Below are some general guidelines that help you analyze your data 
Thinking about this early on, is extremely helpful as it can prevent you from acquired a lot of data without the required inputs. Some things can not be corrected after the fact 

=Create a github page of the project=
Sign up for a github account: github.com 
Create a github page of the project - this page can initially be a private repository if you prefer. Try to give it a reasonably focused name and NOT just Data_Analysis. This type of setup is often required for publication and can be very helpful in the understanding of the study for reproducibility. This excercise is very important in thinking about your end goal - otherwise your data analysis can become a wandering mess. Below are some things that are very helpful to put on a data analysis repository.
==Describe the data acquisition task by task==
Auditory M100 task:
Tone burst auditory stimuli were delivered bilaterally to the subject using the ....

Somatosensory task:
Pneumatic stimulation was performed on the index finger at a rate of approximately 2 times per second with a jitter of 20 ms ...

==For each task describe the auxilliary channels:==
UADC001 was used for left hand patient responses
UADC002 was used for right hand patient responses
UADC016 was used for the projector channel to correct for timing delays
UPPT001 codes the stimuli values

===Describe what each PPT value codes===
2: congruent word stimuli
4: incongruent word stimuli
6: distractor words
8: high noise condition
....

==If your logfile incorporates special data that is not in your meg dataset - list these entries==
The logfile codes out ...

==If there is external data that is collected - describe how this will be incorporated with the data==
External camera data was used to judge facial expressions. Timing triggers were sent to the

==Describe Your Hypothesis About The Results==
We expect to see activation in the left dorsolateral prefrontal area 
Timing - Prior literature has shown that 

=Add Markerfile information / Oragnize Data / QA Data=
[[https://megcore.nih.gov/index.php/BIDS_GUIs BIDS GUI information]]

Organizing an MEG project

2025-01-31T15:02:32Z

Jstout: /* Describe Your Hypothesis About The Results */

Organizing an MEG project

2025-01-31T15:01:41Z

Jstout:

Below are some general guidelines that help you analyze your data 
Thinking about this early on, is extremely helpful as it can prevent you from acquired a lot of data without the required inputs. Some things can not be corrected after the fact 

=Create a github page of the project=
Sign up for a github account: github.com 
Create a github page of the project - this page can initially be a private repository if you prefer. Try to give it a reasonably focused name and NOT just Data_Analysis. This type of setup is often required for publication and can be very helpful in the understanding of the study for reproducibility. This excercise is very important in thinking about your end goal - otherwise your data analysis can become a wandering mess. Below are some things that are very helpful to put on a data analysis repository.
==Describe the data acquisition task by task==
Auditory M100 task:
Tone burst auditory stimuli were delivered bilaterally to the subject using the ....

Somatosensory task:
Pneumatic stimulation was performed on the index finger at a rate of approximately 2 times per second with a jitter of 20 ms ...

==For each task describe the auxilliary channels:==
UADC001 was used for left hand patient responses
UADC002 was used for right hand patient responses
UADC016 was used for the projector channel to correct for timing delays
UPPT001 codes the stimuli values

===Describe what each PPT value codes===
2: congruent word stimuli
4: incongruent word stimuli
6: distractor words
8: high noise condition
....

==If your logfile incorporates special data that is not in your meg dataset - list these entries==
The logfile codes out ...

==If there is external data that is collected - describe how this will be incorporated with the data==
External camera data was used to judge facial expressions. Timing triggers were sent to the

==Describe Your Hypothesis About The Results==
We expect to see activation in the left dorsolateral prefrontal area 
Timing - Prior literature has shown that 

=Add Markerfile information / Oragnize Data / QA Data
[[https://megcore.nih.gov/index.php/BIDS_GUIs | BIDS GUI information]]

BIDS GUIs

2025-01-28T14:54:48Z

Jstout: /* Prep Data for BIDS */

==What is BIDS==
https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

==Biowulf Setup==
https://megcore.nih.gov/index.php/MEG_Biowulf_Setup

==On Biowulf==
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html 
NOTE: Remember to change the resolution to be close to your monitor (top right corner) 

On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=24G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

==Prep Data for BIDS==
Add event coding to the datasets before converting to bids 

