MEG Wiki - User contributions [en]

SQUIGGLES Computer Login

2019-06-26T17:28:32Z

Jeff: /* VNC */

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

==FastX Connection (Preferred Connection):==
FastX is an alternative to VNC connect. It provides a more straightforward connection than VNC. Previously, we have had an issue with a large number of users logging in at once using the VNC. FastX resolves this issue.

The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client

[[File: FastX_config.png]]

Steps to setup the connection: 
1. Open fastX 
2. Click the plus to start a new connection 
3. Enter the Connection Name, host (sguiggles.rcc.mcw.edu), and user (rcc username) 
4. Click the plus to enter a session. Use /etc/X11/xinit/xinitrc for the command 

==VNC (Old method - still works, FastX may be more reliable)==
===VNC User Ports:===
(make sure to log in under your port number)
{| class="wikitable"
|-
! scope="col"|User
! scope="col"|Port
|-
|Jeff Stout
|5910,5911
|-
|Joe Heffernan
|5912
|-
|Candida Ustine
|5914
|-
|Manoj Raghavan
|5913
|-
|Chad Carlson
|5915
|-
|Chris Anderson
|5916
|-
|Serena Thompson
|5917
|-
|Patrick Bauer
|5918
|-
|Jeff Binder
|5919
|-
|Leo Fernandino
|5920
|-
|Lisa Conant
|5921
|-
|Lindsay Nelson
|5922
|-
|Nick Guzowski
|5923
|-
|Zack Harper
|5924
|-
|Bill Gross
|5925
|-
|Michelle Kassel
|5926
|-
|Greg McQuestion
|5927
|-
|Monica Keith
|5928
|-
|Priyanka Shah
|5929
|-
|Vahab Youssofzadeh
|5931
|}

===Connecting to Squiggles===
====For Mac or Linux====
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu

====For Windows====
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

[[File:Putty config2 tunnel.PNG]]

===Logging into VNC session===
Once connected to squiggles over ssh

====Creating a VNC session====
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
vncserver :## -geometry 1900x1200 (This will open a vnc session on port 59## with a resolution of 1900x1200) The ## must match your port number for this to work.
====Connecting to a VNC session====
Use realvnc viewer to log into your VNC session.
=====VNC viewer download=====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
=====Log in using RealVNC=====
Open vncviewer
In the top bar that accepts a VNC Server address 
type localhost:## (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password 
Once the VNC window is open, log into the server using your RCC password

SQUIGGLES Computer Login

2019-06-26T17:13:03Z

Jeff: /* FastX Connection (Prefferred Connection): */

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

==FastX Connection (Prefferred Connection):==
FastX is an alternative to VNC connections. This provides a more straightforward connection than VNC. Also we have had some issues with the large number of users logging in at once with VNC.

The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client

[[File: FastX_config.png]]

See above 
1-Open fastX 
2-Click the plus to start a new connection 
3-Enter Connection Name, host (sguiggles.rcc.mcw.edu), and user (your rcc username) 
4-Click the plus to enter a session. Use /etc/X11/xinit/xinitrc for the command 

==VNC==
===VNC User Ports:===
(make sure to log in under your port number)
{| class="wikitable"
|-
! scope="col"|User
! scope="col"|Port
|-
|Jeff Stout
|5910,5911
|-
|Joe Heffernan
|5912
|-
|Candida Ustine
|5914
|-
|Manoj Raghavan
|5913
|-
|Chad Carlson
|5915
|-
|Chris Anderson
|5916
|-
|Serena Thompson
|5917
|-
|Patrick Bauer
|5918
|-
|Jeff Binder
|5919
|-
|Leo Fernandino
|5920
|-
|Lisa Conant
|5921
|-
|Lindsay Nelson
|5922
|-
|Nick Guzowski
|5923
|-
|Zack Harper
|5924
|-
|Bill Gross
|5925
|-
|Michelle Kassel
|5926
|-
|Greg McQuestion
|5927
|-
|Monica Keith
|5928
|-
|Priyanka Shah
|5929
|-
|Vahab Youssofzadeh
|5931
|}

