Brainsight Coregistration - Revision history

Amnamyst: /* Setting anatomical landmarks */

2026-09-17T14:40:13Z

Setting anatomical landmarks

← Older revision		Revision as of 10:40, 17 September 2026
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	* With the cursor cross-hairs identify the Nasion, LPA (left preauricular), and RPA (right preauricular). Rather than using the tragus, we will choose a point that is less likely to be distorted in the MRI by earplugs or head pads and be clearly identified on the MRI.		* With the cursor cross-hairs identify the Nasion, LPA (left preauricular), and RPA (right preauricular). Rather than using the tragus, we will choose a point that is less likely to be distorted in the MRI by earplugs or head pads and be clearly identified on the MRI.
		⚫	** Previously, we recommended using the supratrageal notch -- notch above the tragus where the tragus joins the upper ear. In practice, we've noticed that even this location can be difficult to unambiguously identify on the MRI, or can be compressed during the scan.
		⚫	** As a better alternative, we recommend marking the end of the [https://elementsofmorphology.nih.gov/anatomy-ear.shtml '''''crux helix'''''] on each ear.

		⚫	* For additional precision, you can select a fourth point on the outer canthus of the eye, the inion, or the tip of the nose. You may use whatever point as long as it is unambiguously identifiable and in a fixed location.
⚫	**Previously, we recommended using the supratrageal notch -- notch above the tragus where the tragus joins the upper ear. In practice, we've noticed that even this location can be difficult to unambiguously identify on the MRI, or can be compressed during the scan.

⚫	**As a better alternative, we recommend marking the end of the [https://elementsofmorphology.nih.gov/anatomy-ear.shtml '''''crux helix'''''] on each ear.

⚫	* For additional precision, you can select a fourth point on the outer canthus of the eye, the inion, or the tip of the nose. You may use whatever point as long as it is unambiguously identifiable and fixed.

	* Now you are ready to start a new session. At this point, you can suspend your project or move directly to the registration session.		* Now you are ready to start a new session. At this point, you can suspend your project or move directly to the registration session.

Amnamyst: /* BRAINSIGHT COREGISTRATION */

2026-09-17T14:36:06Z

BRAINSIGHT COREGISTRATION

← Older revision		Revision as of 10:36, 17 September 2026
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	=== Importing data (May be done before Subject arrives) ===		=== Importing data (May be done before Subject arrives) ===

	* Launch the Brainsight program and select “New Empty Project”. Note: If you do not have access to your subject’s MRI, choose “New MNI Head Project” and follow the Brainsight User Manual instructions for using an average brain template (see chapter 6). This is generally not recommended for our analyses		* Launch the Brainsight program and select “New Empty Project”.
			Note: If you do not have access to your subject’s MRI, choose “New MNI Head Project” and follow the Brainsight User Manual instructions for using an average brain template (see chapter 6). '''This is generally not recommended for our analyses.'''

	* Select subject’s anatomical data. NIfTI files are recommended by MEG Core, but other accepted formats are MINC, Analyze, DICOM, PAR/REC, or BrainVoyager VMR.		* Select subject’s anatomical data. NIfTI files are recommended by MEG Core, but other accepted formats are MINC, Analyze, DICOM, PAR/REC, or BrainVoyager VMR.

Amnamyst: /* Transferring .nii to the Brainsight Mac */

2026-09-17T14:35:02Z

Transferring .nii to the Brainsight Mac

← Older revision		Revision as of 10:35, 17 September 2026
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	* Transfer your .nii file to your data directory on tako		* Transfer your .nii file to your data directory on tako
	* Pull your data from tako to your directory on the Brainsight ~~(requires ethernet connection)~~		* Pull your data from tako to your directory on the Brainsight
			** This requires ethernet connection -- you may use the yellow ethernet cable for this step.

	scp -r [SOURCE]@tako.nimh.nih.gov:/tmp/[MRI data] [DESTINATION]		scp -r [SOURCE]@tako.nimh.nih.gov:/tmp/[MRI data] [DESTINATION]

