inm7 / jubrain-anatomy-toolbox

JuBrain Anatomy Toolbox

JuBrain Anatomy Toolbox v3.0

The JuBrain Anatomy Toolbox (a.k.a. SPM Anatomy Toolbox) is an SPM plugin with probabilistic cytoarchitectonic maps for combination with functional neuroimaging data.

Combining probabilistic cytoarchitectonic maps and functional imaging data.

Licensing

The copyright and all other rights related to the hereby provided products are held by Forschungszentrum Jülich GmbH. The use of the products is only permitted for own educational, scientific or private purposes. The source of the products must be quoted correctly. It is not allowed to revise or amend the provided products or extract only parts of it, e.g. the brain maps, without the explicit permission of Forschungszentrum Jülich GmbH. Likewise it is not allowed to grant sublicences to third partys.

References and Contact

Contact

For any questions and comments regarding the JuBrain Anatomy Toolbox please contact:

• Prof. Simon Eickhoff, Institute for Neuroscience and Medicine - Brain and Behaviour (INM-7), FZJ

For general questions and comments regarding cytoarchitectonic mapping please contact

• Prof.Katrin Amunts, Institute for Neuroscience and Medicine - Structural and functional organisation of the brain (INM-1), FZJ

References for the JuBrain Anatomy toolbox:

Eickhoff S, Stephan KE, Mohlberg H, Grefkes C, Fink GR, Amunts K, Zilles K: A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. NeuroImage 25(4), 1325-1335, 2005

Eickhoff, S.B.; Heim, S.; Zilles, K.; Amunts, K.: Testing anatomically specified hypotheses in functional imaging using cytoarchitectonic maps. NeuroImage 32(2), 570-582, 2006

Eickhoff SB, Paus T, Caspers S, Grosbras MH, Evans A, Zilles K, Amunts K Assignment of functional activations to probabilistic cytoarchitectonic areas revisited. NeuroImage 36(3), 511-521, 2007

References for probabilistic cytoarchitectonic mapping

Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145

Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065

Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602.

References for the individual areal distributed with the current release

Amygdala (superficial, latero-basal and centro-medial complex)

• Amunts,K. et al., (2005). Anat. Embryol. (Berl) 210, 343-352.

Hippocampus

• Amunts,K. et al., (2005). Anat. Embryol. (Berl) 210, 343-352.

Superior Parietal Cortex (Areas 5L, 5M, 5Ci, 7A, 7PC, 7M, 7P)

• Scheperjans et al. (2008a), Cereb. Cortex 18: 846-867
• Scheperjans et al. (2008b), Cereb. Cortex 18: 2141-2157

Inferior Parietal Cortex (Areas PFop, PFt, PF, PFm, PFcm, PGa, PGp)

• Caspers et al. (2006), NeuroImage 33, 430-448
• Caspers et al. (2008), Brain Struct. Funct. 212, 481-495

Intraparietal Sulcus (Areas hIP1, hIP2, hIP3)

• Choi et al. (2006), J. Comp. Neurol. 495, 53-69
• Scheperjans et al. (2008a), Cereb. Cortex 18: 846-867
• Scheperjans et al. (2008b), Cereb. Cortex 18: 2141-2157

BA 17 and BA 18 (V1 / V2)

• Amunts,K et al., (2000). Neuroimage. 11, 66-84.

Broca’s region (Area 44 / Area 45)

• Amunts,K. et al., (1999). J. Comp Neurol. 412, 319-341.
• Amunts,K. et al., (2004). NeuroImage 22, 42-56.

Frontal pole (Areas Fp1 and Fp2)

• Bludau et al., (2013). Neuroimage. 2, 260-275.

Medial orbitofrontal cortex (Areas Fo1 – Fo5)

• Henssen et al., (2015). Cortex. 75, 87-112.

Anterior cingulate cortex (Areas 25, 33, P24a, P24b, P24c, P32, S24 and S32)

• Palomero-Gallagher et al., (2008). J Comp Neurol. 508(6), 906-926.

Fiber tracts

• Burgel,U. et al., (2006). Neuroimage 29, 1092-1105.
• Burgel,U. et al., (1999) Neuroimage. 10(5), 489-99.

Parietal operculum / SII (Areas OP 1 – OP 4)

• Eickhoff,S.B et al., (2006). Cereb. Cortex 16, 254-267.
• Eickhoff,S.B et al., (2006). Cereb. Cortex 16, 268-279.

Premotor cortex (Area 6)

• Geyer,S. (2003). The Microstructural Border Between the Motor and the Cognitive Domain in the Human Cerebral Cortex (Wien: Springer).

Motor cortex (Areas 4a and 4p)

• Geyer,S. et al., (1996). Nature 382, 805-807.

