How can I Download and Install BRANT¶
- You can get the latest version of BRANT from
- Some functions are based on SPM, you can get it from
- Circos in STEP 8 can be downloaded from
- Unzip the brant-master.zip file and move both brant and spm12 folders to
/path/of/toolbox. (The path can be anywhere in your computer as long as it’s in English)
- Configure SPM paths:
- Click Set Path in MATLAB
- Click add folder
- Select SPM’s root folder
spm fmriin MATLAB’s Command Window to let spm add its subfolders. (Note that some SPM’s subfolders are called internally in SPM and should not be added in MATLAB’s search path. Scripts in those folders are conflicting with MATLAB functions, and could cause untraceable errors)
- Configure BRANT paths:
- Click Set Path in MATLAB
- Click Add with subfolders
- Select the unzipped BRANT folder
- Click Save.
- An alternative way to configure both SPM and BRANT Paths:
- Run in MATLAB’s Command Window:
cd('/path/of/unzipped/brant/');% to set current working directory to the unzipped brant
brant_configure_paths;% to add BRANT paths (same as add with subfolders)
brant_configure_paths('/path/of/spm12/');% to add SPM paths
What is BRANT’s Advantage Compared with Other Matlab-based Toolboxes¶
Compared with DPABI v2.3, GRETNA v2.0.0 and CONN v17.f, the differences are listed in the table below.
In conclusion, BRANT can directly support
*.gz for most postprocessing functions, use OPENCL-based parallel computing for time consuming FCD/FCS calculation to save time. Other than focusing on several specific types of rs-fMRI data processing, functions of BRANT cover a wide range of rs-fMRI data processing methods. Also, GUIs are created automatically with a few lines of MATLAB code instead of drawn manually.
How to Format Tables Correctly¶
In some fuctions, you may have to use some
*.csvfiles to input data. If you cannot find any proper existed
*.csvfiles, you can create a
*.csvfile by Excel or Notepad. e.g.
- STEP 4 => FC => Draw ROI => Coordinates in txt or csv file (input type: file)
x y z label 40 -16 50 ROI1 -40 -16 50 ROI2
- STEP 6 => STAT => T-Tests => table
name group age sex NC_02_0001_fMRI grp1 31 0 NC_02_0002_fMRI grp2 27 0 NC_02_0003_fMRI grp1 36 0 NC_02_0004_fMRI grp2 37 1
If you select paired t-test, the table should contain an additional column of paired_t_idx
name group filter age paired_t_idx subj1 stage1 center1 28 1 subj2 stage1 center1 27 2 subj3 stage2 center1 30 1 subj4 stage2 center2 25 2
- STEP 8 => VIEW => Network Visualization => node
x y z label vox_num index -4.6213 15.6 53.2468 A8m_l 235 1 … … … … … …
brant_roi_info.csvfile can be found in the folder as the out dir of ROI Calculation in STEP 4.
- STEP 8 => Embedded => Circos => roi info
x y z label_old label vox_num index module index_module index_node -4.6213 15.6 53.2468 SFG_L_7_1 A8m_l 235 1 SFG 1 1 … … … … … … … … … …
brant_circos_3mm_273.csvfile can be found in the
What can I Do When an Error Occurs¶
- Here are some common errors with their reasons and solutions below. You can also modify parameters with the help of examples and rerun former steps. If these all cannot work, please contact us.
- Reason: Misuse id index.
- Solution: Delete files created before the error occurs. Read example to use id index properly.
- Reason: The preprocessing may be interrupted and create wrong
- Solution: Delete files created during preprocessing, examine your preprocessing settings and run preprocessing again.
- Reason: TR(s) in Preprocessing is zero.
- Solution: Set tr(s) in Silce Timing to a legal value.
- Reason: The table file is incorrect.
- Solution: Confirm that the table file contains a row with group information and contains only one row. Open it with notepad to check if the data in this file is divided by comma.
- Reason: More than one
*.niifiles were found in above directories.
- Solution: Uncheck the delete first N timepoints or convert just one set of data per time.