Open a dataset: 
This will read all trigger lines (analog and digital) and populate lines 
The triggers can be evaluated on upgoing or downgoing portions of the trigger squarewave 
[[File:Trigger_gui_initial_loading.png | 900px]] 
Name all of the appropriate trigger lines (digital and analogue codes) 
Hitting the '''Update Event Names''' button to access the derivative event menu. You can now make events from other events. 
'''DO NOT EDIT THE TOP PANEL AFTER HITTING THIS BUTTON''' 

[[File:Trigger_gui_initial_entry.png | 900px]] 
The derivative event panel allows you to make new events from other events. 
Select a lead event from the dropdown (the menu will display any events that have been established above the current line) 
Select a lag event from the dropdown 
Click the checkbox next to the event that should establish the timing. 
Enter the window to search from the lead event (this can include negative numbers in the initial entry) 
Enter the name that the new derivative event will be called.
Click the '''ADD''' button. This will add a new line and add this event to the dropdown list and the keep events panel at the bottom 
[[File:Trigger_gui_parsemarks_demo.png | 700px]] 

Anything not named cannot be used below to parse two input codes or to save out to the MarkerFile.mrk event code file 

Once finished coding the events - the bottom panel determines which events are written to the Markerfile - intermediary events not selected will be ignored 
D-prime coding is often used (Hit, Miss, False Alarm, Correct Rejection)

Click create script to generate a script that can be used for all subjects under this protocol 
[[File:Event_processing_generated_script.png | 700px]] 

==Create BIDS Dataset Using GUI==
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
[[File:Make_meg_bids_gui_startup.png | 700px]]

=QA GUI Overview=
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

==Project Panel==
[[File:Project_panel_view.png | 700px]]

The project panel consists of tiles with each subject ID. 
'''Subject ID Button''':
* Meg: Number of MEG files
* Mri: If they have an MRI
* FS: Has the freesurfer been run and is successful
* EVT: Events pass QA (Currently this is just green and doesn't QA)

'''QA File''': 
Set the appropriate number of events in a successful meg dataset 

'''Top Right Dropdown''': 
Filter for specific tasks - this will adjust the color coding on the MEG 

'''Run Freesurfer Button''': 
Submits freesurfer sbatch job to biowulf for each missing subject with an mri 

'''Run MEGnet''': 
Currently a placeholder 

'''Prev/Next''': 
Advance to the next panel if more than a single grid of subjects is available 

==Subject Panel==
[[File:Gui_subject_panel.png | 700px]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task 
[[File:Subject_panel_switch_task_epochs.png | 700px]]

==MRI Viewing==
[[File:Plot_mri_views.png | 700px ]]

==MEG Plotting==
Dropdown with MEG plotting options 
[[File:Meg_plotting_options.png | 700px]]

Plot All MEG channels (unorganized view of All channels) 
[[File:Plot_meg_all.png | 700px]]

Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display 
[[File:Plot_meg_fullview.png | 700px]]

Plot Trigger Channels 
Note the auditory delay added to the triggerline pulse 
[[File:Plot_meg_trigview.png | 700px]]

Setting BAD Channels and BAD Epochs (Must do WriteBads afterwards) 
1) Plot a dataset (montage56 is preferable) with a wide bandwidth filter fmin=0.5 and fmax=110. The notch should be checked 
2) BAD Epochs: Click on "Add Description" >> Set the name. The name '''must start''' with '''BAD_''' or it will not be written. 
3) Left click and drag to set a bad time period. 
[[File:Select_bad_epochs.png | 700px]]

4) Clicking on a channel will set it to grey. This sets the channel to BAD ('''!!Warning it is easy to accidentally do this!!'''). 
5) After closing the plot, you can then click the write Bad Channels and Bad Epochs. 
[[File:Write_bads_button.png | 700px]] 
[[File:Bads_write_confirmation.png | 300px]]

BIDS GUIs

2025-01-28T14:54:15Z

Jstout: /* Prep Data for BIDS */

==What is BIDS==
https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

==Biowulf Setup==
https://megcore.nih.gov/index.php/MEG_Biowulf_Setup

==On Biowulf==
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html 
NOTE: Remember to change the resolution to be close to your monitor (top right corner) 

On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=24G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

==Prep Data for BIDS==
Add event coding to the datasets before converting to bids 

