Brainsight Coregistration - Revision history

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.

Amnamyst: /* Setting anatomical landmarks */

2025-02-04T20:46:12Z

Setting anatomical landmarks

← Older revision		Revision as of 16:46, 4 February 2025
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	=== Setting anatomical landmarks ===		=== Setting anatomical landmarks ===
		⚫	[[File:CruxHelix.png\|thumb\|alt=Sagittal MR image of an ear, with crux helix marked with yellow crosshairs\|Location of Crux Helix]]

	''Note: These are anatomical landmarks clearly identifiable from the MRI. You are not placing the marker coils at this step.''		''Note: These are anatomical landmarks clearly identifiable from the MRI. You are not placing the marker coils at this step.''
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	**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.		**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 '''''crux helix''''' on each ear.		**As a better alternative, we recommend marking the end of the [https://elementsofmorphology.nih.gov/anatomy-ear.shtml '''''crux helix'''''] on each ear.

⚫	[[File:CruxHelix.png\|thumb\|alt=Sagittal MR image of an ear, with crux helix marked with yellow crosshairs\|Location of Crux Helix]]

	* 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.		* 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.


	* With the cursor cross-hairs identify the Nasion, LPA (left preauricular), and RPA (right preauricular). Rather than using the tragus, we will use the supratrageal notch -- notch above the tragus where the tragus joins the upper ear. This point is less likely to be distorted in the MRI by earplugs or head pads.

	* For additional precision, you can select a fourth point on the tip of the nose or the outer canthus. 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: /* Setting anatomical landmarks */ Adding Crux Helix as Anatomical Landmark

2025-02-04T20:43:37Z

Setting anatomical landmarks: Adding Crux Helix as Anatomical Landmark

← Older revision		Revision as of 16:43, 4 February 2025
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	* From the “Landmarks” tab, select “Configure Landmarks”. The landmarks window will display the Skin reconstruction and coronal, sagittal, and transverse slices. The cursor cross-hairs will be displayed in all four image windows.		* From the “Landmarks” tab, select “Configure Landmarks”. The landmarks window will display the Skin reconstruction and coronal, sagittal, and transverse slices. The cursor cross-hairs will be displayed in all four image windows.

			* 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 '''''crux helix''''' on each ear.

			[[File:CruxHelix.png\|thumb\|alt=Sagittal MR image of an ear, with crux helix marked with yellow crosshairs\|Location of Crux Helix]]

			* 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.


	* With the cursor cross-hairs identify the Nasion, LPA (left preauricular), and RPA (right preauricular). Rather than using the tragus, we will use the supratrageal notch -- notch above the tragus where the tragus joins the upper ear. This point is less likely to be distorted in the MRI by earplugs or head pads.		* With the cursor cross-hairs identify the Nasion, LPA (left preauricular), and RPA (right preauricular). Rather than using the tragus, we will use the supratrageal notch -- notch above the tragus where the tragus joins the upper ear. This point is less likely to be distorted in the MRI by earplugs or head pads.

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

2022-11-22T15:11:46Z

Downloading/Preparing the MRI data

← Older revision		Revision as of 11:11, 22 November 2022
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	=== Downloading/Preparing the MRI data ===		=== Downloading/Preparing the MRI data ===

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

⚫	If you don’t have access to ~~the~~ ~~archive~~ – talk to your PI.
			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/

		⚫	If you don’t have access to either data repository – talk to your PI.

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

Amnamyst: /* Setting anatomical landmarks */

2022-03-09T21:32:47Z

Setting anatomical landmarks

← Older revision		Revision as of 17:32, 9 March 2022
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	* 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.

			* If you will be using OPMs, proceed to the Targets tab and complete the target trajectory setup for the OPM rig before moving to the registration session:
			** [[Brainsight Coregistration: OPM Rig Setup\|Instructions for OPM Rig Setup]]

	=== Subject Preparation ===		=== Subject Preparation ===

Amnamyst: /* Targets (optional). */

2022-03-09T21:15:47Z

Targets (optional).

← Older revision		Revision as of 17:15, 9 March 2022
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	With the Session window open, go through the following tabs(steps):		With the Session window open, go through the following tabs(steps):

	==== Targets (optional). ====		==== Targets (optional) ====
	The anatomical landmarks selected can be imported here, but this section was intended for other applications (i.e. TMS, surgery).		The anatomical landmarks selected can be imported here, but this section was intended for other applications (i.e. TMS, surgery).
	This section may be updated as we find applications for this section.		This section may be updated as we find applications for this section.

Amnamyst: /* Transferring data to the Brainsight Mac */

2022-01-21T21:12:29Z

Transferring data to the Brainsight Mac

← Older revision		Revision as of 17:12, 21 January 2022
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	* Transfer your data to your directory on tako		* 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)		* 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		* Using the 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: /* NEXT STEPS */

2022-01-21T21:09:14Z

NEXT STEPS

← Older revision		Revision as of 17:09, 21 January 2022
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	* Consult [[MEG Software and Analysis\| MEG Software and Analysis]] for more information on converting the exported Brainsight .txt files to AFNI tags or MNE transforms.		* Consult [[MEG Software and Analysis\| MEG Software and Analysis]] for more information on converting the exported Brainsight .txt files to AFNI tags or MNE transforms.
	::*bstags.py is all you need to convert .txt files to AFNI, and to continue preprocessing for SAM analysis as you would normally.		:*bstags.py is all you need to convert .txt files to AFNI, and to continue preprocessing for SAM analysis as you would normally.
	::*nih2mne pipeline will set you up for preprocessing with MNE.		:*nih2mne pipeline will set you up for preprocessing with MNE.