, Fonov VS, Collins DL, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. NeuroImage 165, 170–179 (2018). Data: github.com/spinalcordtoolbox/PAM50 (release r20250730).
- DOI
- 10.1016/j.neuroimage.2017.10.041 (paper). Data licence: none on disk.
- PMID
- 29061527
- Proposed filename
- not a PDF; need LICENSE in third_party/pam50/
- Relevance
- Scientific target for T/L and brainstem occupancy columns. Paper already full-text-reviewed. SCT LGPLv3 covers the toolbox, not this data repo. neuropoly/template MIT covers the generation scripts, not the PAM50 voxels.
- Date added
- 2026-08-22
- Retrieval
- Checked 2026-08-22: recursive tree of release r20250730 (commit 31443641…) has no LICENSE/LICENCE/COPYING. Investigator decision 2026-08-22: do not use PAM50. A local cache from an earlier pass was deleted. Methods lists this source as not used. A later rights-holder licence file is still wanted if PAM50 is ever reconsidered.
- Stanford OpenURL
- paper only, doi=10.1016/j.neuroimage.2017.10.041
Brainstem Navigator toolkit terms (Bianciardi)
NITRC; v1.0 click-through forbids distributing copies or derived information outside the organization
- Citation
- Bianciardi M et al. Brainstem Navigator toolkit. NITRC. v1.0 released 2024-10-08. DOI 10.25790/bml0cm.96.
- DOI
- 10.25790/bml0cm.96
- PMID
- none for the toolkit
- Proposed filename
- not a PDF; licence text is in third_party/brainstem-navigator/LICENSE; atlas not used
- Relevance
- In-vivo 7 T probabilistic brainstem nuclei in MNI/IIT space. v1.0 terms are research-only and forbid distributing copies or derived information outside the organization. This project does not use the toolkit. AAN v2.0 does not include Sp5c.
- Date added
- 2026-08-22
- Retrieval
- NITRC v1.0 click-through read 2026-08-22 (
downloadlink.php/17381): non-commercial research only; “YOU MAY NOT DISTRIBUTE COPIES of the Brainstem Navigator files, or copies of files or of information derived from them, to others outside your organization.” Terms archived in third_party/brainstem-navigator/LICENSE. Investigator decision 2026-08-22: do not use this toolkit. Methods lists it as not used.
- Stanford OpenURL
- no journal DOI for the toolkit
Valošek et al., 2024 — automatic segmentation of spinal nerve rootlets
OA paper; derived PAM50_rootlets NIfTI shares PAM50’s missing data licence
- Citation
- Valošek J, Mathieu T, Schlienger R, Kowalczyk OS, Cohen-Adad J. Automatic segmentation of the spinal cord nerve rootlets. Imaging Neuroscience 2, imag-2-00218 (2024).
- DOI
- 10.1162/imag_a_00218
- PMID
- 40800300
- PMCID
- PMC12272210
- Proposed filename
- valosek2024-spinal-nerve-rootlets-segmentation.pdf
- Relevance
- Human C2–C8 dorsal rootlets on MRI; the model was also applied to PAM50 T2w to make PAM50_rootlets.nii.gz. That NIfTI is not used (same missing PAM50 data licence). The MIT repo ivadomed/model-spinal-rootlets is code, not the NIfTI.
- Date added
- 2026-08-22
- Retrieval
- Journal is CC BY. PDF not yet saved here. Do not vendor PAM50_rootlets.nii.gz from spinalcordtoolbox/PAM50 (no LICENSE). Methods lists it as not used.
- Stanford OpenURL
- libkey.io doi=10.1162/imag_a_00218