IIT Human Brain Atlas (v.5.0) News

New manual

Konstantinos Arfanakis — Wed, 29 Dec 2021 2:29:32 GMT

We have updated the manual to include recommended track density thresholds for generating masks of major white matter bundles (pages 22-23). Users can apply the recommended thresholds to the track density images of the corresponding major white matter bundles (provided in IIT_bundles.zip) and convert the thresholded track density images to masks of zeroes and ones.

New, more user-friendly look-up tables for the WM labels

Konstantinos Arfanakis — Wed, 16 Sep 2020 1:41:10 GMT

We have updated the look-up tables for the labels of the WM atlas (LUT_WM_0to1.txt and LUT_WM_0to255.txt).
When using the old look-up tables in visualization software such as FSL and ITK-SNAP, only the numerical label ID was displayed e.g. label2776. With the new look-up tables the user can now see not only the numerical label ID, but also the names of the connected regions e.g. ctx-lh-superiorfrontal AND ctx-rh-superiorfrontal.
We have also updated the manual to reflect these changes.

New files provide the length of fiber connections

Konstantinos Arfanakis — Wed, 29 Jul 2020 12:52:35 GMT

New files providing the length of fiber connections of the IIT Human Brain Atlas have been added (IIT_WM_atlas_length.nii.gz and IIT_WM_atlas_length_256.nii.gz). These files demonstrate that the top layers of the multi-layer connectivity-based white matter labels DO NOT correspond to longer connections compared to lower layers (over-representation of long tracts is a known tractography concern). The top layers of the IIT Human Brain Atlas do not over-represent longer connections. The new files serve as a sort of quality check of the connectivity information the atlas is based on. A detailed description of the contents of the new files is provided in the updated manual.

New regionconnect is now available

Konstantinos Arfanakis — Fri, 17 Apr 2020 1:40:39 GMT

A new version of the regionconnect script is now available. The manual of the IIT Human Brain Atlas has also been updated to reflect the changes in regionconnect. All other files of version 5 of the atlas have remained the same.

What changed?
1) The new regionconnect is in python (the old version was in matlab).
2) The new version of regionconnect is faster than the old version.

What is regionconnect?
Regionconnect allows rapid extraction of standardized brain connectivity information for white matter regions with significant findings in voxel-wise neuroimaging studies. Regionconnect addresses a long-standing lack of specificity in terms of brain connectivity when reporting statistically significant findings in white matter. Regionconnect is based on the connectome of the IIT Human Brain Atlas v.5.0. Regionconnect does not require high angular resolution diffusion MRI or any MRI data, and can be used even in populations with certain brain lesions.

New manual (July 20th 2019)`

Konstantinos Arfanakis — Sat, 20 Jul 2019 7:18:44 GMT

The manual has been updated to include the names of the white matter bundles provided with the atlas.

Updates to version 5 of the IIT atlas are now available

Konstantinos Arfanakis — Tue, 09 Jul 2019 1:12:19 GMT

Few updates to version 5 of the IIT atlas are now available. More specifically:
1) An updated manual which now includes a) an updated chapter on how to use the IIT atlas in TBSS, and b) a new chapter on how to use the IIT atlas for ROI analyses in white matter.
2) New white matter bundles files (IIT_bundles.zip, IIT_bundles_skeletonized.zip, IIT_bundles_256.zip, IIT_bundles_skeletonized_256.zip) that now include the anterior commissure, the superior cerebellar peduncle, and updated middle cerebellar peduncle.

In addition, an ISMRM 2019 presentation on the development of the white matter resources of the IIT Human Brain Atlas v.5 has been uploaded to the Documents section, under Other supporting documents.

Version 5.0 of the IIT Human Brain Atlas is here!

Konstantinos Arfanakis — Tue, 14 May 2019 1:18:29 GMT

The new version of the IIT Human Brain Atlas (v.5.0) has been released! This version contains major updates of the gray and white matter atlas resources and structural templates. The new version also includes a new manual containing a description of the available resources and a number of HowTo's.

IIT Brain Atlas is used in paper introducing a new dementia

Konstantinos Arfanakis — Tue, 30 Apr 2019 9:14:21 GMT

The IIT Human Brain Atlas appears in Brain paper introducing a new devastating age-related brain disease: Limbic-predominant Age-related TDP-43 Encephalopathy (LATE).

See paper in the journal Brain here:
https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awz099/5481202?searchresult=1

See news stories on the paper here:
http://time.com/5580623/new-brain-degeneration-mimics-alzheimers/
https://www.apnews.com/791c3ea82e1a40a59d603cfc109d1ad9
https://www.bbc.com/news/health-48092570
https://www.nih.gov/news-events/news-releases/guidelines-proposed-newly-defined-alzheimers-brain-disorder
https://www.cnn.com/2019/04/30/health/dementia-late-alzheimers-study/index.html

Join our team!

Konstantinos Arfanakis — Fri, 01 Jun 2018 9:52:26 GMT

Two (2) Postdoctoral Fellow positions are now available at MRIIT. More details here: www.iit.edu/~mri/assets/img/main/postdoc_ad.pdf

IIT DTI template outperforms study-specific templates

Konstantinos Arfanakis — Fri, 01 Jun 2018 9:50:22 GMT

A comprehensive evaluation of standardized and study specific diffusion tensor templates published in Neuroimage demonstrates that the DTI template of the IIT Human Brain Atlas (v.3.0) outperforms available standardized and even study-specific templates constructed with state-of-the-art approaches. More details here: https://www.ncbi.nlm.nih.gov/pubmed/29414497