BIDS GUIs - Revision history

Jstout: /* Prep Data for BIDS */

2025-01-31T21:50:51Z

Prep Data for BIDS

← Older revision		Revision as of 17:50, 31 January 2025
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	D-prime coding is often used (Hit, Miss, False Alarm, Correct Rejection)		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 <br>		Click '''Write Parser File''' to generate a script that can be used for all subjects under this protocol <br>
	[[File:Event_processing_generated_script.png \| 700px]]<br>		[[File:Event_processing_generated_script.png \| 700px]]<br>
	<br>		<br>

Jstout: /* What is BIDS */

2025-01-31T21:04:11Z

What is BIDS

← Older revision		Revision as of 17:04, 31 January 2025
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	==What is BIDS==		==What is BIDS==
	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.		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.

	https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetoencephalography.html <br>		https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetoencephalography.html <br>

Jstout: /* What is BIDS */

2025-01-31T21:03:43Z

What is BIDS

← Older revision		Revision as of 17:03, 31 January 2025
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	==What is BIDS==		==What is BIDS==
⚫	https://bids-specification.readthedocs.io/en/stable/ <br>
⚫	https://megcore.nih.gov/index.php/Mne_bids_pipeline <br>

	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.		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.

		⚫	https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetoencephalography.html <br>
		⚫	https://megcore.nih.gov/index.php/Mne_bids_pipeline <br>

	==Biowulf Setup==		==Biowulf Setup==

Jstout: /* What is BIDS */

2025-01-31T20:59:00Z

What is BIDS

← Older revision		Revision as of 16:59, 31 January 2025
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	==What is BIDS==		==What is BIDS==
	https://bids-specification.readthedocs.io/en/stable/		https://bids-specification.readthedocs.io/en/stable/ <br>
			https://megcore.nih.gov/index.php/Mne_bids_pipeline <br>

	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.		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.

Jstout: /* MRI Viewing */

2025-01-31T20:21:34Z

MRI Viewing

← Older revision		Revision as of 16:21, 31 January 2025
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	==MRI Viewing==		==MRI Viewing==
	Plot FIDS works on the base MRI and doesn't require any prep.		Plot FIDS works on the base MRI and doesn't require any prep. <br>
	To plot the 3D coreg - Freesurfer must be processed on the subject and the MRI preprocessing must have been completed <br>		To plot the 3D coreg - Freesurfer must be processed on the subject and the MRI preprocessing must have been completed <br>
	[[File:Plot_mri_views.png \| 700px ]]		[[File:Plot_mri_views.png \| 700px ]]

Jstout: /* MRI Viewing */

2025-01-31T20:21:20Z

MRI Viewing

← Older revision		Revision as of 16:21, 31 January 2025
Line 106:		Line 106:

	==MRI Viewing==		==MRI Viewing==
			Plot FIDS works on the base MRI and doesn't require any prep.
	To plot the 3D coreg - Freesurfer must be processed on the subject and the MRI preprocessing must have been completed <br>		To plot the 3D coreg - Freesurfer must be processed on the subject and the MRI preprocessing must have been completed <br>
	[[File:Plot_mri_views.png \| 700px ]]		[[File:Plot_mri_views.png \| 700px ]]

Jstout: /* MRI Viewing */

2025-01-31T20:20:33Z

MRI Viewing

← Older revision		Revision as of 16:20, 31 January 2025
Line 106:		Line 106:

	==MRI Viewing==		==MRI Viewing==
			To plot the 3D coreg - Freesurfer must be processed on the subject and the MRI preprocessing must have been completed <br>
	[[File:Plot_mri_views.png \| 700px ]]		[[File:Plot_mri_views.png \| 700px ]]

Jstout: /* QA GUI Overview */

2025-01-31T20:16:14Z

QA GUI Overview

← Older revision		Revision as of 16:16, 31 January 2025
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	Launch the QA gui		Launch the QA gui
	bids_qa_gui.py -bids_root <<PATH to BIDS dir>>		bids_qa_gui.py -bids_root <<PATH to BIDS dir>>

			If there are issues launch the gui from the BIDS directory
			cd <<PATH to BIDS DIR>>
			bids_qa_gui.py -bids_root $(pwd)

Jstout: /* Prep Data for BIDS */

2025-01-31T19:19:53Z

Prep Data for BIDS

← Older revision		Revision as of 15:19, 31 January 2025
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	==Prep Data for BIDS==		==Prep Data for BIDS==
	Add event coding to the datasets before converting to bids <br>		Add event coding to the datasets before converting to bids <br>

			Launch the GUI: (will eventually add this to the path -- currently needs to call with the full path)
			/vf/users/MEGmodules/modules/mne1.5.1dev_extras/nih_to_mne/nih2mne/GUI/trigger_code_gui.py

	Open a dataset: <br>		Open a dataset: <br>

Jstout: /* Prep Data for BIDS */

2025-01-31T19:13:42Z

Prep Data for BIDS

← Older revision		Revision as of 15:13, 31 January 2025
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	After confirming that the processing script works on your dataset - it is beneficial to add this to your github repository for data reproducability.		After confirming that the processing script works on your dataset - it is beneficial to add this to your github repository for data reproducability.
	You can manually tweak the script as well -- it is just using dataframes to process the event coding.		You can manually tweak the script as well -- it is just using dataframes to process the event coding. For example a separate logfile that has been been processed into a csv can be read into pandas (pd.read_csv) and appended to the larger dataframe. Then events from the logfile can be used to generate derivative events using the parse_marks command.

	==Create BIDS Dataset Using GUI==		==Create BIDS Dataset Using GUI==