Please use our Zenodo based DOI for citing use of mgl in manuscripts:

The Zenodo site has a tool for how to format for different journals, but here is an example:

Gardner, JL, Merriam, EP, Schluppeck, D, Besle, J, & Heeger, DJ (2018). mrTools: Analysis and visualization package for functional magnetic resonance imaging data (Version 4.7). Zenodo. http://doi.org/10.5281/zenodo.1299483

Below is a partial list of publications that have used mrTools. As we did not use the Zenodo DOI until recently we did not explicitly track usage of mrTools and many of even our own papers do not mention its use. Some authors have cited the mrTools wiki documentation in Methods. This list was last updated in August, 2020. Please contact us if you have an update to this publication list.

Aghajari, S., Vinke, L., Ling, S. (2020). Population spatial frequency tuning in human early visual cortex Journal of Neurophysiology 123(2), 773-785. https://dx.doi.org/10.1152/jn.00291.2019

Aquino, K., Sokoliuk, R., Pakenham, D., Sanchez‐Panchuelo, R., Hanslmayr, S., Mayhew, S., Mullinger, K., Francis, S. (2018). Addressing challenges of high spatial resolution UHF fMRI for group analysis of higher‐order cognitive tasks: An inter‐sensory task directing attention between visual and somatosensory domains Human Brain Mapping 40(4), 1298-1316. https://dx.doi.org/10.1002/hbm.24450

Barbot, A., Das, A., Melnick, M., Cavanaugh, M., Merriam, E., Heeger, D., Huxlin, K. (2020). Changes in perilesional V1 underlie training-induced recovery in cortically-blind patients bioRxiv https://dx.doi.org/10.1101/2020.02.28.970285

Berezutskaya, J., Freudenburg, Z., Güçlü, U., Gerven, M., Ramsey, N. (2017). Neural tuning to low-level features of speech throughout the perisylvian cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience 37(33), 7906-7920. https://dx.doi.org/10.1523/jneurosci.0238-17.2017

Besle, J., Sánchez-Panchuelo, R., Bowtell, R., Francis, S., Schluppeck, D. (2013). Event-related fMRI at 7T reveals overlapping cortical representations for adjacent fingertips in S1 of individual subjects. Human brain mapping 35(5), 2027-43. https://dx.doi.org/10.1002/hbm.22310

Besle, J., Sánchez-Panchuelo, R., Bowtell, R., Francis, S., Schluppeck, D. (2013). Single-subject fMRI mapping at 7 T of the representation of fingertips in S1: a comparison of event-related and phase-encoding designs Journal of Neurophysiology 109(9), 2293-2305. https://dx.doi.org/10.1152/jn.00499.2012

Birman, D., Gardner, J. (2019). A flexible readout mechanism of human sensory representations. Nature communications 10(1), 3500. https://dx.doi.org/10.1038/s41467-019-11448-7

Birman, D., Gardner, J. (2018). A quantitative framework for motion visibility in human cortex. Journal of neurophysiology 120(4), 1824 1839. https://dx.doi.org/10.1152/jn.00433.2018

Connolly, J., Kentridge, R., Cavina-Pratesi, C. (2015). Coding of attention across the human intraparietal sulcus. Experimental brain research 234(3), 917-30. https://dx.doi.org/10.1007/s00221-015-4507-2

Connolly, J., Vuong, Q., Thiele, A. (2013). Gaze-dependent topography in human posterior parietal cortex. Cerebral cortex (New York, N.Y. : 1991) 25(6), 1519-26. https://dx.doi.org/10.1093/cercor/bht344

Dobs, K., Schultz, J., Bülthoff, I., Gardner, J. (2018). Task-dependent enhancement of facial expression and identity representations in human cortex. NeuroImage 172(), 689 702. https://dx.doi.org/10.1016/j.neuroimage.2018.02.013

Freeman, J., Brouwer, G., Heeger, D., Merriam, E. (2011). Orientation decoding depends on maps, not columns. Journal of Neuroscience 31(13), 4792 4804. https://dx.doi.org/10.1523/jneurosci.5160-10.2011

Freeman, J., Heeger, D., Merriam, E. (2013). Coarse-Scale Biases for Spirals and Orientation in Human Visual Cortex The Journal of neuroscience : the official journal of the Society for Neuroscience 33(50), 19695 19703. https://dx.doi.org/10.1523/jneurosci.0889-13.2013

Gaglianese, A., Vansteensel, M., Harvey, B., Dumoulin, S., Petridou, N., Ramsey, N. (2017). Correspondence between fMRI and electrophysiology during visual motion processing in human MT+ NeuroImage 155(), 480-489. https://dx.doi.org/10.1016/j.neuroimage.2017.04.007

Gaglianese, A., Costagli, M., Bernardi, G., Ricciardi, E., Pietrini, P. (2012). Evidence of a direct influence between the thalamus and hMT+ independent of V1 in the human brain as measured by fMRI. NeuroImage 60(2), 1440-7. https://dx.doi.org/10.1016/j.neuroimage.2012.01.093

Gaglianese, A., Costagli, M., Ueno, K., Ricciardi, E., Bernardi, G., Pietrini, P., Cheng, K. (2014). The direct, not V1-mediated, functional influence between the thalamus and middle temporal complex in the human brain is modulated by the speed of visual motion. Neuroscience 284(), 833-44. https://dx.doi.org/10.1016/j.neuroscience.2014.10.042