Open a dataset: 
This will read all trigger lines (analog and digital) and populate lines 
The triggers can be evaluated on upgoing or downgoing portions of the trigger squarewave 
[[File:Trigger_gui_initial_loading.png | 900px]] 
Name all of the appropriate trigger lines (digital and analogue codes) 
Hitting the '''Update Event Names''' button to access the derivative event menu. You can now make events from other events. 
'''DO NOT EDIT THE TOP PANEL AFTER HITTING THIS BUTTON''' 

[[File:Trigger_gui_initial_entry.png | 700px]] 
The derivative event panel allows you to make new events from other events. 
Select a lead event from the dropdown (the menu will display any events that have been established above the current line) 
Select a lag event from the dropdown 
Click the checkbox next to the event that should establish the timing. 
Enter the window to search from the lead event (this can include negative numbers in the initial entry) 
Enter the name that the new derivative event will be called.
Click the '''ADD''' button. This will add a new line and add this event to the dropdown list and the keep events panel at the bottom 
[[File:Trigger_gui_parsemarks_demo.png | 700px]] 

Anything not named cannot be used below to parse two input codes or to save out to the MarkerFile.mrk event code file 

Once finished coding the events - the bottom panel determines which events are written to the Markerfile - intermediary events not selected will be ignored 
D-prime coding is often used (Hit, Miss, False Alarm, Correct Rejection)

Click create script to generate a script that can be used for all subjects under this protocol 
[[File:Event_processing_generated_script.png | 700px]] 

==Create BIDS Dataset Using GUI==
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
[[File:Make_meg_bids_gui_startup.png | 700px]]

=QA GUI Overview=
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

==Project Panel==
[[File:Project_panel_view.png | 700px]]

The project panel consists of tiles with each subject ID. 
'''Subject ID Button''':
* Meg: Number of MEG files
* Mri: If they have an MRI
* FS: Has the freesurfer been run and is successful
* EVT: Events pass QA (Currently this is just green and doesn't QA)

'''QA File''': 
Set the appropriate number of events in a successful meg dataset 

'''Top Right Dropdown''': 
Filter for specific tasks - this will adjust the color coding on the MEG 

'''Run Freesurfer Button''': 
Submits freesurfer sbatch job to biowulf for each missing subject with an mri 

'''Run MEGnet''': 
Currently a placeholder 

'''Prev/Next''': 
Advance to the next panel if more than a single grid of subjects is available 

==Subject Panel==
[[File:Gui_subject_panel.png | 700px]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task 
[[File:Subject_panel_switch_task_epochs.png | 700px]]

==MRI Viewing==
[[File:Plot_mri_views.png | 700px ]]

==MEG Plotting==
Dropdown with MEG plotting options 
[[File:Meg_plotting_options.png | 700px]]

Plot All MEG channels (unorganized view of All channels) 
[[File:Plot_meg_all.png | 700px]]

Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display 
[[File:Plot_meg_fullview.png | 700px]]

Plot Trigger Channels 
Note the auditory delay added to the triggerline pulse 
[[File:Plot_meg_trigview.png | 700px]]

Setting BAD Channels and BAD Epochs (Must do WriteBads afterwards) 
1) Plot a dataset (montage56 is preferable) with a wide bandwidth filter fmin=0.5 and fmax=110. The notch should be checked 
2) BAD Epochs: Click on "Add Description" >> Set the name. The name '''must start''' with '''BAD_''' or it will not be written. 
3) Left click and drag to set a bad time period. 
[[File:Select_bad_epochs.png | 700px]]

4) Clicking on a channel will set it to grey. This sets the channel to BAD ('''!!Warning it is easy to accidentally do this!!'''). 
5) After closing the plot, you can then click the write Bad Channels and Bad Epochs. 
[[File:Write_bads_button.png | 700px]] 
[[File:Bads_write_confirmation.png | 300px]]

BIDS GUIs

2025-01-28T14:48:02Z

Jstout: /* Prep Data for BIDS */

==What is BIDS==
https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

==Biowulf Setup==
https://megcore.nih.gov/index.php/MEG_Biowulf_Setup

==On Biowulf==
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html 
NOTE: Remember to change the resolution to be close to your monitor (top right corner) 

On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=24G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

==Prep Data for BIDS==
Add event coding to the datasets before converting to bids 

