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FAQs
==============================
How can I Download and Install BRANT
-------------------------------------
* You can get latest version of BRANT from
https://github.com/kbxu/brant/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. Move the brant folder and spm12 folder to :file:`\*/Matlab/toolbox`.
* Open Matlab, use *Set Path* and add folders above with subfolders or use the configuration function in BRANT(**recommended**).
.. tip::
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.
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