Preprocessing codes for the rat rs-fMRI database www.nitrc.org/projects/rat_rsfmri.
- GIFT ICA toolbox. (https://www.nitrc.org/projects/gift)
- jsonlab. (https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files)
- Tools for NIfTI and ANALYZE image (https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image)
- despiking.m
Discard frames with excessive motion in data (aka motion scrubbing). - alignment_checking_tool.m
A graphcial user interface (GUI) to manually coregister a rsfMRI scan to a template. - pre_ic_labeling.m
Motion correction (save motion parameters);
Run independent component analysis (ICA) with the GIFT ICA toolbox to identify noisy independent components (ICs);
Spatial smoothing;
Save averaged WM/CSF signal. - copy_ica_results_4labeling.m
Copy ICA results to an temporary folder for the ease of manual labeling.
Save spatial maps, time courses, and frequency spetrums of the ICs to figures. - ica_cleaning_view.m
A GUI to manually label the ICs. - copy_labels.m
Copy IC labels to the database folder. - post_ic_labeling.m
Soft IC-regressing the spatially-smoothed images, along with the motion parameters and averaged WM/CSF signal;
Temporal filtering.
./
├── rat001
│ ├── rat001_info.json [Sequence names, acquisition dates, number of frames, and corresponding names inside folders]
│ ├── raw [Nifti files converted from raw Bruker data using Bru2Nii (https://github.com/neurolabusc/Bru2Nii)]
│ │ ├── X2P1.nii
│ │ ├── X4P1.nii
│ │ ├── X7P1.nii
│ │ ├── X8P1.nii
│ │ └── ...
│ ├── rfmri_unprocessed [rsfMRI scans from the folder 'raw']
│ │ ├── 01.nii
│ │ ├── 02.nii
│ │ ├── 03.nii
│ │ └── 04.nii
│ ├── rfmri_intermediate [Intermediate files generated from preprocessing]
│ │ ├── 01_despiked.json
│ │ ├── 01_despiked.nii.gz [Not further processed since more than 10% of the frames were motion-scrubbed]
│ │ ├── 02_despiked.json
│ │ ├── 02_despiked.nii.gz [Despiked image]
│ │ ├── 02_registered.json
│ │ ├── 02_registered.nii.gz [Manually coregistered image]
│ │ ├── 02_motioncorrected.json
│ │ ├── 02_motioncorrected.nii.gz [Motion corrected image]
│ │ ├── 02_motion.json
│ │ ├── 02_motion.txt [Motion parameters]
│ │ ├── 02.gift_ica [Results from single-scan ICA]
│ │ │ ├── ica__ica_br1.mat
│ │ │ ├── ica__ica_c1-1.mat
│ │ │ ├── ica__ica.mat
│ │ │ ├── ica__icasso_results.mat
│ │ │ ├── ica_Mask.hdr
│ │ │ ├── ica_Mask.img
│ │ │ ├── ica__pca_r1-1.mat
│ │ │ ├── ica__postprocess_results.mat
│ │ │ ├── ica__results.log
│ │ │ ├── ica__sub01\_component\_ica\_s1_.mat
│ │ │ ├── ica__sub01\_component\_ica\_s1_.nii
│ │ │ ├── ica__sub01\_timecourses\_ica\_s1_.nii
│ │ │ ├── ica_Subject.mat
│ │ │ └── labels.csv [IC labels: only the ones labeled with 'noise' were soft-regressed]
│ │ ├── 02\_WMCSF_timeseries.json
│ │ ├── 02\_WMCSF_timeseries.txt [Averaged signal from white matter and ventricle voxels]
│ │ ├── ...
│ └── rfmri_processed [Preprocessed images]
│ ├── 02.json
│ ├── 02.nii
│ ├── 04.json
│ └── 04.nii
├── rat002
│ ├── ...