Mne bids pipeline - Revision history

Jstout: /* Use on biowulf */

2023-07-03T15:12:09Z

Use on biowulf

← Older revision		Revision as of 11:12, 3 July 2023
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	sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly - subjects will run in parrallel		sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50 #adjust mem and cpus accordingly - subjects will run in parrallel

	===Create BIDS data from ~~MEG data~~===		===Option 1: Create BIDS data from commandline===
	module load mne_scripts		module load mne_scripts

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	make_meg_bids.py -meg_input_dir ${MEGFOLDER} -mri_bsight ${MRI_BSIGHT}.nii -mri_bsight_elec ${EXPORTED_BRAINSIGHT}.txt		make_meg_bids.py -meg_input_dir ${MEGFOLDER} -mri_bsight ${MRI_BSIGHT}.nii -mri_bsight_elec ${EXPORTED_BRAINSIGHT}.txt

			===Option 2: Use CSV file to create BIDS (rest data only)===
			Instructions and more info: https://github.com/nih-megcore/enigma_anonymization_lite <br>
			Fill out the csv with all of the appropriate entries <br>
			module load enigma_meg
			enigma_anonymization_mne.py -topdir TOPDIR -csvfile CSVFILE -njobs NJOBS -linefreq LINEFREQ -bidsonly #Use the bidsonly flag if not anonymizing

			==MNE BIDS Pipeline==
	===Freesurfer Processing===		===Freesurfer Processing===
	If you have already processed your freesurfer data - just copy or link the freesurfer data(see below). You can also set the freesurfer directory in mne-bids-pipeline config file. Alternatively, you can have the pipieline calculate freesurfer as part of the processing. This will take time - adjust sinteractive session (see below).		If you have already processed your freesurfer data - just copy or link the freesurfer data(see below). You can also set the freesurfer directory in mne-bids-pipeline config file. Alternatively, you can have the pipieline calculate freesurfer as part of the processing. This will take time - adjust sinteractive session (see below).

Jstout at 15:35, 27 October 2022

2022-10-27T15:35:39Z

← Older revision		Revision as of 11:35, 27 October 2022
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	''Open sub-ON02747_ses-01_task-airpuff_report.html in an internet browser to view the report''		''Open sub-ON02747_ses-01_task-airpuff_report.html in an internet browser to view the report''

			==Setup for running on a headless server (no monitor attached)==
			#(add this to the bashrc and run start_xvfb before running):
			alias start_xvfb='Xvfb :99 & export DISPLAY=:99'
			export MESA_GL_VERSION_OVERRIDE=3.3
			export MNE_3D_OPTION_ANTIALIAS=false

Jstout: /* Example Output Images */

2022-10-21T20:15:52Z

Example Output Images

← Older revision		Revision as of 16:15, 21 October 2022
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	#--subject=SUBJECTID(without the sub- prefix)		#--subject=SUBJECTID(without the sub- prefix)

	====Example Output Images====		====Example Output Images (from anonymized data - the pipeline does not anonymize)====
	[[File : MNE BIDS PIPELINE output.png \| 1000px ]]		[[File : MNE BIDS PIPELINE output.png \| 1000px ]]

Jstout: /* Process data using MNE Bids Pipeline */

2022-10-21T20:14:19Z

Process data using MNE Bids Pipeline

← Older revision		Revision as of 16:14, 21 October 2022
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	#--subject=SUBJECTID(without the sub- prefix)		#--subject=SUBJECTID(without the sub- prefix)

			====Example Output Images====
	[[Example Ouput \| MNE_BIDS_PIPELINE_output.png]]
			[[File : MNE BIDS PIPELINE output.png \| 1000px ]]

	==TEST DATA for biowulf==		==TEST DATA for biowulf==

Jstout: /* Process data using MNE Bids Pipeline */

2022-10-21T20:09:35Z

Process data using MNE Bids Pipeline

← Older revision		Revision as of 16:09, 21 October 2022
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	#--steps=preprocessing,sensor,source,report or all (default) - Can be a list of steps or a single step		#--steps=preprocessing,sensor,source,report or all (default) - Can be a list of steps or a single step
	#--subject=SUBJECTID(without the sub- prefix)		#--subject=SUBJECTID(without the sub- prefix)

			[[Example Ouput \| MNE_BIDS_PIPELINE_output.png]]

