MNE BIDS MEG Anonymization - Revision history

Jstout: /* OPTION 2 */

2021-08-31T14:35:35Z

OPTION 2

← Older revision		Revision as of 10:35, 31 August 2021
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	== OPTION 2 ==		== OPTION 2 ==
	Create a link file (csv format) that links the MEG subjectID to the MRI subjectID <br>		Create a link file (csv format) that links the MEG subjectID to the MRI subjectID <br>
	Provide the MEG path <br>		Provide the top level MEG path <br>
	Provide the MRI path <br>		Provide the top level MRI path <br>

	== OPTION 3 ==		== OPTION 3 ==

Jstout: /* Data Curating before anonymization */

2021-08-31T14:35:04Z

Data Curating before anonymization

← Older revision		Revision as of 10:35, 31 August 2021
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	EG - Subj1.ds Subj1.nii OR LastName_FirstName.fif LastName_FirstName.nii		EG - Subj1.ds Subj1.nii OR LastName_FirstName.fif LastName_FirstName.nii

	== OPTION 2 ==		== OPTION 2 ==
			Create a link file (csv format) that links the MEG subjectID to the MRI subjectID <br>
⚫	Manually generate the ~~master_list~~.csv by hand using the template csv. <br>
			Provide the MEG path <br>
			Provide the MRI path <br>

			== OPTION 3 ==
		⚫	Manually generate the Master_List.csv by hand using the template csv. <br>
	Troubleshooting can be tedious due to typing errors in the path.		Troubleshooting can be tedious due to typing errors in the path.

Jstout: /* Data Curating before anonymization */

2021-08-31T14:17:36Z

Data Curating before anonymization

@@ Line 23: / Line 23: @@
 = Data Curating before anonymization =
@@ Line 33: / Line 38: @@
   MRIs and MEG datasets must have the same prefix.
-  EG - Subj1.ds  Subj1.nii   OR  LastName_FirstName.fif  LastName_FirstName.nii   OR
+  EG - Subj1.ds  Subj1.nii   OR  LastName_FirstName.fif  LastName_FirstName.nii

Jstout: /* Introduction to Import/Upload Process */

2021-08-31T13:58:34Z

Introduction to Import/Upload Process

← Older revision		Revision as of 09:58, 31 August 2021
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	= Introduction to Import/Upload Process =		= Introduction to Import/Upload Process =
	Datasets must be organized prior to anonymization. <br>		Datasets must be organized prior to anonymization. <br>
	Several organizational options will be provided to assist in recognizing the datasets. <br>		Several organizational options will be provided to assist in recognizing and linking the datasets. <br>
	There are a variety of options ranging from extensive renaming of files to manipulating search expressions (choose the option most appropriate for your lab)		There are a variety of options ranging from extensive renaming of files to manipulating search expressions (choose the option most appropriate for your lab)
	Prior to anonymization - a "master_list" will be created linking the appropriate input information.		Prior to anonymization - a "master_list" will be created linking the appropriate input information.

Jstout: /* OPTION 1 */

2021-08-31T13:55:44Z

OPTION 1

@@ Line 26: / Line 26: @@
 == OPTION 1 ==
 All MEG datasets must be single files or directories:  .ds, .fif, .sqd, 4D-dataset (?)
   MRIs and MEG datasets must have the same prefix.
   EG - Subj1.ds  Subj1.nii   OR  LastName_FirstName.fif  LastName_FirstName.nii   OR

Jstout: /* Introduction to Import/Upload Process */

2021-08-31T13:48:20Z

Introduction to Import/Upload Process

← Older revision		Revision as of 09:48, 31 August 2021
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	Datasets must be organized prior to anonymization. <br>		Datasets must be organized prior to anonymization. <br>
	Several organizational options will be provided to assist in recognizing the datasets. <br>		Several organizational options will be provided to assist in recognizing the datasets. <br>
	There are a variety of options ranging from ~~high~~ ~~levels~~ of ~~renaming~~ files to ~~high level of~~ search expressions.		There are a variety of options ranging from extensive renaming of files to manipulating search expressions (choose the option most appropriate for your lab)
			Prior to anonymization - a "master_list" will be created linking the appropriate input information.


	= Setup Container =		= Setup Container =

Jstout at 13:17, 31 August 2021

2021-08-31T13:17:09Z

← Older revision		Revision as of 09:17, 31 August 2021
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	UNDER CONSTRUCTION		UNDER CONSTRUCTION

	~~===~~= Introduction to Import/Upload Process ~~===~~=		= Introduction to Import/Upload Process =
	Datasets must be organized prior to anonymization. <br>		Datasets must be organized prior to anonymization. <br>
	Several organizational options will be provided to assist in recognizing the datasets. <br>		Several organizational options will be provided to assist in recognizing the datasets. <br>
Line 7:		Line 7:


	~~===~~= Setup Container ~~===~~=		= Setup Container =
	#This installs mne_docker / mne-bids / mne-bids-pipeline		#This installs mne_docker / mne-bids / mne-bids-pipeline
	git clone git@tako:mne_singularity		git clone git@tako:mne_singularity
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	~~===~~= Create Head Surface to view anonymization ~~===~~=		= Create Head Surface to view anonymization =
	#Create		#Create
	enigma/import/import_mri.sh		enigma/import/import_mri.sh


	~~===~~= Data Curating before anonymization ~~===~~=		= Data Curating before anonymization =


	=== OPTION 1 ===		== OPTION 1 ==
	Organize all data into the same folder.		Organize all data into the same folder.
	All MRIs must be of .nii or .mgz		All MRIs must be of .nii or .mgz

Jstout at 13:16, 31 August 2021

2021-08-31T13:16:04Z

@@ Line 1: / Line 1: @@
 UNDER CONSTRUCTION
   #This installs mne_docker / mne-bids / mne-bids-pipeline
   git clone git@tako:mne_singularity
@@ Line 7: / Line 15: @@
 Link freesurfer or build from singularity:
   ln -s PATH_TO_FREESURFER ./freesurfer

Jstout: Initial

2021-08-30T19:54:25Z

Initial

New page

UNDER CONSTRUCTION
#This installs mne_docker / mne-bids / mne-bids-pipeline
git clone git@tako:mne_singularity
cd mne_singularity
sudo singularity build singularity_build.sif singularity_build.def

Link freesurfer or build from singularity:
ln -s PATH_TO_FREESURFER ./freesurfer

====For admin setup====
# From the mne docker website -- https://github.com/mne-tools/mne-docker
singularity pull docker://ghcr.io/mne-tools/mne-python-jupyter:main