replace older links that result in a redirect by the new links

Author: robertoostenveld

_includes/shared/particular_data.md

@@ -4,80 +4,80 @@ In general you should get started with the [tutorials](/tutorial). The pages tha
 
 ## Getting started with particular MEG data types
 
-- [Getting started with CTF data](/getting_started/ctf)
-- [Getting started with BTi/4D data](/getting_started/bti)
-- [Getting started with Neuromag/Elekta/Megin data](/getting_started/neuromag)
-- [Getting started with BabySQUID data](/getting_started/babysquid)
-- [Getting started with Yokogawa data](/getting_started/yokogawa)
-- [Getting started with Ricoh data](/getting_started/ricoh)
-- [Getting started with OPM data recorded at the FIL](/getting_started/opm_fil)
-- [Getting started with Cerca OPM data](/getting_started/cerca)
-- [Getting started with FieldLine OPM data](/getting_started/fieldline)
+- [Getting started with CTF data](/getting_started/meg/ctf)
+- [Getting started with BTi/4D data](/getting_started/meg/bti)
+- [Getting started with Neuromag/Elekta/Megin data](/getting_started/meg/neuromag)
+- [Getting started with BabySQUID data](/getting_started/meg/babysquid)
+- [Getting started with Yokogawa data](/getting_started/meg/yokogawa)
+- [Getting started with Ricoh data](/getting_started/meg/ricoh)
+- [Getting started with OPM data recorded at the FIL](/getting_started/meg/opm_fil)
+- [Getting started with Cerca OPM data](/getting_started/meg/cerca)
+- [Getting started with FieldLine OPM data](/getting_started/meg/fieldline)
 
 ## Getting started with particular EEG data types
 
-- [Getting started with BrainVision Analyzer and Easycap](/getting_started/brainvision)
-- [Getting started with 20%, 10% and 5% electrode arrangements](/getting_started/1020)
-- [Getting started with ANT-Neuro, ASA and EEProbe data](/getting_started/antneuro)
-- [Getting started with Advanced Brain Monitoring (ABM)'s B-Alert EEG data](/getting_started/b_alert)
-- [Getting started with BESA data](/getting_started/besa)
-- [Getting started with Biosemi BDF data](/getting_started/biosemi)
-- [Getting started with EDF data](/getting_started/edf)
-- [Getting started with EGI/Philips/Magstim data](/getting_started/egi)
-- [Getting started with Nicolet data](/getting_started/nicolet)
-- [Getting started with TMSi data](/getting_started/tmsi)
+- [Getting started with BrainVision Analyzer and Easycap](/getting_started/eeg/brainvision)
+- [Getting started with 20%, 10% and 5% electrode arrangements](/getting_started/eeg/1020)
+- [Getting started with ANT-Neuro, ASA and EEProbe data](/getting_started/eeg/antneuro)
+- [Getting started with Advanced Brain Monitoring (ABM)'s B-Alert EEG data](/getting_started/eeg/b_alert)
+- [Getting started with BESA data](/getting_started/eeg/besa)
+- [Getting started with Biosemi BDF data](/getting_started/eeg/biosemi)
+- [Getting started with EDF data](/getting_started/eeg/edf)
+- [Getting started with EGI/Philips/Magstim data](/getting_started/eeg/egi)
+- [Getting started with Nicolet data](/getting_started/eeg/nicolet)
+- [Getting started with TMSi data](/getting_started/eeg/tmsi)
 
 ## Getting started with intracranial data
 
-- [Getting started with Blackrock data](/getting_started/blackrock)
-- [Getting started with Cyberkinetics data](/getting_started/cyberkinetics)
-- [Getting started with Neuralynx data](/getting_started/neuralynx)
-- [Getting started with Neuralynx data recorded at the Donders Institute](/getting_started/neuralynx_fcdc)
-- [Getting started with Plexon data](/getting_started/plexon)
-- [Getting started with animal electrophysiology data, including spikes](/getting_started/animal)
-- [Getting started with human intracranial electrophysiology data](/getting_started/human_ecog)
-- [Getting started with Neurodata Without Borders (NWB) data](/getting_started/nwb)
+- [Getting started with Blackrock data](/getting_started/intracranial/blackrock)
+- [Getting started with Cyberkinetics data](/getting_started/intracranial/cyberkinetics)
+- [Getting started with Neuralynx data](/getting_started/intracranial/neuralynx)
+- [Getting started with Neuralynx data recorded at the Donders Institute](/getting_started/intracranial/neuralynx_fcdc)
+- [Getting started with Plexon data](/getting_started/intracranial/plexon)
+- [Getting started with animal electrophysiology data, including spikes](/getting_started/intracranial/animal)
+- [Getting started with human intracranial electrophysiology data](/getting_started/intracranial/human_ecog)
+- [Getting started with Neurodata Without Borders (NWB) data](/getting_started/intracranial/nwb)
 