===Connecting to Squiggles===
====For Mac or Linux====
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu

====For Windows====
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

[[File:Putty config2 tunnel.PNG]]

===Logging into VNC session===
Once connected to squiggles over ssh

====Creating a VNC session====
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
vncserver :## -geometry 1900x1200 (This will open a vnc session on port 59## with a resolution of 1900x1200) The ## must match your port number for this to work.
====Connecting to a VNC session====
Use realvnc viewer to log into your VNC session.
=====VNC viewer download=====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
=====Log in using RealVNC=====
Open vncviewer
In the top bar that accepts a VNC Server address 
type localhost:## (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password 
Once the VNC window is open, log into the server using your RCC password

SQUIGGLES Computer Login

2019-06-26T17:10:01Z

Jeff: /* FastX Connection (Prefferred Connection): */

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

==FastX Connection (Prefferred Connection):==
FastX is an alternative to VNC connections. This provides a more straightforward connection than VNC. Also we have had some issues with the large number of users logging in at once with VNC.

The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client

[[File: FastX_config.png]]

See above 
1-Open fastX 
2-Click the plus to start a new connection 
3-Enter Connection Name, host (sguiggles.rcc.mcw.edu), and user (your rcc username) 
4-Click play 
5-There are at least two different session windows (you can click the pencil and enter either gnome-session or /etc/X11/xinit/xinitrc). The xinitrc was being used by vnc. 

==VNC==
===VNC User Ports:===
(make sure to log in under your port number)
{| class="wikitable"
|-
! scope="col"|User
! scope="col"|Port
|-
|Jeff Stout
|5910,5911
|-
|Joe Heffernan
|5912
|-
|Candida Ustine
|5914
|-
|Manoj Raghavan
|5913
|-
|Chad Carlson
|5915
|-
|Chris Anderson
|5916
|-
|Serena Thompson
|5917
|-
|Patrick Bauer
|5918
|-
|Jeff Binder
|5919
|-
|Leo Fernandino
|5920
|-
|Lisa Conant
|5921
|-
|Lindsay Nelson
|5922
|-
|Nick Guzowski
|5923
|-
|Zack Harper
|5924
|-
|Bill Gross
|5925
|-
|Michelle Kassel
|5926
|-
|Greg McQuestion
|5927
|-
|Monica Keith
|5928
|-
|Priyanka Shah
|5929
|-
|Vahab Youssofzadeh
|5931
|}

===Connecting to Squiggles===
====For Mac or Linux====
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu

====For Windows====
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

[[File:Putty config2 tunnel.PNG]]

===Logging into VNC session===
Once connected to squiggles over ssh

====Creating a VNC session====
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
vncserver :## -geometry 1900x1200 (This will open a vnc session on port 59## with a resolution of 1900x1200) The ## must match your port number for this to work.
====Connecting to a VNC session====
Use realvnc viewer to log into your VNC session.
=====VNC viewer download=====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
=====Log in using RealVNC=====
Open vncviewer
In the top bar that accepts a VNC Server address 
type localhost:## (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password 
Once the VNC window is open, log into the server using your RCC password

2019-06-26T16:13:14Z

Jeff:

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

==FastX Connection:==
FastX is an alternative to VNC connections. This provides a more straightforward connection than VNC. Also we have had some issues with the large number of users logging in at once with VNC.

The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client

[[File: FastX_login_mod.png]]

See above
1-Open fastX
2-Click the plus to start a new connection
3-Enter Connection Name, host (sguiggles.rcc.mcw.edu), and user (your rcc username)
4-Click play
5-There are at least two different session windows (you can click the pencil and enter either gnome-session or /etc/X11/xinit/xinitrc). The xinitrc was being used by vnc.

