test

source/Embedded_Circos.txt

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+Circos
+--------------
+
+.. image:: _images/circos.png
+   :align: right
+
+* **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:
+    * **label**: label of each sub-areas.
+    * **module**: to which lobe/module does the sub-area belong.
+    * **index_module**: order of the arranged module.
+    * **index_node**: order of sub-areas within one module.
+
+**Before using the function, please download and install circos 0.69 or higher.**
+
+- **Buttons**:
+    - **S**: Save parameters of the current panel to a *\*.mat* file. The *\*.mat* can be further loaded for the panel or be used in a script processing.
+    - **L**: Load parameters from *\*.mat* for the current panel.
+    - **?**: Help information.
+

source/Embedded_Diffusion_Kit.txt

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+Diffusion Kit
+---------------
+
+*A batch processing GUI-interface for DiffusionKit*
+
+.. image:: _images/diffusionkit.png
+   :align: right
+
+* **D.K. dir**: path of installed DiffusionKit, e.g. *C:/Program Files (x86)/DiffusionKit*
+* **id index**: identifier to find unique string for each subject
+* **filetype**: files in the filetype will be searched in input directories.
+* **4D nifti files**: if the input data is 4D, check this item. Otherwise uncheck.
+* **input dirs**: directories can be input either using a *.txt* file or spm select window.
+
+* **Choose below options to perform in each directory.**
+
+  * eddy correction
+  * reconstruction--DTI
+  * tracking--DTI
+  * reconstruction--HARDI(ODF)
+  * reconstruction--HARDI(FOD)
+
+Results will be saved in each input directory.
+
+- **Buttons**:
+    - **S**: Save parameters of the current panel to a *\*.mat* file. The *\*.mat* can be further loaded for the panel or be used in a script processing.
+    - **L**: Load parameters from *\*.mat* for the current panel.
+    - **?**: Help information.
+
+**For more information, please visit**
+http://diffusion.brainnetome.org/
+
+* **Reference**:
+1. Sangma Xie, Liangfu Chen, Nianming Zuo and Tianzi Jiang. DiffusionKit: A Light One-Stop Solution for Diffusion MRI Data Analysis. *Journal of Neuroscience Methods*. vol. 273, pp. 107-119, 2016.

source/FAQs.txt

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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/download/spm12_updates
+
+* 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 *\*/Matlab/toolbox*.
+
+* Open Matlab, use *Set Path* and add folders above with their subfolders. You can also print *brant_configure_paths* in matlab to config BRANT.
+
+How to Format Tables Correctly
+---------------------------------------
+* In some fictions, 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
+	================ ====== === ====
+
+
+    * 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*.
+
+
+
+.. _`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.1 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.2 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.
+
+3.
+
+.. figure:: _images/faqs_error_new_5.png
+   :align: center
+
+   fig.3 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.4 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.5 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.
+
+.. _`examples`: Menu_examples.html

source/FC_Draw_ROI.txt

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+Draw ROI
+------------------------------
+
+.. image:: _images/draw_roi.png
+   :align: right
+
+* **type**: draw roi as sphere or cube
+* **unit**: unit of input radius
+* **radius**: radius of sphere or 1/2 edge length for cubic
+* **input type**: 
+    * manual: input coordinates seperated by ';'
+     e.g::
+
+      25,5,10;10,15,10
+
+    * file: input a csv file with 3 columns for x,y,z (the first line should be 'x', 'y' and 'z')
+
+* **mask roi afterwards**: mask generated roi using input mask
+* **output to one roi file**: instead of output one file for each roi, BRANT will generate one roi file with each roi labeled by number
+* **ref&mask**: reference and mask file. for extracting information of origin, voxel size, bounding box, etc..
+* **out dir**: directory for output
+
+- **Buttons**:
+    - **S**: Save parameters of the current panel to a *\*.mat* file. The *\*.mat* can be further loaded for the panel or be used in a script processing.
+    - **L**: Load parameters from *\*.mat* for the current panel.
+    - **?**: Help information.

