Project_larynx

General information:

• Data in this repository has been acquired as part of Nicole Eichert's PhD project at the University of Oxford, which was supervised by Rogier B. Mars and Kate E. Watkins.

• Funding for this project was provided by the Wellcome Trust [203730/Z/16/Z]

• Data in this repository has been used in multiple projects that involved different collaborators. For project-specific authorship and acknowledgements, please refer to the relevant references.

• Main data papers:

  • Eichert N, Robinson EC, Bryant KL, Jbabdi S, Jenkinson M, Li L, Krug K, Watkins KE, Mars RB. 2020. Cross-species cortical alignment identifies different types of anatomical reorganization in the primate temporal lobe. eLife 9. doi:10.7554/eLife.53232
  • Eichert N, Papp D, Mars RB, Watkins KE. 2020. Mapping Human Laryngeal Motor Cortex during Vocalization. Cerebral Cortex 30:6254–6269. doi:10.1093/cercor/bhaa182
  • Eichert N, Watkins KE, Mars RB, Petrides M. 2020. Morphological and functional variability in central and subcentral motor cortex of the human brain. Brain Structure and Function (accepted). doi:10.1007/s00429-020-02180-w

• not all scripts in the related code repositories run directly on the OpenNeuro dataset because it does not contain all intermediate data

• all missing intermediate data can, in principle, be reconstructed using the provided code, but file paths might have to be adapted

Data related to Eichert et al. 2020 eLife:

• related processing code and result scene files can be found at https://git.fmrib.ox.ac.uk/neichert/project_msm
• relevant data are subfolder /dwi, surface reconstructions and T1w/T2w myelin maps

Data related to Eichert et al. 2020 Cerebral Cortex:

• related processing code can be found at https://git.fmrib.ox.ac.uk/neichert/project_larynx

• the first 25 volumes of all individual bold task scans need to be discarded prior to analysis. These volumes were acquired during the time, where noise-cancelling headphones 'learned' the scanner noise

• the fieldmap for subject 11 can only be applied to the 'ArtVoc' bold task scan and not to the 'Factorial' bold task scan

• average inflated surfaces are stored in /derivatives/group/anat/group.{hemi}.inflated.32k_fs_LR.surf.gii (and 164k)

• individual native midthickness surfaces are stored in /derivatives/sub-{sub}/anat/sub-{sub}.{hemi}.midthickness.native.surf.gii

• Figure 1C - breathing traces:

  • cropped individual breathing traces are stored in /derivatives/sub-{sub}/beh/sub-{sub}_breathing-traces.pkl. The file can be loaded using Python's pandas package.
  • raw data containing subject's breathing traces during the functional scan is stored in /sub-{sub}/beh/sub-{sub}/sub-{sub}_biopac.mat

• Figure 2 and Figure 3 - group level fMRI results:

  • task: 'ArtVoc' for the basic localizer task and 'Factorial' for the syllable production task
  • contrast: lip, tongue, vowel for 'ArtVoc' (Figure 3); vocalization, articulation for 'Factorial' (Figure 2)
  • volumetric results in MNI space are stored in /derivatives/group/func/task/group_task-{task}_{contrast}_zstat1.nii.gz
  • surface count maps are stored in /derivatives/group/func/task/group_task-{task}_{contrast}_{hemi}_32k_fs_LR.func.gii

• Figure 4 - surface metrics

  • average T1w/T2w and thickness maps are stored in /derivatives/group/anat
  • averate mpm maps are stored in /derivatives/group/mpm
  • individual surface maps are stored in derivatives/sub-{sub}/anat and derivatives/sub-{sub}/mpm

• Figure 5 - quantitative analysis

  • numerical values underlying the figures are stored as csv-files in /derivatives/group/mpm/*csv

Data related to Eichert et al. 2020 Brain Structure and Function:

• related processing code can be found at https://git.fmrib.ox.ac.uk/neichert/project_variability

• Subject-IDs 01 - 20 refer to the subjects that contributed both structural and functional data (also used for the other two papers)

• Subject-IDs 21 - 50 refer to the HCP subjects that only contributed structural data (to be shared)

• Fig. 1B - individual example

  • data of sub-20 is shown

• Fig. 3 - probability maps

  • volumetric and surface probability maps are stored in /derivatives/group/sulci/

• Fig. 4 - Anatomical measures:

  • numerical values are provided in the file /derivatives/group/sulci/anatomical_quantifications.csv

• Fig. 5 - All individual sulci and peaks

  • all individual sulcal labels and functional activation peaks in native space are provided in the files /derivatives/sub-{sub}/anat/sulci_{hemi}.label.gii and derivatives/sub-{sub}/func/peaks_{hemi}.func.gii
  • the manually drawn ventral ROI to extract the ventral peak is provided in /derivatives/sub-{sub}/anat/ventral_ROI_{hemi}.func.gii
  • they can be displayed together with the native surface in /derivatives/sub-{sub}/anat/sub-{sub}.{hemi}.midthickness.native.surf.gii

• Fig. 6 - Effect of registrations

  • numerical values are provided in the file /derivatives/group/anat/sulci/peak_distances.csv

• Fig. 7 (Supplementary Material) - Anatomical measures per morphological type

  • numerical values are provided in the file /derivatives/group/sulci/anatomical_quantifications.csv

• Table 1 - Morphological types

  • numbers can be inferred from the provided csv file /derivatives/group/sulci/structure_function_links.csv

• Table 2 - Coordinates

  • can be derived from volumetric probability maps

• Table 3 - Structure-function-relationships

  • numbers can be inferred from the provided csv file /derivatives/group/sulci/structure_function_links.csv

https://openneuro.org/datasets/ds002634