==User Ports:==
(make sure to log in under your port number)
{| class="wikitable"
|-
! scope="col"|User
! scope="col"|Port
|-
|Jeff Stout
|5910,5911
|-
|Joe Heffernan
|5912
|-
|Candida Ustine
|5914
|-
|Manoj Raghavan
|5913
|-
|Chad Carlson
|5915
|-
|Chris Anderson
|5916
|-
|Serena Thompson
|5917
|-
|Patrick Bauer
|5918
|-
|Jeff Binder
|5919
|-
|Leo Fernandino
|5920
|-
|Lisa Conant
|5921
|-
|Lindsay Nelson
|5922
|-
|Nick Guzowski
|5923
|-
|Zack Harper
|5924
|-
|Bill Gross
|5925
|-
|Michelle Kassel
|5926
|-
|Greg McQuestion
|5927
|-
|Monica Keith
|5928
|-
|Priyanka Shah
|5929
|-
|Vahab Youssofzadeh
|5931
|}

==Connecting to Squiggles==
===For Mac or Linux===
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu

===For Windows===
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

[[File:Putty config2 tunnel.PNG]]

==Logging into VNC session==
Once connected to squiggles over ssh

===Creating a VNC session===
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
vncserver :## -geometry 1900x1200 (This will open a vnc session on port 59## with a resolution of 1900x1200) The ## must match your port number for this to work.
===Connecting to a VNC session===
Use realvnc viewer to log into your VNC session.
====VNC viewer download====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
====Log in using RealVNC====
Open vncviewer
In the top bar that accepts a VNC Server address 
type localhost:## (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password 
Once the VNC window is open, log into the server using your RCC password

File:FastX login mod.png

2019-06-26T16:07:48Z

Jeff:

SQUIGGLES Computer Login

2019-06-26T16:06:44Z

Jeff:

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

==FastX Connection:==
SECTION UNDER CONSTRUCTION
FastX is an alternative to VNC connections. This provides a more straightforward connection than VNC. Also we have had some issues with the large number of users logging in at once with VNC.

The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client

Open the FastX software --- image

Click connect ---image

Enter either gnome-session or /etc/X11/xinit/xinitrc (<< this is the style used with VNC)

==User Ports:==
(make sure to log in under your port number)
{| class="wikitable"
|-
! scope="col"|User
! scope="col"|Port
|-
|Jeff Stout
|5910,5911
|-
|Joe Heffernan
|5912
|-
|Candida Ustine
|5914
|-
|Manoj Raghavan
|5913
|-
|Chad Carlson
|5915
|-
|Chris Anderson
|5916
|-
|Serena Thompson
|5917
|-
|Patrick Bauer
|5918
|-
|Jeff Binder
|5919
|-
|Leo Fernandino
|5920
|-
|Lisa Conant
|5921
|-
|Lindsay Nelson
|5922
|-
|Nick Guzowski
|5923
|-
|Zack Harper
|5924
|-
|Bill Gross
|5925
|-
|Michelle Kassel
|5926
|-
|Greg McQuestion
|5927
|-
|Monica Keith
|5928
|-
|Priyanka Shah
|5929
|-
|Vahab Youssofzadeh
|5931
|}

==Connecting to Squiggles==
===For Mac or Linux===
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu

===For Windows===
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

[[File:Putty config2 tunnel.PNG]]

==Logging into VNC session==
Once connected to squiggles over ssh

===Creating a VNC session===
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
vncserver :## -geometry 1900x1200 (This will open a vnc session on port 59## with a resolution of 1900x1200) The ## must match your port number for this to work.
===Connecting to a VNC session===
Use realvnc viewer to log into your VNC session.
====VNC viewer download====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
====Log in using RealVNC====
Open vncviewer
In the top bar that accepts a VNC Server address 
type localhost:## (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password 
Once the VNC window is open, log into the server using your RCC password

SQUIGGLES Computer Login

2019-06-26T15:28:31Z

Jeff:

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

==FastX Connection:==
SECTION UNDER CONSTRUCTION
FastX is an alternative to VNC connections. This provides a more straightforward connection than VNC. Also we have had some issues with the large number of users logging in at once with VNC.

