Use this file to discover all available pages before exploring further.
DCEMapper supports four distinct ways to open data, all accessible through File → Open in the top menu bar. Whether you are starting from a raw Bruker scanner export, a BIDS-organized study, a single NIfTI scan, or a previously generated parametric map, there is a loading mode designed for your workflow.
File → Open → Open BIDSUse this mode when your data is organized according to the Brain Imaging Data Structure (BIDS) standard. DCEMapper will recursively scan the selected folder for all NIfTI files and queue them for batch analysis.Steps:
Click File → Open → Open BIDS.
In the directory picker, select the root folder of your BIDS dataset (e.g., my_study/).
DCEMapper calls get_files_to_process() internally to discover all .nii.gz and .nii files across subjects and sessions.
The first subject is loaded immediately. Use File → Next and File → Previous to navigate between subjects.
DCEMapper writes preprocessed and processed outputs into a derivatives/ subfolder alongside the source data.
The Next and Previous menu actions are only enabled when more than one subject file was found by get_files_to_process(). For a single-file BIDS folder they remain disabled.
File → Open → Open NIfTI FileUse this mode to load one DCE-MRI scan directly, without requiring a BIDS folder structure. This is the quickest way to inspect an individual acquisition.Steps:
Click File → Open → Open NIfTI File.
A file dialog opens filtered to *.nii.gz and *.nii files.
Select your NIfTI file and click Open.
The viewer loads the 4-D volume immediately.
The parent directory of the selected file is used as the derivative_folder for any outputs generated during preprocessing or processing. Subject navigation (Next/Previous) is disabled in this mode.Supported formats:
File → Open → Open Process FileUse this mode to reload a parametric map that was previously generated by DCEMapper’s semi-quantitative pipeline (for example rce_process.nii.gz, rce_max_process.nii.gz, or tto_rce_max_process.nii.gz). The viewer is preconfigured for inspecting output maps.Steps:
Click File → Open → Open Process File.
In the file dialog (filtered to *.nii.gz and *.nii), navigate to your derivatives folder and select any of the three process output files.
DCEMapper automatically locates the companion rce_process, rce_max_process, and tto_rce_max_process files in the same directory.
The canvas switches to the jet colormap and the viewer toolbar enables the RCE / MAX RCE / TTP view-toggle buttons.
If you select rce_max_process.nii.gz or tto_rce_max_process.nii.gz, DCEMapper normalises the path internally and still loads the full set of three maps, so you can switch between views without reloading.
File → Open → Open Bruker FileUse this mode when your data comes directly off a Bruker MRI system. DCEMapper calls convert_studies_from_bruker() to convert the proprietary Bruker format to NIfTI/JSON files organised in a BIDS-like sourcedata/ structure, then loads the results automatically.Steps:
Click File → Open → Open Bruker File.
Select the folder that contains Bruker subject files or .zip archives.
DCEMapper scans for all nested subject manifests and ZIP archives.
For each study, convert_studies_from_bruker() is called:
Each scan/reconstruction pair is extracted with brkraw.
Images are saved as <subject>_ses-<session>_acq-<scan_id>_run-<reco_id>_<modality>.nii.gz.
BIDS-compatible JSON sidecar files are written alongside each NIfTI.
Time fields (RepetitionTime, EchoTime, InversionTime) are automatically converted from milliseconds to seconds.
Converted files are placed under <input_parent>/sourcedata/.
DCEMapper then calls get_files_to_process() on the converted output and loads the first DCE file.
Output structure:
sourcedata/└── sub-B060326_ses-WTF1/ ├── func/ │ ├── sub-B060326_ses-WTF1_acq-10_run-1_dce.nii.gz │ └── sub-B060326_ses-WTF1_acq-10_run-1_dce.json └── ...conversion_report.log ← only written when errors occurred
If any scan or reconstruction fails to convert, the error is recorded in conversion_report.log in the parent output directory. Successfully converted studies are still loaded; only the failed scans are skipped.
Derived and parametric maps (Bruker DERIVED_ISA series) are automatically excluded from conversion.
Once a file is loaded, DCEMapper displays a resizable three-panel workspace:
Left Panel — Slice Selector
A scrollable thumbnail grid showing all axial slices of the volume at time-point 0. Click any thumbnail to jump directly to that Z-slice in the main canvas. The column count adjusts automatically as you resize the panel.
Center Panel — Main Canvas
The primary matplotlib figure displaying the currently selected slice at the current time point. The matplotlib navigation toolbar (pan, zoom, home, zoom history) is docked above the canvas.
Right Panel — Intensity Graph
An IntensityGraph widget plotting the time-series signal for the last voxel clicked, alongside a scrollable Clicks record log showing X, Y, Z coordinates and percentage intensity increase for every click.
Drag the dividers between panels to redistribute horizontal space. Press R to restore the default panel proportions at any time.
The Mask submenu is found at File → Mask and contains two actions:
Save current Mask — saves the current 3-D ROI mask as a NIfTI file to a directory you choose.
Open mask — loads a previously saved mask NIfTI and applies it to the currently loaded volume.
These actions are available immediately after a file is loaded. See ROI Tools for details on drawing and managing masks.