Open a dataset: 
This will read all trigger lines (analog and digital) and populate lines 
The triggers can be evaluated on upgoing or downgoing portions of the trigger squarewave 
[[File:Trigger_gui_initial_loading.png | 700px]] 
Name all of the appropriate trigger lines (digital and analogue codes) 
Hitting the '''Update Event Names''' button to access the derivative event menu. You can now make events from other events. 
'''DO NOT EDIT THE TOP PANEL AFTER HITTING THIS BUTTON''' 

[[File:Trigger_gui_initial_entry.png | 700px]] 
The derivative event panel allows you to make new events from other events. 
Select a lead event from the dropdown (the menu will display any events that have been established above the current line) 
Select a lag event from the dropdown 
Click the checkbox next to the event that should establish the timing. 
Enter the window to search from the lead event (this can include negative numbers in the initial entry) 
Enter the name that the new derivative event will be called.
Click the '''ADD''' button. This will add a new line and add this event to the dropdown list and the keep events panel at the bottom 
[[File:Trigger_gui_parsemarks_demo.png | 700px]] 

Anything not named cannot be used below to parse two input codes or to save out to the MarkerFile.mrk event code file 

Once finished coding the events - the bottom panel determines which events are written to the Markerfile - intermediary events not selected will be ignored 
D-prime coding is often used (Hit, Miss, False Alarm, Correct Rejection)

Click create script to generate a script that can be used for all subjects under this protocol 
[[File:Event_processing_generated_script.png | 700px]] 

==Create BIDS Dataset Using GUI==
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
[[File:Make_meg_bids_gui_startup.png | 700px]]

=QA GUI Overview=
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

==Project Panel==
[[File:Project_panel_view.png | 700px]]

The project panel consists of tiles with each subject ID. 
'''Subject ID Button''':
* Meg: Number of MEG files
* Mri: If they have an MRI
* FS: Has the freesurfer been run and is successful
* EVT: Events pass QA (Currently this is just green and doesn't QA)

'''QA File''': 
Set the appropriate number of events in a successful meg dataset 

'''Top Right Dropdown''': 
Filter for specific tasks - this will adjust the color coding on the MEG 

'''Run Freesurfer Button''': 
Submits freesurfer sbatch job to biowulf for each missing subject with an mri 

'''Run MEGnet''': 
Currently a placeholder 

'''Prev/Next''': 
Advance to the next panel if more than a single grid of subjects is available 

==Subject Panel==
[[File:Gui_subject_panel.png | 700px]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task 
[[File:Subject_panel_switch_task_epochs.png | 700px]]

==MRI Viewing==
[[File:Plot_mri_views.png | 700px ]]

==MEG Plotting==
Dropdown with MEG plotting options 
[[File:Meg_plotting_options.png | 700px]]

Plot All MEG channels (unorganized view of All channels) 
[[File:Plot_meg_all.png | 700px]]

Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display 
[[File:Plot_meg_fullview.png | 700px]]

Plot Trigger Channels 
Note the auditory delay added to the triggerline pulse 
[[File:Plot_meg_trigview.png | 700px]]

Setting BAD Channels and BAD Epochs (Must do WriteBads afterwards) 
1) Plot a dataset (montage56 is preferable) with a wide bandwidth filter fmin=0.5 and fmax=110. The notch should be checked 
2) BAD Epochs: Click on "Add Description" >> Set the name. The name '''must start''' with '''BAD_''' or it will not be written. 
3) Left click and drag to set a bad time period. 
[[File:Select_bad_epochs.png | 700px]]

4) Clicking on a channel will set it to grey. This sets the channel to BAD ('''!!Warning it is easy to accidentally do this!!'''). 
5) After closing the plot, you can then click the write Bad Channels and Bad Epochs. 
[[File:Write_bads_button.png | 700px]] 
[[File:Bads_write_confirmation.png | 300px]]

File:Event processing generated script.png

2025-01-28T14:46:23Z

Jstout:

BIDS GUIs

2025-01-28T14:44:43Z

Jstout: /* Prep Data for BIDS */

==What is BIDS==
https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

==Biowulf Setup==
https://megcore.nih.gov/index.php/MEG_Biowulf_Setup

==On Biowulf==
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html 
NOTE: Remember to change the resolution to be close to your monitor (top right corner) 