Gardner, J., Merriam, E., Movshon, J., Heeger, D. (2008). Maps of visual space in human occipital cortex are retinotopic, not spatiotopic. The Journal of neuroscience : the official journal of the Society for Neuroscience 28(15), 3988 3999. https://dx.doi.org/10.1523/jneurosci.5476-07.2008

Hara, Y., Pestilli, F., Gardner, J. (2014). Differing effects of attention in single-units and populations are well predicted by heterogeneous tuning and the normalization model of attention. Frontiers in computational neuroscience 8(), 12. https://dx.doi.org/10.3389/fncom.2014.00012

Hara, Y., Gardner, J. (2014). Encoding of graded changes in spatial specificity of prior cues in human visual cortex Journal of Neurophysiology 112(11), 2834-2849. https://dx.doi.org/10.1152/jn.00729.2013

Lennartsson, F., Nilsson, M., Flodmark, O., Jacobson, L., Larsson, J. (2018). Injuries to the Immature Optic Radiation Show Correlated Thinning of the Macular Ganglion Cell Layer Frontiers in Neurology 9(), 321. https://dx.doi.org/10.3389/fneur.2018.00321

Liu, T., Hospadaruk, L., Zhu, D., Gardner, J. (2011). Feature-specific attentional priority signals in human cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience 31(12), 4484 4495. https://dx.doi.org/10.1523/jneurosci.5745-10.2011

Liu, T., Cable, D., Gardner, J. (2017). Inverted encoding models of human population response conflate noise and neural tuning width. The Journal of Neuroscience 38(2), 398-408. https://dx.doi.org/10.1523/jneurosci.2453-17.2017

Merriam, E., Gardner, J., Movshon, J., Heeger, D. (2013). Modulation of visual responses by gaze direction in human visual cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience 33(24), 9879 9889. https://dx.doi.org/10.1523/jneurosci.0500-12.2013

Olman, C., Harel, N., Feinberg, D., He, S., Zhang, P., Ugurbil, K., Yacoub, E. (2012). Layer-specific fMRI reflects different neuronal computations at different depths in human V1. PloS one 7(3), e32536. https://dx.doi.org/10.1371/journal.pone.0032536

O’Neill, G., Sengupta, A., Asghar, M., Barratt, E., Besle, J., Schluppeck, D., Francis, S., Panchuelo, R. (2020). A probabilistic atlas of finger dominance in the primary somatosensory cortex NeuroImage 217(), 116880. https://dx.doi.org/10.1016/j.neuroimage.2020.116880

Panchuelo, R., Besle, J., Schluppeck, D., Humberstone, M., Francis, S. (2018). Somatotopy in the Human Somatosensory System Frontiers in Human Neuroscience 12(), 235. https://dx.doi.org/10.3389/fnhum.2018.00235

Pestilli, F., Carrasco, M., Heeger, D., Gardner, J. (2011). Attentional enhancement via selection and pooling of early sensory responses in human visual cortex. Neuron 72(5), 832 846. https://dx.doi.org/10.1016/j.neuron.2011.09.025

Roth, Z., Heeger, D., Merriam, E. (2018). Stimulus vignetting and orientation selectivity in human visual cortex eLife 7(), e37241. https://dx.doi.org/10.7554/elife.37241

Sanchez-Panchuelo, R., Francis, S., Bowtell, R., Schluppeck, D. (2010). Mapping Human Somatosensory Cortex in Individual Subjects With 7T Functional MRI Journal of Neurophysiology 103(5), 2544-2556. https://dx.doi.org/10.1152/jn.01017.2009

Sanchez-Panchuelo, R., Besle, J., Beckett, A., Bowtell, R., Schluppeck, D., Francis, S. (2012). Within-digit functional parcellation of Brodmann areas of the human primary somatosensory cortex using functional magnetic resonance imaging at 7 tesla. The Journal of neuroscience : the official journal of the Society for Neuroscience 32(45), 15815 15822. https://dx.doi.org/10.1523/jneurosci.2501-12.2012

Sánchez-Panchuelo, R., Besle, J., Mougin, O., Gowland, P., Bowtell, R., Schluppeck, D., Francis, S. (2013). Regional structural differences across functionally parcellated Brodmann areas of human primary somatosensory cortex. NeuroImage 93 Pt 2(), 221-30. https://dx.doi.org/10.1016/j.neuroimage.2013.03.044

Sun, P., Gardner, J., Costagli, M., Ueno, K., Waggoner, R., Tanaka, K., Cheng, K. (2013). Demonstration of Tuning to Stimulus Orientation in the Human Visual Cortex: A High-Resolution fMRI Study with a Novel Continuous and Periodic Stimulation Paradigm Cerebral Cortex 23(7), 1618-1629. https://dx.doi.org/10.1093/cercor/bhs149

Vintch, B., Gardner, J. (2014). Cortical correlates of human motion perception biases. Journal of Neuroscience 34(7), 2592 2604. https://dx.doi.org/10.1523/jneurosci.2809-13.2014

Wang, H., Merriam, E., Freeman, J., Heeger, D. (2014). Motion Direction Biases and Decoding in Human Visual Cortex The Journal of neuroscience : the official journal of the Society for Neuroscience 34(37), 12601 12615. https://dx.doi.org/10.1523/jneurosci.1034-14.2014

Wardle, S., Ritchie, J., Seymour, K., Carlson, T. (2016). Edge-related activity is not necessary to explain orientation decoding in human visual cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience 37(5), 1187-1196. https://dx.doi.org/10.1523/jneurosci.2690-16.2016