	* Alternative: Pull the data from tako to one of Linux computers in the MEG Lab (gusoku, namako or kani). ~~uthe~~ dedicated MEG Lab flash drive, transfer your data to the Mac and file it in the appropriate MEGLAB directory for your study		* Alternative: Pull the data from tako to one of Linux computers in the MEG Lab (gusoku, namako or kani). Using the dedicated MEG Lab flash drive (held by the pink squid!), transfer your data to the Mac and file it in the appropriate MEGLAB directory for your study

	== BRAINSIGHT COREGISTRATION ==		== BRAINSIGHT COREGISTRATION ==

Amnamyst: /* Downloading/Preparing the MRI data */

2026-09-17T14:32:55Z

Downloading/Preparing the MRI data

← Older revision		Revision as of 10:32, 17 September 2026
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	=== Downloading/Preparing the MRI data ===		=== Downloading/Preparing the MRI data ===

⚫	If ~~your~~ ~~participant’s~~ ~~data was collected here prior to October 2022~~, you can download ~~their~~ data from the FMRIF ~~DICOM~~ Archive:
⚫	https://~~gold~~.nimh.nih.gov/

			Ask your PI/Study coordinator how to access your participant or patient's MRI.
	If your participant’s data was collected here '''AFTER October 2022''', you can download their data from the FMRIF XNAT Archive:
	https://fmrif-xnat.nimh.nih.gov/

		⚫	For most NIMH studies, you can download study data from the FMRIF XNAT Archive:
	If you don’t have access to either data repository – talk to your PI.
		⚫	https://fmrif-xnat.nimh.nih.gov/

	==== Transform the DICOM to NIfTI (.nii) format ====		==== Transform the DICOM to NIfTI (.nii) format ====

	'''1. Locate the ~~MPRAGE~~'''		'''1. Locate the correct scan in your subject's directory'''

		⚫	We recommend using an MPRAGE for coregistration. If your subject doesn’t have an MPRAGE, you can use a suitable alternative (i.e. SPGR). You want the resolution to be 1mm. If you’re unsure, consult your PI or MEG Core staff.
	The README file from the session will tell you which directory to use.
⚫	If your subject doesn’t have an MPRAGE, you can use a suitable alternative (i.e. SPGR). You want the resolution to be 1mm.
	If you’re unsure, consult your PI or MEG Core staff.

	'''2. Use dcm2niix to convert the .dcm files to .nii'''		'''2. Use dcm2niix to convert the .dcm files to .nii'''

Amnamyst: /* POST-REGISTRATION */ 2026 Updates

2026-09-17T14:14:44Z

POST-REGISTRATION: 2026 Updates

← Older revision		Revision as of 10:14, 17 September 2026
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	* Prep subject for entering the MSR as usual (bathroom, demetal, apply marker coils, etc.)		* Prep subject for entering the MSR as usual (bathroom, demetal, apply marker coils, etc.)
	* Save registration date to flash drive ~~and~~ ~~transfer~~ to ~~end~~ ~~destination~~.		* Save registration date to flash drive or push to tako, your lab server, or helix. Data on the Brainsight Mac is not backed up -- '''treat it as a temporary repository.'''
	* Turn off the Mac if you are finished, or lock the screen to secure it, if you plan to use it later in your session.		* Turn off the Mac if you are finished, or lock the screen to secure it, if you plan to use it later in your session.
	* ~~Turn off~~ the Polaris ~~Vicra~~ ~~via~~ ~~the upper rocker switch on the~~ ~~control~~ ~~unit~~.		* Disconnect the Polaris Lyra and store it carefully.
	* The lower rocker switch controls power to the whole unit. If you are finished, turn off.

	* '''Disinfect''' the Brainsight stylus and surfaces using a hospital approved disinfectant such as Hydrogen Peroxide, 70-90% ethyl alcohol or isopropyl alcohol after each subject/patient use.		* '''Disinfect''' the Brainsight stylus and surfaces using a hospital approved disinfectant such as Hydrogen Peroxide, 70-90% ethyl alcohol or isopropyl alcohol after each subject/patient use and allow to air dry.