The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/ (I am currently unsure if we have a university download or if you need to start a trial ---UPDATE)

Open the FastX software --- image

Click connect ---image

Enter either gnome-session or /etc/X11/xinit/xinitrc (<< this is the style used with VNC)

==User Ports:==
(make sure to log in under your port number)
{| class="wikitable"
|-
! scope="col"|User
! scope="col"|Port
|-
|Jeff Stout
|5910,5911
|-
|Joe Heffernan
|5912
|-
|Candida Ustine
|5914
|-
|Manoj Raghavan
|5913
|-
|Chad Carlson
|5915
|-
|Chris Anderson
|5916
|-
|Serena Thompson
|5917
|-
|Patrick Bauer
|5918
|-
|Jeff Binder
|5919
|-
|Leo Fernandino
|5920
|-
|Lisa Conant
|5921
|-
|Lindsay Nelson
|5922
|-
|Nick Guzowski
|5923
|-
|Zack Harper
|5924
|-
|Bill Gross
|5925
|-
|Michelle Kassel
|5926
|-
|Greg McQuestion
|5927
|-
|Monica Keith
|5928
|-
|Priyanka Shah
|5929
|-
|Vahab Youssofzadeh
|5931
|}

==Connecting to Squiggles==
===For Mac or Linux===
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu

===For Windows===
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

[[File:Putty config2 tunnel.PNG]]

==Logging into VNC session==
Once connected to squiggles over ssh

===Creating a VNC session===
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
vncserver :## -geometry 1900x1200 (This will open a vnc session on port 59## with a resolution of 1900x1200) The ## must match your port number for this to work.
===Connecting to a VNC session===
Use realvnc viewer to log into your VNC session.
====VNC viewer download====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
====Log in using RealVNC====
Open vncviewer
In the top bar that accepts a VNC Server address 
type localhost:## (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password 
Once the VNC window is open, log into the server using your RCC password

ECP MEG Data Folders

2019-06-10T20:19:39Z

Jeff: /* Cleaning */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]

===Processing===
====Initialization - Subject Dataframe ====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|400px]]
 
The Contents of the subject dataframe are stored in a .csv file which can be opened using LibreOffice
The data file is stored in the row, and all of the documented processing steps are the columns
[[file:Subject DataFrame.PNG|1400px]]

====Initialization - Subject Processing Folders====
init_subject_process - A process folder is created for each dataset type (multiple runs are copied into each folder)
The _tsss.fif files are links to the tSSS folder. If these folders are deleted, it will not affect the data in the tSSS folder
[[file:Process setup.png|300px]]

=====Cleaning=====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
The processing creates a folder called Process_*DataType*/Clean with the output of the baddata analysis
[[file:Clean data.png|400px]]

ECP MEG Data Folders

2019-06-10T20:16:16Z

Jeff:

ECP MEG Data Folders

2019-06-10T20:15:20Z

Jeff: /* Initialization - Subject Dataframe */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]

===Processing===
====Initialization - Subject Dataframe ====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|400px]]
 
The Contents of the subject dataframe are stored in a .csv file which can be opened using LibreOffice
The data file is stored in the row, and all of the documented processing steps are the columns
[[file:Subject DataFrame.PNG|1400px]]

====Initialization - Subject Processing Folders====
init_subject_process - A process folder is created for each dataset type (multiple runs are copied into each folder)
The _tsss.fif files are links to the tSSS folder. If these folders are deleted, it will not affect the data in the tSSS folder
[[file:Process setup.png|300px]]

=====Cleaning=====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T20:14:12Z

Jeff: /* Initialization - Subject Processing Folders */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]

===Processing===
====Initialization - Subject Dataframe ====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|400px]]
 
The Contents of the subject dataframe are stored in a .csv file which can be opened using LibreOffice
[[file:Subject DataFrame.PNG|1400px]]

====Initialization - Subject Processing Folders====
init_subject_process - A process folder is created for each dataset type (multiple runs are copied into each folder)
The _tsss.fif files are links to the tSSS folder. If these folders are deleted, it will not affect the data in the tSSS folder
[[file:Process setup.png|300px]]

=====Cleaning=====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T20:13:01Z

Jeff: /* Initialization - Subject Processing Folders */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]

===Processing===
====Initialization - Subject Dataframe ====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|400px]]
 
The Contents of the subject dataframe are stored in a .csv file which can be opened using LibreOffice
[[file:Subject DataFrame.PNG|1400px]]