 ## Getting started with NIRS data
 
-- [Getting started with Artinis NIRS data](/getting_started/artinis)
-- [Getting started with Hitachi NIRS data](/getting_started/hitachi)
-- [Getting started with NIRx NIRS data](/getting_started/nirx)
-- [Getting started with Shimadzu NIRS data](/getting_started/shimadzu)
-- [Getting started with SNIRF NIRS data](/getting_started/snirf)
+- [Getting started with Artinis NIRS data](/getting_started/nirs/artinis)
+- [Getting started with Hitachi NIRS data](/getting_started/nirs/hitachi)
+- [Getting started with NIRx NIRS data](/getting_started/nirs/nirx)
+- [Getting started with Shimadzu NIRS data](/getting_started/nirs/shimadzu)
+- [Getting started with SNIRF NIRS data](/getting_started/nirs/snirf)
 
 ## Getting started with eyetracker data
 
-- [Getting started with SR-Research EyeLink eye-tracker data](/getting_started/eyelink)
+- [Getting started with SR-Research EyeLink eye-tracker data](/getting_started/eyetracker/eyelink)
 
 ## Getting started with motion capture data
 
-- [Getting started with XSens motion capture data](/getting_started/xsens)
+- [Getting started with XSens motion capture data](/getting_started/motion/xsens)
 
 ## Getting started with other types of data
 
-- [Getting started with fMRI timeseries data](/getting_started/fmri)
-- [Getting started with video data](/getting_started/video)
-- [Getting started with audio data](/getting_started/audio)
+- [Getting started with fMRI timeseries data](/getting_started/otherdata/fmri)
+- [Getting started with video data](/getting_started/otherdata/video)
+- [Getting started with audio data](/getting_started/otherdata/audio)
 
 ## Getting started with (data from) other software
 
-- [Getting started with BIDS](/getting_started/bids)
-- [Getting started with AnyWave](/getting_started/anywave)
-- [Getting started with Seg3D](/getting_started/seg3d)
-- [Getting started with ParaView](/getting_started/paraview)
-- [Getting started with MeshLab](/getting_started/meshlab)
-- [Getting started with LIMO EEG](/getting_started/limo)
-- [Getting started with data from EEGLAB](/getting_started/eeglab)
-- [Getting started with data from SPM](/getting_started/spm)
-- [Getting started with data from LORETA](/getting_started/loreta)
-- [Getting started with data from the BIOIMAGE suite](/getting_started/bioimage)
-- [Getting started with data from Homer](/getting_started/homer)
-- [Getting started with MNE(-python)](/getting_started/mne)
-- [Getting started with SimNIBS](/getting_started/simnibs)
+- [Getting started with BIDS](/getting_started/othersoftware/bids)
+- [Getting started with AnyWave](/getting_started/othersoftware/anywave)
+- [Getting started with Seg3D](/getting_started/othersoftware/seg3d)
+- [Getting started with ParaView](/getting_started/othersoftware/paraview)
+- [Getting started with MeshLab](/getting_started/othersoftware/meshlab)
+- [Getting started with LIMO EEG](/getting_started/othersoftware/limo)
+- [Getting started with data from EEGLAB](/getting_started/othersoftware/eeglab)
+- [Getting started with data from SPM](/getting_started/othersoftware/spm)
+- [Getting started with data from LORETA](/getting_started/othersoftware/loreta)
+- [Getting started with data from the BIOIMAGE suite](/getting_started/othersoftware/bioimage)
+- [Getting started with data from Homer](/getting_started/othersoftware/homer)
+- [Getting started with MNE(-python)](/getting_started/othersoftware/mne)
+- [Getting started with SimNIBS](/getting_started/othersoftware/simnibs)
 