	The stylus handle and tracker headband can be washed as usual, but special care must be taken with the reflective spheres. The spheres ~~must~~ be dipped in hydrogen peroxide (container provided) and allowed to air dry.		The stylus handle and tracker headband can be washed as usual, but special care must be taken with the reflective spheres so as not to damage the special reflective coating. The spheres may be dipped in hydrogen peroxide (container provided) and allowed to air dry.

	== NEXT STEPS ==		== NEXT STEPS ==

Amnamyst: /* Registration */

2026-09-17T13:44:02Z

Registration

← Older revision		Revision as of 09:44, 17 September 2026
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	''Note: It is important not to press too deeply into the participant's skin. This will distort the registration. Likewise, be sure not to move or the location will be incorrectly recorded.''		''Note: It is important not to press too deeply into the participant's skin. This will distort the registration. Likewise, be sure not to move or the location will be incorrectly recorded.''

	* Click the “Speech Recognition” ~~or “I/OBox Switch” option boxes~~ to sample independently.		* Click the “Speech Recognition” to sample independently.
			The “I/OBox Switch” option box no longer functions, as we have disconnected the I/O box.

	* Identify the landmark with the stylus		* Identify the landmark with the stylus.

	* Holding the stylus steady, say “SAMPLE” ~~or step on the foot pedal~~.		* Holding the stylus steady, say “SAMPLE”.

	* If you have an assistant, they can click “Sample & Go to Next Landmark” for you, and give you feedback on the camera view (green or red) for the subject tracker and stylus.		* If you have an assistant, they can click “Sample & Go to Next Landmark” for you, and give you feedback on the camera view (green or red) for the subject tracker and stylus.

Amnamyst: /* Polaris */ Updating from Polaris Vicra to Polaris Lyra

2026-09-17T13:39:26Z

Polaris: Updating from Polaris Vicra to Polaris Lyra

← Older revision		Revision as of 09:39, 17 September 2026
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	==== Polaris ====		==== Polaris ====
	Ensure that the Polaris ~~Vicra~~ is on ~~and~~ ~~operational.~~ We ~~recommend~~ ~~turning~~ on ~~the~~ ~~Polaris~~ as ~~soon as you arrive so~~ it ~~has~~ ~~time~~ to ~~warm up~~.		Ensure that the Polaris Lyra is connected to the Brainsight Mac. You will hear a "beep" when it is on and operational.

			1. Plug in the Lyra power supply/splitter.
			This is a grey cable with blue plug.
			The splitter box is mounted below the Brainsight Mac.
			2. Connect the blue ethernet cable to the Polaris Lyra.
			3. Connect the black ethernet cable to the Brainsight Mac.


	Troubleshooting:		Troubleshooting:

Amnamyst: Updated instructions for /* Transferring data to the Brainsight Mac */

2025-02-25T00:02:55Z

Updated instructions for Transferring data to the Brainsight Mac

← Older revision		Revision as of 20:02, 24 February 2025
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	PII may still be buried in the header text of the data; treat the files accordingly.		PII may still be buried in the header text of the data; treat the files accordingly.

	=== Transferring ~~data~~ to the Brainsight Mac ===		=== Transferring .nii to the Brainsight Mac ===

		⚫	* Transfer your .nii file to your data directory on tako
			* Pull your data from tako to your directory on the Brainsight (requires ethernet connection)

⚫	* Transfer your ~~data~~ to your directory on tako
	* Transfer your data from tako to one of Linux computers in the MEG Lab (namako or kani)
	scp -r [SOURCE]@tako.nimh.nih.gov:/tmp/[MRI data] [DESTINATION]		scp -r [SOURCE]@tako.nimh.nih.gov:/tmp/[MRI data] [DESTINATION]

	* ~~Using~~ the dedicated MEG Lab flash drive, transfer your data to the Mac and file it in the appropriate MEGLAB directory for your study		* Alternative: Pull the data from tako to one of Linux computers in the MEG Lab (gusoku, namako or kani). uthe dedicated MEG Lab flash drive, transfer your data to the Mac and file it in the appropriate MEGLAB directory for your study