====Initialization - Subject Processing Folders====
init_subject_process - A process folder is created for each dataset type (multiple runs are copied into each folder)
[[file:Process setup.png|300px]]

=====Cleaning=====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T20:12:53Z

Jeff: /* Initialization - Subject Processing Folders */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]

===Processing===
====Initialization - Subject Dataframe ====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|400px]]
 
The Contents of the subject dataframe are stored in a .csv file which can be opened using LibreOffice
[[file:Subject DataFrame.PNG|1400px]]

====Initialization - Subject Processing Folders====
init_subject_process - A process folder is created for each dataset type (multiple runs are copied into each folder)
[[file:Process setup.png|400px]]

=====Cleaning=====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

2019-06-10T19:47:38Z

Jeff:

ECP MEG Data Folders

2019-06-10T19:46:21Z

Jeff: /* Initialization */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]
====Proc Folders====
The Process_*DataType* folders are created after

===Processing===
====Initialization====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|400px]]

====Import??====
init_subject_process - creates a folder for each data type and creates a link to the original dataset
====Cleaning====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T19:46:13Z

Jeff: /* Initialization */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]
====Proc Folders====
The Process_*DataType* folders are created after

===Processing===
====Initialization====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|300px]]

====Import??====
init_subject_process - creates a folder for each data type and creates a link to the original dataset
====Cleaning====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T19:46:03Z

Jeff: /* Initialization */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]
====Proc Folders====
The Process_*DataType* folders are created after

===Processing===
====Initialization====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
[[file:AProject Folder.png|200px]]

====Import??====
init_subject_process - creates a folder for each data type and creates a link to the original dataset
====Cleaning====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T19:45:13Z

Jeff: /* Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work */

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders (the format of the data can be seen below)
[[file: RAW format.PNG | 300px]]
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work for further processing

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with the following folders: Anatomy, RAW, tSSS, Process_*DataType*
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
The data is labelled with Subjid+_+DataType+_run+RunNumber+_raw.fif
[[file: RAW format.PNG | 300px]]
====Proc Folders====
The Process_*DataType* folders are created after

===Processing===
====Initialization====
init_subject_dataframe - initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
====Import??====
init_subject_process - creates a folder for each data type and creates a link to the original dataset
====Cleaning====
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

2019-06-10T18:35:04Z

Jeff:

ECP MEG Data Folders

2019-06-10T18:31:32Z

Jeff:

==At the MEG lab:==
Data is acquired to the MEG_acq/ecp/ folder
Data is tSSS processed and organized into raw and tSSS folders
Data is uploaded to to the RCC using scp (/rcc/stor1/projects/ECP/MEG/MEG_Orig)
Data is copied into /rcc/stor1/projects/ECP/MEG/MEG_Work

==Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work==
All subjects have a folder with both the anatomy, RAW, tSSS, Preprocessed, and Processed Data
[[file:ECP Subject.PNG|200px]]

===Anatomy Layout===
Typical Freesurfer layout with BEM process performed
The folder is always labelled Anatomy (a hack to make all folders homogeneous and easier to process)
The Anatomy-trans.fif is created during the MNE python coregistration step
[[file:ECP MEG Anatomy.png|400px]]

===Data Layout===
====RAW and tSSS====
[[file ]]

====Initialized=====
Initialization creates a subject pandas dataframe saved as a csv file in the aProjects folder at the top of the MEG Project folder
Preproc Initialization creates a folder for each data type and creates a link to the original dataset
Cleaning (baddata pipeline) performs ICA removal of heartbeat and eyeblink artifact that is correlated to EOG and ECG electrodes at a threshold of (r=???)
[[file:Clean data.png|400px]]

==RCC preprocessing==
The data is then copied to a folder /rcc/stor1/projects/ECP/MEG/MEG_Work
[[image:Folder layout.png]]

ECP MEG Data Folders

2019-06-10T17:57:23Z

Jeff: /* RAW and tSSS */

ECP MEG Data Folders

2019-06-10T17:55:32Z

Jeff: /* Folder Layout /rcc/stor1/projects/ECP/MEG/MEG_Work */