	==TEST DATA for biowulf==		==TEST DATA for biowulf==

Jstout: /* MNE bids pipeline background */

2022-10-21T20:04:51Z

MNE bids pipeline background

← Older revision		Revision as of 16:04, 21 October 2022
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	study_name = 'TESTSTudy'		study_name = 'TESTSTudy'
	bids_root = 'YOUR_BIDS_DIR' #<< Modify		bids_root = 'YOUR_BIDS_DIR' #<< Modify
			task = 'TASKNAME' #If this is left empty, it will likely find another task and throw an error
	l_freq = 1.0		l_freq = 1.0
	h_freq = 100.		h_freq = 100.
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	ch_types = ['meg']		ch_types = ['meg']
	conditions = ['stim'] #<< list of conditions		conditions = ['stim'] #<< list of conditions
			N_JOBS=4 #On biowulf - leave this empty - it will set N_JOBS equal to the cpu cores assigned in sinteractive
	N_JOBS=4
			on_error = 'continue' # This is often helpful when doing multiple subjects. If 1 subject fails processing stops

	#crop_runs = [0, 900] #Can be useful for long tasks that are ended early		#crop_runs = [0, 900] #Can be useful for long tasks that are ended early but full file is written.

	==Use on biowulf==		==Use on biowulf==

Jstout at 19:32, 26 May 2022

2022-05-26T19:32:19Z

← Older revision		Revision as of 15:32, 26 May 2022
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	===BIDS website===		===BIDS website===
	https://bids-specification.readthedocs.io/en/stable/		https://bids-specification.readthedocs.io/en/stable/

		⚫	===Bids data organization===
		⚫	[[File:BIDS_data_organization.png\|1000px\|Bids data organization]]

	==MNE Bids==		==MNE Bids==
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	===MNE Bids website===		===MNE Bids website===
	https://mne.tools/mne-bids/stable/index.html		https://mne.tools/mne-bids/stable/index.html

⚫	===Bids data organization===
⚫	[[File:BIDS_data_organization.png\|1000px\|Bids data organization]]

	==MNE bids pipeline background==		==MNE bids pipeline background==

Jstout: /* MNE Bids */

2022-05-26T18:54:10Z

MNE Bids

← Older revision		Revision as of 14:54, 26 May 2022
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	===MNE Bids website===		===MNE Bids website===
	https://mne.tools/mne-bids/stable/index.html		https://mne.tools/mne-bids/stable/index.html

			===Bids data organization===
			[[File:BIDS_data_organization.png\|1000px\|Bids data organization]]

	==MNE bids pipeline background==		==MNE bids pipeline background==

Jstout: /* Freesurfer Processing */

2022-05-25T20:55:39Z

Freesurfer Processing

← Older revision		Revision as of 16:55, 25 May 2022
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	===Freesurfer Processing===		===Freesurfer Processing===
	If you have already processed your freesurfer data - just copy or link the freesurfer data. You can also set the freesurfer directory in mne-bids-pipeline config file. Alternatively, you can have the pipieline calculate freesurfer as part of the processing. This will take time.		If you have already processed your freesurfer data - just copy or link the freesurfer data(see below). You can also set the freesurfer directory in mne-bids-pipeline config file. Alternatively, you can have the pipieline calculate freesurfer as part of the processing. This will take time - adjust sinteractive session (see below).
	====Already Processed - Copy Data====		====Already Processed - Copy Data====
	mkdir -p ${bids_dir}/derivatives/freesurfer/subjects #If this folder doesn't already exists		mkdir -p ${bids_dir}/derivatives/freesurfer/subjects #If this folder doesn't already exists

Jstout: /* Freesurfer Processing */

2022-05-25T20:54:56Z

Freesurfer Processing

← Older revision		Revision as of 16:54, 25 May 2022
Line 67:		Line 67:

	===Freesurfer Processing===		===Freesurfer Processing===
			If you have already processed your freesurfer data - just copy or link the freesurfer data. You can also set the freesurfer directory in mne-bids-pipeline config file. Alternatively, you can have the pipieline calculate freesurfer as part of the processing. This will take time.
	====Already Processed - Copy Data====		====Already Processed - Copy Data====
	mkdir -p ${bids_dir}/derivatives/freesurfer/subjects #If this folder doesn't already exists		mkdir -p ${bids_dir}/derivatives/freesurfer/subjects #If this folder doesn't already exists