add result files

YongLiuLab · Jul 26, 2018 · 6fd4a9b · 6fd4a9b
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diff --git a/source/Embedded_Circos.txt b/source/Embedded_Circos.txt
@@ -7,7 +7,7 @@ Circos
 * **circos dir**: Path of unzipped circos folder. */circos_path/bin*
 * **conf dir**: Path of circos configure file.
 * **roi info**: CSV table which defines sub-areas and lobes, there is an example in *brant-master/circos/brant_circos_3mm_273.csv*
-* In the table should have at least four columns:
+* There should be at least four columns in the table:
     * **label**: label of each sub-areas.
     * **module**: to which lobe/module does the sub-area belong.
     * **index_module**: order of the arranged module.

diff --git a/source/FAQs.txt b/source/FAQs.txt
@@ -80,6 +80,16 @@ How to Format Tables Correctly
 .. _`STEP 4`: example_4.html 
 
 
+What is BRANT's Advantages 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.
+
+.. figure:: _images/result1.tif
+   :align: center
+
+   fig.1 differences among four Matlab-based toolboxes
 
 What can I Do When an Error Occurs
 -------------------------------------
@@ -91,7 +101,7 @@ What can I Do When an Error Occurs
 .. figure:: _images/faqs_error_new_2.png
    :align: center
 
-   fig.1 error during DICOM Convert
+   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.
@@ -103,7 +113,7 @@ What can I Do When an Error Occurs
 .. figure:: _images/faqs_error_new_1.png
    :align: center
 
-   fig.2 error after preprocessing
+   fig.3 error after preprocessing
 
 * 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.
@@ -113,7 +123,7 @@ What can I Do When an Error Occurs
 .. figure:: _images/faqs_error_new_5.png
    :align: center
 
-   fig.3 error during preprocessing
+   fig.4 error during preprocessing
 
 * Reason: TR(s) in Preprocessing is zero.
 * Solution: Set tr(s) in *Silce Timing* to a legal value.
@@ -123,7 +133,7 @@ What can I Do When an Error Occurs
 .. figure:: _images/faqs_error_new_3.png
    :align: center
 
-   fig.4 error during STAT
+   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. 
@@ -133,7 +143,7 @@ What can I Do When an Error Occurs
 .. figure:: _images/faqs_error_new_4.png
    :align: center
 
-   fig.5 error after DICOM Convert
+   fig.6 error after DICOM Convert
 
 * 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.

diff --git a/source/_images/Thumbs.db b/source/_images/Thumbs.db
diff --git a/source/_images/arrangement.png b/source/_images/arrangement.png
diff --git a/source/_images/example/Thumbs.db b/source/_images/example/Thumbs.db
diff --git a/source/_images/result1.tif b/source/_images/result1.tif
diff --git a/source/_images/result2.tif b/source/_images/result2.tif
diff --git a/source/_images/result3.tif b/source/_images/result3.tif
diff --git a/source/example_result.txt b/source/example_result.txt
@@ -9,5 +9,18 @@ The MR images were acquired on a 3.0-T MR scanner (Magnetom Trio, Siemens, Germa
 
 No significant differences (P>0.05) of age (two-tailed two sample t-test), gender (chi-squared test) and education (two-tailed two sample t-test) were found between each patient group and NC group. T-statistic maps of fALFF, ReHo and results of FCs (P<0.001, uncorrected) based on different toolkits have quite similar patterns, which suggest BRANT is another optimal toolkit for rs-fMRI research community. In the results, the minor differences can be induced by 489 different implementations of trends removal, covariance regression and band-pass filter. For the results, we didn’t draw a strong conclusion, since the interpretation requires multiple comparison corrections and is not the main point of the current study.
 
+We have listed the differences among BRANT and other Matlab-based toolboxes in `FAQs`_. We can also find that t-statistic maps of fALFF, ReHo and results of FCs (P<0.001, uncorrected) based on different toolkits have quite similar patterns, which suggest BRANT is another optimal toolkit for rs-fMRI research community.
 
-.. _`online`: https://github.com/yongliulab
+.. figure:: _images/result2.tif
+   :align: center
+
+   fig.1 T-statistic maps of fALFF and ReHo based on different toolkits
+
+.. figure:: _images/result3.tif
+   :align: center
+
+   fig.1 results of FCs based on different toolkits
+
+.. _`online`: https://github.com/yongliulab
+
+.. _`FAQs`: FAQs.html#what-is-brant-s-advantages-compared-with-other-matlab-based-toolboxes
diff --git a/source/index.txt b/source/index.txt
@@ -5,15 +5,20 @@
 
 Welcome to Brant!
 ===================================
+
+Here is some good news that our paper on BRANT has been published, for further details and information on BRANT and other toolkits related, you can get the paper *BRANT: A Versatile and Extendable Resting-state fMRI Toolkit* `online`_.
+
+
 To facilitate data processing and deal with above listed issues, we’ve written an extendable MATLAB based toolbox BRANT (BRAinNetome Toolkit), which integrates fMRI data preprocessing, voxel-wise spontaneous activity analysis, functional connectivity analysis, complex network analysis, statistical analysis, data visualization as well as several useful utilities. We designed the toolbox using dynamically generated GUIs, with which other developers can generate their own GUIs by adding a few lines of MATLAB code. Also, to simplify the input process during using BRANT, most functions are initialized with default settings, users will only need to specify several necessary parameters, with free access to all.
 
 Functions of BRANT are arranged into 7 modules, which are preprocessing, functional connectivity (FC), spontaneous activity (SPON), complex network analysis (NET), statistics (STAT), visualization (View) and utilities. More details on proper module can be found in its own part.
 
-Here is some good news that our paper on BRANT has been published, for further details and information on BRANT and other toolkits related, you can get the paper *BRANT: A Versatile and Extendable Resting-state fMRI Toolkit* `online`_.
-
 .. image:: _images/main_gui.png
    :align: center
 
+.. image:: _images/arrangement.png
+   :align: center
+
 .. toctree::
    :maxdepth: 2
    :glob: