Viewers

Which file opens where

The Editor picks the viewer from the file's name and folder, without reading the file (DICOM is the one exception: its first bytes are read).

A BrainVision recording opens from its .vhdr, not from its .eeg or .vmrk.

The image viewer

The toolbar, from left to right: the layout; Time course (for a 4-D image); Slice; Volume and Play for a 4-D image; QC (the quality check and the maps of a series); Tools (overlays, the header and sidecar, the next run, echo, session or subject, a fieldmap of this image drawn over it); Save (a screenshot, a mosaic figure, a preset, a scene, the command line); and at the right the keyboard icon, which lists the shortcuts. Advanced controls is the strip on the right edge of the images (⌘I on macOS, Ctrl+I on Windows and Linux). Comparing two images is in the Editor's Tools > Compare images....

Advanced controls opens a column with every control, in sections: the layers (each image and overlay, its colour map, window, gamma and opacity), the slice views, the layout, and for 3-D its look, the clip planes and the lighting.

The viewer remembers how you last looked at each kind of image: a BOLD run opens with its time course, a T1w with what you set for anatomical images. Restore every viewer default... puts back the defaults.

Keys

On a Mac, ⌘ is Command, ⌥ Option, ⌃ Control and ⇧ Shift. Keys are shown for the system this page was opened on; where it cannot tell, for both.

Mouse, on a slice

Mouse, in 3-D

The signal viewer

For MEG, EEG and physiological recordings. The toolbar sets how many channels are shown, the scaling, the time span and the filter; Advanced controls chooses the channel type or single channels, and Events there (or E) draws the task's events over the traces; QC checks the recording channel by channel; Annotate marks bad channels and segments; PSD opens the power spectrum. The overview bar at the bottom shows the whole recording; drag in it to move.

Save to dataset writes the bad channels into the status column of the recording's channels.tsv, and the bad segments as BAD_ rows of its events.tsv (which MNE-BIDS reads back as annotations), as one operation recorded in the project. The task's own events are kept.

Keys

On a Mac, ⌘ is Command, ⌥ Option, ⌃ Control and ⇧ Shift. Keys are shown for the system this page was opened on; where it cannot tell, for both.

Mouse

The spectrum viewer

For MR spectroscopy. The spectrum is drawn against chemical shift in ppm, from right to left, with the main metabolites marked; FID shows the signal over time. Advanced controls sets the line broadening, the phase (or Auto phase), which repeat is shown, and the reference; On anatomy shows the voxel on the participant's anatomical image.

Keys

On a Mac, ⌘ is Command, ⌥ Option, ⌃ Control and ⇧ Shift. Keys are shown for the system this page was opened on; where it cannot tell, for both.

Saving what you see

A preset or a scene applies only what an image has: a time-course setting is ignored on an anatomical image.

From the command line

bidsmgr-view opens an image, a scene or an overlay in the viewer without the rest of BIDS Manager. With --render it draws the view into a PNG with no window at all, which works on a server.

$ bidsmgr-view sub-001/ses-01/anat/sub-001_ses-01_acq-tfl3p2_T1w.nii.gz
$ bidsmgr-view T1w.nii.gz --render t1.png --planes axial coronal --height 400

Every option is in Command line.