source/FC_Merge_Extract_ROI.txt

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+Merge/Extract ROIs
+------------------------------
+
+.. image:: _images/merge_roi.png
+   :align: right
+
+* **Operation**: select to merge 3D rois into one, or extract ROIs from an atlas.    
+ - **Merge**:
+  * **filetype**: files in the filetype will be searched in input directories.
+  * **data dir**: directory in which stores 3D rois.
+  * **out fn**: output filename
+  * **out dir**: output directory
+
+ - **Extract**:
+  * **roi file**: ROIs in one nifti file
+  * **roi info***: (* means optional) labels of tagged ROIs in a *.csv* file. For example::
+
+     1,SFG
+     2,MFG
+     3,IFG
+
+  * **roi index**: a vector of integers. used for selecting wanted ROIs.
+  * **output to single file**: choose to output to only one file.
+  * **out dir**: output directory
+
+.. image:: _images/extract_roi.png
+   :align: right 
+
+- **Buttons**:
+    - **S**: Save parameters of the current panel to a *\*.mat* file. The *\*.mat* can be further loaded for the panel or be used in a script processing.
+    - **L**: Load parameters from *\*.mat* for the current panel.
+    - **?**: Help information.

source/FC_ROI_Calculation.txt

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+ROI Calculation
+----------------------------------------------------
+
+.. image:: _images/roi_calculation.png
+   :align: right 
+
+* **roi file**: ROIs in one nifti file
+* **roi index(*)**: optional. labels of tagged ROIs in a *.csv* file. 
+  For example::
+
+    1,SFG
+    2,MFG
+    3,IFG
+
+* **clustersize thr**: threshold of cluster size.
+* **mask**: could be whole brain mask or gray matter mask.
+* **id index**: identifier to find unique string for each subject
+* **filetype**: files in the filetype will be searched in input directories.
+* **4D nifti files**: if the input data is 4D, check this item. Otherwise uncheck.
+* **input dirs**: directories can be input either using a *.txt* file or spm select window.
+
+* **extract mean**: extract mean time series for each ROI
+* **roi to roi correlation**: calculate correlation between pairs of ROI
+* **roi to whole brain correlation**: calculate correlation between each ROI's mean time series and voxels in the mask.
+
+* **Partial correlation**: (check to use Partial correlation, uncheck to use Pearson's correlation) when calculating correlation, between one roi mean time series and voxels/other time series, the rest of roi mean time serieses will be regressed out from the calculation.
+
+* **out dir**: output directory for saving results.
+
+- **Buttons**:
+    - **S**: Save parameters of the current panel to a *\*.mat* file. The *\*.mat* can be further loaded for the panel or be used in a script processing.
+    - **L**: Load parameters from *\*.mat* for the current panel.
+    - **?**: Help information.

source/Menu_Embedded.txt

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+.. Brant documentation master file, created by
+   sphinx-quickstart on Fri May 26 16:27:58 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Embedded
+===================================
+
+.. toctree::
+   :maxdepth: 2
+
+   Embedded_Diffusion_Kit
+
+   Embedded_Circos

source/Menu_FC.txt

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+.. Brant documentation master file, created by
+   sphinx-quickstart on Fri May 26 16:27:58 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+FC
+===================================
+
+.. toctree::
+   :maxdepth: 2
+
+   FC_Draw_ROI
+
+   FC_Merge_Extract_ROI
+
+   FC_ROI_Calculation
+
+
+

source/Menu_NET.txt

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+.. Brant documentation master file, created by
+   sphinx-quickstart on Fri May 26 16:27:58 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+NET
+===================================
+
+.. toctree::
+   :maxdepth: 2
+
+   NET_Threshold_Estimation
+
+   NET_Network_Calculation
+
+   NET_Network_Statistics
+
+
+

source/Menu_Preprocess.txt

@@ -0,0 +1,20 @@
+.. Brant documentation master file, created by
+   sphinx-quickstart on Fri May 26 16:27:58 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Preprocess
+===================================
+
+
+.. toctree::
+   :maxdepth: 2
+
+   Preprocess_System_Configuration
+
+   Preprocess_Directories
+
+   Preprocess_Modules
+
+
+

source/Menu_SPON.txt

@@ -0,0 +1,21 @@
+.. Brant documentation master file, created by
+   sphinx-quickstart on Fri May 26 16:27:58 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+SPON
+===================================
+
+.. toctree::
+   :maxdepth: 2
+
+   SPON_AM
+
+   SPON_ALFF_FALFF
+
+   SPON_ReHo
+
+   SPON_FCD
+
+
+