 ## Getting started with real-time data analysis
 
-- [Getting started with real-time analysis for BCI and neurofeedback](/getting_started/realtime)
-- [Getting started with real-time MEG head localization](/getting_started/realtime_headlocalizer)
-- [Getting started with real-time fMRI analysis](/getting_started/realtime_fmri)
+- [Getting started with real-time analysis for BCI and neurofeedback](/getting_started/realtime/bci)
+- [Getting started with real-time MEG head localization](/getting_started/realtime/headlocalizer)
+- [Getting started with real-time fMRI analysis](/getting_started/realtime/fmri)

development/realtime.md

@@ -13,7 +13,7 @@ This page is part of the documentation series of the FieldTrip buffer for realti
 2.  definition of the [buffer protocol](/development/realtime/buffer_protocol),
 3.  the [reference implementation](/development/realtime/reference_implementation), and
 4.  specific [implementations](/development/realtime/implementation) that interface with acquisition software, or software platforms.
-5.  the [getting started](/getting_started/realtime) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
+5.  the [getting started](/getting_started/realtime/bci) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
 
 The page [scratchpad](/development/realtime/scratchpad) contains some loose ends that have no clear place.
 

development/realtime/buffer.md

@@ -13,7 +13,7 @@ This page is part of the documentation series of the FieldTrip buffer for realti
 2.  definition of the [buffer protocol](/development/realtime/buffer_protocol),
 3.  the [reference implementation](/development/realtime/reference_implementation), and
 4.  specific [implementations](/development/realtime/implementation) that interface with acquisition software, or software platforms.
-5.  the [getting started](/getting_started/realtime) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
+5.  the [getting started](/getting_started/realtime/bci) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
 
 This page documents the general concept behind the FieldTrip buffer.
 

development/realtime/buffer_protocol.md

@@ -11,7 +11,7 @@ This page is part of the documentation series of the FieldTrip buffer for realti
 2.  definition of the [buffer protocol](/development/realtime/buffer_protocol),
 3.  the [reference implementation](/development/realtime/reference_implementation), and
 4.  specific [implementations](/development/realtime/implementation) that interface with acquisition software, or software platforms.
-5.  the [getting started](/getting_started/realtime) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
+5.  the [getting started](/getting_started/realtime/bci) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
 
 This page provides a formal description of how the communication over the network is performed between the FieldTrip buffer server and clients.
 

development/realtime/closing_the_loop.md

@@ -7,7 +7,7 @@ tags: [realtime]
 
 To close the loop in your BCI application, you have to communicate the control signal from the application/computer that does the feature extraction and feature translation to the application that is controlled by the BCI system. The application that is controlled by the BCI signal can be anything from a generic stimulus presentation software (e.g., NeuroBS Presentation, ERTS, ANT EEvoke, ...) to a spelling device or to custom-built hardware device (e.g., robot arm).
 
-Before you attempt to close the loop, please make sure that the data is streaming properly and that you are able to process it fast enough. Some examples are given in the [getting started](/getting_started/realtime) section.
+Before you attempt to close the loop, please make sure that the data is streaming properly and that you are able to process it fast enough. Some examples are given in the [getting started](/getting_started/realtime/bci) section.
 
 ## Communicating over a serial port connection
 

development/realtime/implementation.md

@@ -11,7 +11,7 @@ This page is part of the documentation series of the FieldTrip buffer for realti
 2.  definition of the [buffer protocol](/development/realtime/buffer_protocol),
 3.  the [reference implementation](/development/realtime/reference_implementation), and
 4.  specific [implementations](/development/realtime/implementation) that interface with acquisition software, or software platforms.
-5.  the [getting started](/getting_started/realtime) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
+5.  the [getting started](/getting_started/realtime/bci) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
 
 This page deals with specific implemenations of the FieldTrip buffer protocol. This includes interfacing with specific hardware (e.g., TMSi, Biosemi, CTF, Unicorn), software platforms (e.g., BCI2000, BrainStream) and links to the implementation in specific programming languages (e.g., MATLAB, Java, C/C++, Python).
 
@@ -31,7 +31,7 @@ This page deals with specific implemenations of the FieldTrip buffer protocol. T
 - [Neurosky ThinkCap](/development/realtime/neurosky)
 - [OpenBCI](/development/realtime/openbci)
 - [Sound card input](/development/realtime/audio2ft)
-- [Siemens fMRI](/getting_started/realtime_fmri)
+- [Siemens fMRI](/getting_started/realtime/fmri)
 - [TMSI](/development/realtime/tmsi)
 - [TOBI](/development/realtime/tobi)
 - [Unicorn Hybrid Black](/development/realtime/unicorn)
@@ -48,11 +48,11 @@ This page deals with specific implemenations of the FieldTrip buffer protocol. T
 ## Additional useful tools
 
