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FAQs
==============================
How can I Download and Install BRANT
-------------------------------------
* You can get the latest version of BRANT from
https://github.com/YongLiuLab/brant-stable/archive/master.zip
* Some functions are based on SPM, you can get it from
http://www.fil.ion.ucl.ac.uk/spm/software/spm12
* Circos in STEP 8 can be downloaded from
http://circos.ca/distribution/circos-0.69-5.tgz
* Unzip the *brant-master.zip* file and move both brant and spm12 folders to :file:`/path/of/toolbox`. (The path can be anywhere in your computer as long as it's in English)
* Configure SPM paths:
1. Click *Set Path* in MATLAB
2. Click *add folder*
3. Select SPM's root folder
4. Run ``spm fmri`` in 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:
1. Click *Set Path* in MATLAB
2. Click *Add with subfolders*
3. Select the unzipped BRANT folder
4. Click *Save*.
.. tip::
* 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 :file:`\*.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.
.. figure:: _images/result1.png
:align: center
fig.1 differences among four Matlab-based toolboxes
How to Format Tables Correctly
---------------------------------------
* In some fuctions, you may have to use some :file:`\*.csv` files to input data. If you cannot find any proper existed :file:`\*.csv` files, you can create a :file:`\*.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 :file:`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 :file:`brant_circos_3mm_273.csv` file can be found in the :file:`\*/Matlab/toolbox/brant-master/circos`.
.. _`STEP 4`: example_4.html
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.
1.
.. figure:: _images/faqs_error_new_2.png
:align: center
fig.2 error during DICOM Convert
* Reason: Misuse id index.
* Solution: Delete files created before the error occurs. Read `example`_ to use id index properly.
.. _`example`: example_1.html
2.
.. figure:: _images/faqs_error_new_1.png
:align: center
fig.3 error after preprocessing
* Reason: The preprocessing may be interrupted and create wrong :file:`\*.nii` files.
* Solution: Delete files created during preprocessing, examine your preprocessing settings and run preprocessing again.
3.
.. figure:: _images/faqs_error_new_5.png
:align: center
fig.4 error during preprocessing
* Reason: TR(s) in Preprocessing is zero.
* Solution: Set tr(s) in *Silce Timing* to a legal value.
4.
.. figure:: _images/faqs_error_new_3.png
:align: center
fig.5 error during STAT
* 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.
5.
.. figure:: _images/faqs_error_new_4.png
:align: center
fig.6 error after DICOM Convert
* Reason: More than one :file:`\*.nii` files were found in above directories.
* Solution: Uncheck the *delete first N timepoints* or convert just one set of data per time.
.. _`examples`: Menu_examples.html