On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=24G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

==Prep Data for BIDS==
Add event coding to the datasets before converting to bids
This section is under construction

Open a dataset: 
This will read all trigger lines (analog and digital) and populate lines 
The triggers can be evaluated on upgoing or downgoing portions of the trigger squarewave 
[[File:Trigger_gui_initial_loading.png | 700px]] 
Name all of the appropriate trigger lines (digital and analogue codes) 
Hitting the '''Update Event Names''' button to access the derivative event menu. You can now make events from other events. 
'''DO NOT EDIT THE TOP PANEL AFTER HITTING THIS BUTTON''' 

[[File:Trigger_gui_initial_entry.png | 700px]] 
The derivative event panel allows you to make new events from other events. 
Select a lead event from the dropdown (the menu will display any events that have been established above the current line) 
Select a lag event from the dropdown 
Click the checkbox next to the event that should establish the timing. 
Enter the window to search from the lead event (this can include negative numbers in the initial entry) 
Enter the name that the new derivative event will be called.
Click the '''ADD''' button. This will add a new line and add this event to the dropdown list and the keep events panel at the bottom 
[[File:Trigger_gui_parsemarks_demo.png | 700px]] 

Anything not named cannot be used below to parse two input codes or to save out to the MarkerFile.mrk event code file 

Once finished coding the events - the bottom panel determines which events are written to the Markerfile - intermediary events not selected will be ignored 
D-prime coding is often used (Hit, Miss, False Alarm, Correct Rejection)

==Create BIDS Dataset Using GUI==
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
[[File:Make_meg_bids_gui_startup.png | 700px]]

=QA GUI Overview=
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

==Project Panel==
[[File:Project_panel_view.png | 700px]]

The project panel consists of tiles with each subject ID. 
'''Subject ID Button''':
* Meg: Number of MEG files
* Mri: If they have an MRI
* FS: Has the freesurfer been run and is successful
* EVT: Events pass QA (Currently this is just green and doesn't QA)

'''QA File''': 
Set the appropriate number of events in a successful meg dataset 

'''Top Right Dropdown''': 
Filter for specific tasks - this will adjust the color coding on the MEG 

'''Run Freesurfer Button''': 
Submits freesurfer sbatch job to biowulf for each missing subject with an mri 

'''Run MEGnet''': 
Currently a placeholder 

'''Prev/Next''': 
Advance to the next panel if more than a single grid of subjects is available 

==Subject Panel==
[[File:Gui_subject_panel.png | 700px]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task 
[[File:Subject_panel_switch_task_epochs.png | 700px]]

==MRI Viewing==
[[File:Plot_mri_views.png | 700px ]]

==MEG Plotting==
Dropdown with MEG plotting options 
[[File:Meg_plotting_options.png | 700px]]

Plot All MEG channels (unorganized view of All channels) 
[[File:Plot_meg_all.png | 700px]]

Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display 
[[File:Plot_meg_fullview.png | 700px]]

Plot Trigger Channels 
Note the auditory delay added to the triggerline pulse 
[[File:Plot_meg_trigview.png | 700px]]

Setting BAD Channels and BAD Epochs (Must do WriteBads afterwards) 
1) Plot a dataset (montage56 is preferable) with a wide bandwidth filter fmin=0.5 and fmax=110. The notch should be checked 
2) BAD Epochs: Click on "Add Description" >> Set the name. The name '''must start''' with '''BAD_''' or it will not be written. 
3) Left click and drag to set a bad time period. 
[[File:Select_bad_epochs.png | 700px]]

4) Clicking on a channel will set it to grey. This sets the channel to BAD ('''!!Warning it is easy to accidentally do this!!'''). 
5) After closing the plot, you can then click the write Bad Channels and Bad Epochs. 
[[File:Write_bads_button.png | 700px]] 
[[File:Bads_write_confirmation.png | 300px]]

BIDS GUIs

2025-01-28T14:32:39Z

Jstout: /* Prep Data for BIDS */

==What is BIDS==
https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

==Biowulf Setup==
https://megcore.nih.gov/index.php/MEG_Biowulf_Setup

==On Biowulf==
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html 
NOTE: Remember to change the resolution to be close to your monitor (top right corner) 

On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=24G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