Primary somatosensory cortex (Areas 3a, 3b, 1)

• Geyer,S. et al., (1999). Neuroimage. 10, 63-83.
• Geyer,S. et al., (2000). Neuroimage. 11, 684-696.

Primary somatosensory cortex (Areas 2)

• Grefkes,C. et al., (2001). Neuroimage. 14, 617-631.

hOC5 (V5 / MT+)

• Malikovic,A., et al., (2007). Cereb. Cortex 17, 562-574.

Primary auditory cortex (Areas TE 1.0, TE 1.1 and TE 1.2)

• Morosan,P. et al., (2001) Neuroimage 13, 684-701.

Posterior insula (Areas Ig1, Ig2, Id1)

• Kurth,F. et al., (2010) Cerebral Cortex 20(6): 1448-1461.

Ventral extrastriate cortex (V3v / V4)

• Rottschy,C., et al., (2007). Hum Brain Mapp. 28(10):1045-1059.

Dorsal extrastriate cortex (hOC3d / hOC4d)

• Kujovic et al., Brain Struct. Funct. 10.1007/s00429-012-0390-9, 2012.

Gyrus fusiformis (FG1, FG2)

• J. Caspers et al., Brain Struct. Funct., 10.1007/s00429-012-0411-8, 2012.

Mid-Fusiform Gyrus (Areas FG3 and FG4)

• Lorenz et al., (2015). Cereb Cortex. pii: bhv225

Lateral occipital cortex (extrastriate areas hOc4la and hOc4lp)

• Malikovic et al., (2016). Brain Struct Funct. 221(4), 1877-1897.

Frontal pole (Fp1, Fp2)

• S. Bludau et al., (2014) Neuroimage, 93(2), 260–275

Basal Forebrain (Ch1-3, Ch4)

• L. Zaborszky et al., (2008) Neuroimage, 42(3), 1127–1141

Cerebellar nuclei (DDN, VDN, EN, GN, FN)

• Tellmann et al., (2015). Front Neuroanat. 13, 9-54.

The JuBrain Anatomy Toolbox also include the Cerebellar atlas by Diedrichsen

Cerebellar atlas Diedrichsen,J. et al., (2009) Neuroimage. 46(1), 39-46. http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm

The JuBrain Anatomy Toolbox also include the Thalamic Connectivity atlas by Behrens

Behrens TE et al., (2003) Nat Neurosci. 6(7):750-7. http://www.fmrib.ox.ac.uk/connect/

jubrain-anatomy-toolbox's Issues

Fixed download - zipping bug in v3.0 distribution from Oct 2022

Hi,

Thanks a lot for this valuable software. I have been using it for over 12 years and it has always worked very well for me. However, today I faced an issue with it for the first time while setting up my new PC (Windows 10 Pro, Matlab 2022b) and thought of reporting it here along with the solution in the hope that it will help others.

In a nutshell, it looks like the current compression process is additionally zipping the JuBrain_Data_v30.mat into its own compressed folder. Currently, to use the software, that file must be unzipped and moved in the toolbox's root folder to complete the installation process, so that JuBrain_Data_v30.mat can then be selected when the user is prompted to "Select JuBrain Data file" (for some reason the .nii version is not visible via the GUI on my system). This is very easy to fix, so I am attaching a version of the toolbox with the fixed name and folder structure below.

On two other minor points:

1. The link to the official download webpage is broken - no file was downloaded from the forwarded link (notice the "Invalid date" warning in the screenshot below)

https://www.fz-juelich.de/en/inm/inm-7/resources/jubrain-anatomy-toolbox/jubrain-toolbox/toolbox_3/@@download/file

2. As it has been noted in the other Issues, currently one has to change the folder name from "jubrain-anatomy-toolbox-master" to "Anatomy" for the toolbox to appear within the spm12 GUI toolbox toggle.

Here is a version of the toolbox with the correct name and folder structure: https://drive.google.com/drive/folders/1qnaQtaM-ibJYbBX0RwAH2CBVAHV4bUtm?usp=sharing

Thanks again and best wishes,
Stav

Calculation of Maximum Probability Maps in v2.2

I need to calculate maximum probability maps for several regions (precisely, the amygdala subregions), but this option does not seem to be available anymore in the v2.2 release. The manual on the Jülich homepage ( https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html ) still contains this feature and I cannot find an updated manual. Is there still a way to do this in the new release?

Best wishes,
Maurizio

Version 3.0 doesn't launch from the Toolbox toggle in SPM anymore

Hey, thanks for your work on this useful toolbox. In all previous versions, we added the anatomy toolbox to the Toolbox folder in our SPM distribution. Anatomy Toolbox would then show up in the Toolbox toggle in the SPM GUI. This is no longer the case, and your manual doesn't specify a different install method. How should we set this up?

Thanks,

Douglas Garrett
Max Planck UCL Centre for Computational Psychiatry and Ageing Research
Berlin, Germany