	== BRAINSIGHT COREGISTRATION ==		== BRAINSIGHT COREGISTRATION ==

Amnamyst: /* Transform the DICOM to NIfTI (.nii) format */

2025-02-24T23:50:27Z

Transform the DICOM to NIfTI (.nii) format

← Older revision		Revision as of 19:50, 24 February 2025
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	==== Transform the DICOM to NIfTI (.nii) format ====		==== Transform the DICOM to NIfTI (.nii) format ====

	1. '''Locate the MPRAGE'''		'''1. Locate the MPRAGE'''

	~~<br>~~The README file from the session will tell you which directory to use.		The README file from the session will tell you which directory to use.
	If your subject doesn’t have an MPRAGE, you can use a suitable alternative (i.e. SPGR). You want the resolution to be 1mm.		If your subject doesn’t have an MPRAGE, you can use a suitable alternative (i.e. SPGR). You want the resolution to be 1mm.
	If you’re unsure, consult your PI or MEG Core staff.		If you’re unsure, consult your PI or MEG Core staff.

	2. '''Use dcm2niix to convert the .dcm files to .nii'''		'''2. Use dcm2niix to convert the .dcm files to .nii'''

	* Documentation for using dcm2niix on your computer:		* Documentation for using dcm2niix on your computer:
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	** https://hpc.nih.gov/apps/dcm2niix.html		** https://hpc.nih.gov/apps/dcm2niix.html

	3. Generate MEG Hashcode for your subject		'''3. Generate MEG Hashcode for your subject'''

	If you don’t have the opportunity to do it before your study, label your file something generic (I.e. SubjectXDate.nii).		If you don’t have the opportunity to do it before your study, label your file something generic (I.e. SubjectXDate.nii).
	You will be able to rename it later; the primary goal is to remove any PII in the filename.		You will be able to rename it later; the primary goal is to remove any PII in the filename.

Amnamyst: Update to /* Transform the DICOM to NIfTI (.nii) format */

2025-02-24T23:49:19Z

Update to Transform the DICOM to NIfTI (.nii) format

← Older revision		Revision as of 19:49, 24 February 2025
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	==== Transform the DICOM to NIfTI (.nii) format ====		==== Transform the DICOM to NIfTI (.nii) format ====

	* Locate the ~~MP RAGE~~		1. '''Locate the MPRAGE'''
	The README file from the session will tell you which directory to use.		<br>The README file from the session will tell you which directory to use.
	If your subject doesn’t have an MPRAGE, you can use a suitable alternative (i.e. SPGR).		If your subject doesn’t have an MPRAGE, you can use a suitable alternative (i.e. SPGR). You want the resolution to be 1mm.
	If you’re unsure, consult your PI or MEG Core staff.		If you’re unsure, consult your PI or MEG Core staff.

			2. '''Use dcm2niix to convert the .dcm files to .nii'''
	* Navigate to that directory in terminal and use the following command:
	Dimon -infile_prefix anat_t1w_mp_rage_1mm_abcd -GERT_Rico -gert_write_as_nifti –gert_create_dataset

			* Documentation for using dcm2niix on your computer:
	(If you use something other than MPRAGE, replace the prefix ‘anat_t1w_mp_rage_1mm_abcd’ accordingly.)
			** https://github.com/rordenlab/dcm2niix

			* Documentation for using dcm2niix on Biowulf
	For more information on Dimon-- https://afni.nimh.nih.gov/pub/dist/doc/program_help/Dimon.html
			** https://hpc.nih.gov/apps/dcm2niix.html

	* Generate MEG Hashcode for your subject		3. Generate MEG Hashcode for your subject
	If you don’t have the opportunity to do it before your study, label your file something generic (I.e. SubjectXDate.nii).		If you don’t have the opportunity to do it before your study, label your file something generic (I.e. SubjectXDate.nii).
	You will be able to rename it later; the primary goal is to remove ~~the~~ PII ~~that NMRIF includes~~ in the filename.		You will be able to rename it later; the primary goal is to remove any PII in the filename.

	PII may still be buried in the header text of the data; treat the files accordingly.		PII may still be buried in the header text of the data; treat the files accordingly.