How can I Download and Install BRANT¶
- You can get 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. Move the brant folder and spm12 folder to */Matlab/toolbox.
- Open Matlab, use Set Path and add folders above with subfolders or use the configuration function in BRANT(recommended).
There is a configuration function in BRANT. Use cd(‘*/Matlab/toolbox’) to set the directory of matlab, then print brant_configure_paths in matlab to configure BRANT or print brant_configure_paths(‘*/Matlab/toolbox/spm12’) to configure spm.
How to Format Tables Correctly¶
In some fuctions, you may have to use some .csv files to input data. If you cannot find any proper existed .csv files, you can create a .csv file 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 ... ... ... ... ... ...
This brant_roi_info.csv file 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 ... ... ... ... ... ... ... ... ... ...
This brant_circos_3mm_273.csv file can be found in the */Matlab/toolbox/brant-master/circos.
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 .nii files.
- 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 *.nii files were found in above directories.
- Solution: Uncheck the delete first N timepoints or convert just one set of data per time.