==Prep Data for BIDS==
Add event coding to the datasets before converting to bids
This section is under construction

Open a dataset: 
This will read all trigger lines (analog and digital) and populate lines 
The triggers can be evaluated on upgoing or downgoing portions of the trigger squarewave 
[[File:Trigger_gui_initial_loading.png | 700px]] 
Name all of the appropriate trigger lines (digital and analogue codes) 
Hitting the '''Update Event Names''' button to access the derivative event menu. You can now make events from other events. 
'''DO NOT EDIT THE TOP PANEL AFTER HITTING THIS BUTTON''' 

[[File:Trigger_gui_initial_entry.png | 700px]] 
The derivative event panel allows you to make new events from other events. 
Select a lead event from the dropdown (the menu will display any events that have been established above the current line) 
Select a lag event from the dropdown 
Click the checkbox next to the event that should establish the timing. 
Enter the window to search from the lead event (this can include negative numbers in the initial entry) 
Enter the name that the new derivative event will be called.
Click the '''ADD''' button. This will add a new line and add this event to the dropdown list and the keep events panel at the bottom 
[[File:Trigger_gui_parsemarks_demo.png | 700px]] 

Anything not named cannot be used below to parse two input codes or to save out to the MarkerFile.mrk event code file 

Parse marks takes two "named" inputs from above and allows you to compare their trigger timing to create a new event. Use the dropdown menus to select an event for comparison. The checkboxes next to the dropdowns determine which event codes the timing of the derived event. The new name of the event is entered at the end of the line. Hit the set button to add this new event to the list of names. Hit the add button to create a new line for parsing -- the event that you just created can now be used to parse additional events. 
Once finished coding the events - the bottom panel determines which events are written to the Markerfile - intermediary events can be ignored 
D-prime coding is often used (Hit, Miss, False Alarm, ...)

==Create BIDS Dataset Using GUI==
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
[[File:Make_meg_bids_gui_startup.png | 700px]]

=QA GUI Overview=
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

==Project Panel==
[[File:Project_panel_view.png | 700px]]

The project panel consists of tiles with each subject ID. 
'''Subject ID Button''':
* Meg: Number of MEG files
* Mri: If they have an MRI
* FS: Has the freesurfer been run and is successful
* EVT: Events pass QA (Currently this is just green and doesn't QA)

'''QA File''': 
Set the appropriate number of events in a successful meg dataset 

'''Top Right Dropdown''': 
Filter for specific tasks - this will adjust the color coding on the MEG 

'''Run Freesurfer Button''': 
Submits freesurfer sbatch job to biowulf for each missing subject with an mri 

'''Run MEGnet''': 
Currently a placeholder 

'''Prev/Next''': 
Advance to the next panel if more than a single grid of subjects is available 

==Subject Panel==
[[File:Gui_subject_panel.png | 700px]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task 
[[File:Subject_panel_switch_task_epochs.png | 700px]]

==MRI Viewing==
[[File:Plot_mri_views.png | 700px ]]

==MEG Plotting==
Dropdown with MEG plotting options 
[[File:Meg_plotting_options.png | 700px]]

Plot All MEG channels (unorganized view of All channels) 
[[File:Plot_meg_all.png | 700px]]

Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display 
[[File:Plot_meg_fullview.png | 700px]]

Plot Trigger Channels 
Note the auditory delay added to the triggerline pulse 
[[File:Plot_meg_trigview.png | 700px]]

Setting BAD Channels and BAD Epochs (Must do WriteBads afterwards) 
1) Plot a dataset (montage56 is preferable) with a wide bandwidth filter fmin=0.5 and fmax=110. The notch should be checked 
2) BAD Epochs: Click on "Add Description" >> Set the name. The name '''must start''' with '''BAD_''' or it will not be written. 
3) Left click and drag to set a bad time period. 
[[File:Select_bad_epochs.png | 700px]]

4) Clicking on a channel will set it to grey. This sets the channel to BAD ('''!!Warning it is easy to accidentally do this!!'''). 
5) After closing the plot, you can then click the write Bad Channels and Bad Epochs. 
[[File:Write_bads_button.png | 700px]] 
[[File:Bads_write_confirmation.png | 300px]]

BIDS GUIs

2025-01-28T14:30:45Z

2025-01-24T21:50:19Z

Jstout:

==What is BIDS==
https://bids-specification.readthedocs.io/en/stable/

BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG). BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/... The main advantage is that common code can be generated to process data organized in a standard format. Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...). Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

==Biowulf Setup==
https://megcore.nih.gov/index.php/MEG_Biowulf_Setup

==On Biowulf==
Log into biowulf using NoMachine. Setup instructions here: https://hpc.nih.gov/docs/nx.html 
NOTE: Remember to change the resolution to be close to your monitor (top right corner) 

On biowulf open a terminal and start a compute node using the commands below
sinteractive --mem=16G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly

module use --append /data/MEGmodules/modulefiles
module load mne/dev1.5.1

==Prep Data for BIDS==
Add event coding to the datasets before converting to bids
This section is under construction

Open a dataset: 

Name all of the appropriate trigger lines (digital and analogue codes) 
The triggers can be evaluated on upgoing or downgoing portions of the trigger squarewave 
Anything not named cannot be used below to parse two input codes or to save out to the MarkerFile.mrk event code file 

Parse marks takes two "named" inputs from above and allows you to compare their trigger timing to create a new event. Use the dropdown menus to select an event for comparison. The checkboxes next to the dropdowns determine which event codes the timing of the derived event. The new name of the event is entered at the end of the line. Hit the set button to add this new event to the list of names. Hit the add button to create a new line for parsing -- the event that you just created can now be used to parse additional events. 
Once finished coding the events - the bottom panel determines which events are written to the Markerfile - intermediary events can be ignored 
D-prime coding is often used (Hit, Miss, False Alarm, ...)

==Create BIDS Dataset Using GUI==
https://megcore.nih.gov/MEG/BIDS_gui_080224_anon.pdf
make_meg_bids_gui.py
[[File:Make_meg_bids_gui_startup.png | 700px]]

=QA GUI Overview=
Launch the QA gui
bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

==Project Panel==
[[File:Project_panel_view.png | 700px]]

The project panel consists of tiles with each subject ID. 
'''Subject ID Button''':
* Meg: Number of MEG files
* Mri: If they have an MRI
* FS: Has the freesurfer been run and is successful
* EVT: Events pass QA (Currently this is just green and doesn't QA)

'''QA File''': 
Set the appropriate number of events in a successful meg dataset 

'''Top Right Dropdown''': 
Filter for specific tasks - this will adjust the color coding on the MEG 

'''Run Freesurfer Button''': 
Submits freesurfer sbatch job to biowulf for each missing subject with an mri 

'''Run MEGnet''': 
Currently a placeholder 

'''Prev/Next''': 
Advance to the next panel if more than a single grid of subjects is available 

==Subject Panel==
[[File:Gui_subject_panel.png | 700px]]

==Task Switcher==
Changing the task - shows the number of epochs in the selected task 
[[File:Subject_panel_switch_task_epochs.png | 700px]]

==MRI Viewing==
[[File:Plot_mri_views.png | 700px ]]

==MEG Plotting==
Dropdown with MEG plotting options 
[[File:Meg_plotting_options.png | 700px]]

Plot All MEG channels (unorganized view of All channels) 
[[File:Plot_meg_all.png | 700px]]

Plot whole head - subset of meg channels representing the Left (top half) to Right (bottom half) display 
[[File:Plot_meg_fullview.png | 700px]]

Plot Trigger Channels 
Note the auditory delay added to the triggerline pulse 
[[File:Plot_meg_trigview.png | 700px]]

Setting BAD Channels and BAD Epochs (Must do WriteBads afterwards) 
1) Plot a dataset (montage56 is preferable) with a wide bandwidth filter fmin=0.5 and fmax=110. The notch should be checked 
2) BAD Epochs: Click on "Add Description" >> Set the name. The name '''must start''' with '''BAD_''' or it will not be written. 
3) Left click and drag to set a bad time period. 
[[File:Select_bad_epochs.png | 700px]]

4) Clicking on a channel will set it to grey. This sets the channel to BAD ('''!!Warning it is easy to accidentally do this!!'''). 
5) After closing the plot, you can then click the write Bad Channels and Bad Epochs. 
[[File:Write_bads_button.png | 700px]] 
[[File:Bads_write_confirmation.png | 300px]]