Updated documentation files

docs/_sidebar.md

@@ -62,6 +62,7 @@
   - [FreeSurfer](methods/freesurfer.md)
   - [QSIprep-based dMRI Processing](methods/QSIprep_based_DWI_processing.md)
   - [fMRI Processing](methods/fMRI-Processing.md)
+  - [Downloading Public Data (NDA)](other/Downloading-Public-Data.md)
   - [Software](other/Software.md)
   - [SOP Tracking Documents](other/SOP-Tracking-Documents.md)
   - [Editing Documentation](other/Editing-Documentation.md)

docs/other/Downloading-Public-Data.md

@@ -0,0 +1,74 @@
+# Downloading Public NDA Data from NIMH Data Archive
+
+## **1) Introduction to NDA**
+
+Central hub for accessing large neuroimaging datasets, such as HCP.
+
+**Website:**
+https://nda.nih.gov/
+
+**Example:**
+HCP data: https://www.humanconnectome.org/storage/app/media/documentation/HCP-EP1.1/HCP-EP_Release_1.1_Manual.pdf 
+
+## 2) Steps to Access and Download Data
+**Step 1: Sign In**
+
+* Navigate to **NDA** website.
+* Click **My Account** → **Sign In with RAS**.
+* Select **login gov** 
+
+**Step 2: Get Study Data**
+
+* Go to **Get Data**.
+* Select **Connectomes Related to Human Disease** from the left bar.
+* Choose **Access Shared Data Package**.
+* Note your Data **Package ID**.
+
+##  3) Command-Line Download Setup
+
+**Prerequisite: Install Miniconda**
+
+`Sudo su clevis`
+
+```
+#install Miniconda
+mkdir ~/conda; cd ~/conda
+
+wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash Miniconda3-latest-Linux-x86_64.sh
+```
+
+**Optional: Avoid base env auto-activation:**
+
+ ```
+export PATH="/home/clevis/miniconda3/bin:$PATH"
+conda config --set auto_activate_base false
+```
+**Install nda-tools:**
+```
+#Install nda-tools
+conda create -n nda-tools pip
+conda activate nda-tools
+pip install nda-tools
+```
+
+## 4) Download Data Using Terminal
+
+**Command Structure:**
+
+```
+downloadcmd -dp <studyid> -u <NDA ID> -p <password> -d <directory you want to save data>
+```
+
+**Example:**
+
+```
+downloadcmd -dp  1190786  -u ghazale  -d /scratch/clevis/NDA
+```
+
+* Enter your NDA password when prompted.
+
+**Keyring Error Fix:** pip install keyrings.alt
+
+* Avoid saving directly in /external due to permission issues.
+