__Please note that none of these files/folders have been made available online__, because the MRI data were acquired prior to this study and belong to other researchers, and because the metadata sometimes contains the initials of participants (in the scan names). The following description is only included here for the sake of completeness. # File structure Each subject has one folder, with the name of the MRI scan. The coupling between the subject IDs ("S01", "S28", etc.) and the folder/scan names is in `screenshot_notes.csv`. See the following subsections for description of the contents of each subject folder. ## Screenshots Inside each subject folder, there should be at least 4 image files (subjects with functional data have more screenshots with it overlaid). These are screenshots of the neuroanatomical markers that are required for the neuronavigation procedure: * `_nasion.png`: marks the coordinates of the nasion. * `_LPA.png`: marks the coordinates of the Left Pre-Auricular point, in this case defined as the intersection between the tragus and the helix. * `_RPA.png`: same as `_LPA.png`, but for the right ear. * `_rFEF.png`: marks the presumed coordinates of the right Frontal Eye Field. ## `from_neuronav` folder These files were all generated by / taken from the neuronavigation PC: * `.nii` file: This is the NIfTI file that was used on the neuronavigation PC (it could not read compressed NIfTI files). This is not necessarily the same as the original `.nii` file we received, as sometimes these were not read in correctly by the neuronavigation software. In that case, we resaved the file (thereby modifying the header information) using [MRIcron software][mricron]. * `_mrk.png` file: This is a screenshot of the marker that was placed using the neuronavigation software. Note that this marker was placed 5mm more posterior (i.e. subtracted 5 voxels in the Y-direction) than the presumed FEF location (as depicted in `_rFEF.png`) * `.asc` file: Information on markers generated by the neuronavigation software (we did not use this for anything). [mricron]: www.mccauslandcenter.sc.edu/crnl/mricron/ ## `orig` folder If a subject has an `orig` folder, these will be the MRI files as we got them from the researcher. Usually this will be a compressed NIfTI file (`.nii.gz`); sometimes we (also) got the original PAR/REC files as they came from the scanner. ## `registration` folder These files are the processed MRI data and were created with [FSL][fsl]. Files created as output of the `src/func/mni_coords.sh` shell script (see the `code` component): * `_reorient.nii.gz`: created using `fslreorient2std`, such that the orientations of the scans matches that of the MRI template * `_reorient_brain.nii.gz`: skull-stripped scan (using FSL `bet`) * `_reorient_brain_toMNI1mm.nii.gz`: scan registered to the MNI152 1mm template (using FSL `flirt`) * `_native2mNI.mat`: file with transformation matrix created by `flirt` Files created as output of the `src/func/fef_rois.sh` shell script: * `_FEF_vox.nii.gz`: mask of the MNI template where all voxels are set to an intensity of 0, and the voxel with the presumed FEF location is set to 1 * `_FEF_sphere.nii.gz`: same `_FEF_vox.nii.gz`, but then the region with intensity of 1 consists of a sphere inflated around the FEF voxel. These files can be used to visualize the location of the individual frontal eye fields. [fsl]: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki ## `func` folder Only subjects with functional data have this folder, which contains .nii and .txt files that were used to pick the cluster assumed to be the FEF. # Coordinates and corrections We manually checked whether the procedure for identifying the FEF was followed correctly, which is detailed in `screenshot_notes.csv`. This table contains the following columns: * __subject__: the subject ID ("S01", "S28", etc.) * __folder__: the name of the folder housing the MRI data (named after the scan) * __scan__: the full name that is prefixed to the MRI scans * __FEF screenshot coordinate__: Coordinate as show on the `_rFEF.png` screenshot, which was taken before the data were entered into the neuronavigation system. * __"Neuronavigation marker coordinate"__ Coordinate as show on the `from_neuronav/*_mrk.png` screenshot, which was taken on the neuronavigation system after the data were entered there. * __Match between coordinates?__: The X- and Z-coordinates should be identical; the Y-coordinate of the neuronavigation coordinate on the `from_neuronav/*_mrk.png` screenshot should be 5 less than the coordinate in `_rFEF.png`, because of the placement procedure. If they don't match, the `_rFEF.png` screenshot could be outdated, for instance because the rFEF location was re-determined, but no screenshot was taken. * __"Match between neuronavigation scan and FEF screenshot?"__ For this check, the `from_neuronav/.nii` scan taken from the neuronavigation system was loaded into *MRIcron* (this program was almost exclusively used to take the screenshots). Navigating to the coordinate from the `_rFEF.png` should yield the same slice view as in the screenshot. If it doesn't match, the screenshot was taken on a different scan, i.e. the data that was entered into the neuronavigation system was different from the original, e.g. because it was altered before neuronavigation. This means the coordinate from the FEF screenshot cannot be used verbatim. * __Match between neuronavigation scan and marker screenshot?__ For this check, the `from_neuronav/*.nii` scan taken from the neuronavigation system was loaded into *MRIcron* (this program was almost exclusively used to take the screenshots). Navigating to the coordinate from the `from_neuronav/*_mrk.png` should yield the same slice view as in the screenshot. If it doesn't match, this means the neuronavigation did not read in the data the same way as *MRIcron* did. * __Match between FSL and MRIcron?__ If the coordinates from the screenshot are to be used in FSL, FSL must read in the scan the same way as MRIcron does, but this is not always the case. Note that the coordinate system in the two viewers is always slightly different: MRIcron coordinates start at 1, FSL coordinates start at 0. So this correction always has to be taken into account. Another problem is that the X-coordinate axis in FSL is sometimes flipped, such that the coordinates selected in MRIcron are suddenly in the left hemisphere instead of the right. In these cases MRIcron counts right-to-left, from e.g. 256 to 1, while FSL counts left-to-right, from e.g. 0-255. Whenever this happens, the coordinates can be corrected as follows: - from MRIcron to FSL: FSL_coord = max_MRIcron_coord - MRIcron_coord - from FSL to MRIcron: MRIcron_coord = (max_FSL_coord + 1) - FSL_coord * __Corrections__: Sometimes, the checks in the 4 previous columns were not passed. This column describes how that was corrected for; the most frequent corrections being: 1. If the coordinate can not be determined from the FEF screenshot, it can be determined from the neuronavigation screenshot instead, by adding +5 voxels (i.e. more anterior) to the Y-coordinate. 2. For the neuronav data, the x-axis in FSL is sometimes, but not always +R (i.e. X voxel coordinates increase when moving rightwards) instead of +L like in MRIcron. In that case the x-axis correction has to be applied to the FEF coordinate. Here is a graphical representation of the entire checking and correction procedure (which can be rendered with [mermaid]): [mermaid]: https://mermaidjs.github.io/ ```mermaid graph TD A[Match between coordinates?] B[Match neuronav and FEF screenshot?] C[Match neuronav and marker screenshot?] D[Match between FSL and MRIcron?] corr{Corrrectable?} neuronav(Use neuronav coord) add(Add 5 mm to Y-coord) vis(Visually match to neuronav screenshot) neuronav_corr(Correct neuronav coord) A -->|yes/no| B B --> |yes| C B --> |no| C C --> |yes| D C --> |no| vis vis --> D D--> |yes| neuronav D--> |no| corr corr-.-> |yes| neuronav_corr corr-.-> |no| vis neuronav-->add vis--> add neuronav_corr--> add ```