add result file and add urf in index(incompleted)

source/Menu_examples.txt

@@ -27,5 +27,7 @@ Examples
 
    filename
 
+   example_result
+
 
 

source/example_result.txt

@@ -0,0 +1,13 @@
+Result of rs-fMRI data analysis
+---------------------------------------------
+
+To validate the efficacy of our toolkit, we used the same preprocessing pipelines provided by BRANT and DPABI v2.3, to compare ReHo, fALFF and FCs using a rs-fMRI dataset consists of 18 patients with mild cognitive impairment (MCI), 17 patients with mild Alzheimer's disease (mAD), 18 patients with severe Alzheimer's disease (sAD) and 21 normal controls (NC). This dataset is available `online`_.
+
+AD subjects were diagnosed using standard operationalized criteria (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV); American Psychiatric Association 1994 and National Institute of Neurological and Communicative Disorders and Stroke - Alzheimer's Disease and Related Disorders Association (NINCDS-ADRDA)). The severity of dementia was assessed using the Clinical Dementia Rating (CDR) scale. Patients with a diagnosis of AD and CDR score of 1 were classified as mild AD and those with a CDR score of 2 or 3 were diagnosed as severe AD. MCI was diagnosed according to standard criteria, which included subjective memory loss with objective evidence of memory impairment in the context of normal or near-normal performance on other domains of cognitive functioning; minimal impairment of activities of daily living with a CDR score of 0.5. Normal volunteers have a CDR score of 0.
+
+The MR images were acquired on a 3.0-T MR scanner (Magnetom Trio, Siemens, Germany). Functional MRI data were acquired using an echo planar imaging (EPI) sequence sensitive to BOLD contrast: Repetition time (TR) = 2000 ms, echo time (TE) = 30 ms, flip angle (FA) = 90°, matrix = 64 × 64, field of view (FOV) = 220 mm × 220 mm, slice thickness = 3 mm with inter-slice gap = 1 mm. Each brain volume comprised 32 axial slices, and each scanning session lasted for 360 s. Sagittal T1-weighted MR images were acquired by a magnetization-prepared rapid gradient-echo sequence (TR/TE = 2000/2.6 ms, FA = 9°, matrix = 256 × 224, FOV = 256 mm × 224 mm, 176 continuous sagittal slices with 1 mm thickness).
+
+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.
+
+
+.. _`online`: https://github.com/yongliulab

source/index.txt

@@ -9,6 +9,8 @@ To facilitate data processing and deal with above listed issues, we’ve written
 
 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
 
@@ -38,6 +40,5 @@ Functions of BRANT are arranged into 7 modules, which are preprocessing, functio
 
    Menu_Contact
 
-
-
+.. _`online`: https://github.com/yongliulab