 - [viewer](/development/realtime/viewer) is a graphical C++ application to visualize online signals from the FieldTrip buffer
-- [serial_event](/development/realtime/serial_event) is a C application that turns incoming characters from a serial port into FieldTrip buffer events (used for translating TTL pulses in [realtime fMRI](/getting_started/realtime_fmri))
+- [serial_event](/development/realtime/serial_event) is a C application that turns incoming characters from a serial port into FieldTrip buffer events (used for translating TTL pulses in [realtime fMRI](/getting_started/realtime/fmri))
 - [buffer_java#MidiToBuffer](/development/realtime/buffer_java#MidiToBuffer) is a Java application that turns MIDI messages into FieldTrip buffer events
 - [buffer_java#MarkerGUI](/development/realtime/buffer_java#MarkerGUI) is a graphical Java application that allows to write FieldTrip buffer events with a freely chosen _type_ and _value_ string.
 - [Testing with sine waves and pre-recorded EEG data](/development/realtime/eeg)
-- [Testing with pre-recorded fMRI data](/getting_started/realtime_fmri#testing_with_pre-recorded_fmri_data)
+- [Testing with pre-recorded fMRI data](/getting_started/realtime/fmri#testing_with_pre-recorded_fmri_data)
 
 ## Recording and playing back online experiments
 

development/realtime/neuromag.md

@@ -10,7 +10,7 @@ Volume 2011) in any work that uses it.
 
 The rtMEG software relays signals from a 306-channel Neuromag/Elekta/Megin MEG device in real-time to a FieldTrip buffer. This buffer can then be read by any computer in the same network as the computer hosting the buffer. The data is still stored by the Acquisition computer (i.e. where you run the Acquisition software by Neuromag) as a FIF file, and it can be read by as many computers in the network as necessary. The rtMEG software has the capability of running the FieldTrip buffer by itself, or it can output the data to a separate computer hosting the buffer when necessary. The delay introduced by the software to the data being relayed has been measured to be smaller than 50ms, which is sufficient for most real-time studies.
 
-For more information on how to read from a FieldTrip buffer, please check [here](/development/realtime) for a collection of technical documents or the [getting started section](/getting_started/realtime).
+For more information on how to read from a FieldTrip buffer, please check [here](/development/realtime) for a collection of technical documents or the [getting started section](/getting_started/realtime/bci).
 
 ## Usage
 

development/realtime/reference_implementation.md

@@ -11,7 +11,7 @@ This page is part of the documentation series of the FieldTrip buffer for realti
 2.  definition of the [buffer protocol](/development/realtime/buffer_protocol),
 3.  the [reference implementation](/development/realtime/reference_implementation), and
 4.  specific [implementations](/development/realtime/implementation) that interface with acquisition software, or software platforms.
-5.  the [getting started](/getting_started/realtime) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
+5.  the [getting started](/getting_started/realtime/bci) documentation which takes you through the first steps of real-time data streaming and analysis in MATLAB
 
 This page deals with the cross-platform reference implementation in C.
 

development/realtime/scratchpad.md

@@ -9,7 +9,7 @@ This page contains some loose ends and random pieces that don't fit elsewhere.
 
 - [closing the loop](/development/realtime/closing_the_loop) lists some methods for interacting with, and controlling the external world (i.e. outside the analysis computer)
 - [pipeline](/development/realtime/pipeline) contains example fMRI pipeline description
-- [Siemens fMRI](/getting_started/realtime_fmri) also contains some fMRI details
+- [Siemens fMRI](/getting_started/realtime/fmri) also contains some fMRI details
 
 ## Various notes and comments
 

development/realtime/serial_event.md

@@ -9,7 +9,7 @@ This page describes the tool **serial2event**, which is located in the directory
 The user has the option to either only react on specific characters, and to write events with
 a fixed _type_ and _value_, or to forward the received character as the _value_ of the event.
 The _sample_ field of the event can be auto-incremented, and reset by sending the string "RESET"
-to the UDP port (default = 1990) on which the tool listens. The latter feature is used in the DCCN's MRI lab to reset the sample counter when a new sequence is started on the scanner host (which is then picked up by the [fMRI gui_streamer](/getting_started/realtime_fmri) tool).
+to the UDP port (default = 1990) on which the tool listens. The latter feature is used in the DCCN's MRI lab to reset the sample counter when a new sequence is started on the scanner host (which is then picked up by the [fMRI gui_streamer](/getting_started/realtime/fmri) tool).
 
 The tool is started from the command line by typing