Setting up protocols page - Revision history

Akerr at 21:41, 3 April 2026

2026-04-03T21:41:30Z

← Older revision		Revision as of 21:41, 3 April 2026
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	[[Image:Slide03.png\|thumb\|200px\|none\|Subject Data Entry]]		[[Image:Slide03.png\|thumb\|200px\|none\|Subject Data Entry]]
	'''Subject Data Entry'''		'''Subject Data Entry'''
	Key data fields that must be entered include: ~~Subject Name~~, Subject Weight~~, Subject Date of Birth~~, and Operator Name		Key data fields that must be entered include: Patient ID, Subject Weight, and Operator Name.
	~~The subject’s weigh must be included in the weight field for SAR calculations otherwise the scanner will not run.~~
	~~For data retrieval and archiving please make sure that your data is stored in the your correct lab folder~~.
	The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[Anonymous Subject ID]@[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)		The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[Anonymous Subject ID]@[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)
	Examples are:		Examples are:
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	sub_345@wandell/abc,		sub_345@wandell/abc,
	kalanit/xyz754.		kalanit/xyz754.
			The subject’s weight must be included in the weight field for SAR calculations otherwise the scanner will not run.
			Please do NOT include any PHI for the subject in any of the fields (e.g. Name, Date of Birth, any identifying numbers-other than weight.)
			For data retrieval and archiving please make sure that your data is stored in the your correct lab folder.

	Click on Start Exam (circled in red) to proceed to protocol list.		Click on Start Exam (circled in red) to proceed to protocol list.

Akerr at 21:24, 3 April 2026

2026-04-03T21:24:56Z

← Older revision		Revision as of 21:24, 3 April 2026
Line 12:		Line 12:
	The subject’s weigh must be included in the weight field for SAR calculations otherwise the scanner will not run.		The subject’s weigh must be included in the weight field for SAR calculations otherwise the scanner will not run.
	For data retrieval and archiving please make sure that your data is stored in the your correct lab folder.		For data retrieval and archiving please make sure that your data is stored in the your correct lab folder.
	The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)		The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[Anonymous Subject ID]@[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)
	Examples are:		Examples are:
	gross/study1,		s101@gross/study1,
	wandell/abc,		sub_345@wandell/abc,
	kalanit/xyz754.		kalanit/xyz754.
	Click on Start Exam (circled in red) to proceed to protocol list.		Click on Start Exam (circled in red) to proceed to protocol list.

imported>Wandell: /* Screenshots: Setting up protocols */

2017-05-05T19:42:32Z

Screenshots: Setting up protocols

← Older revision		Revision as of 19:42, 5 May 2017
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	=Screenshots~~: Setting up protocols~~ =		=Screenshots =
	The following set of slides remind you about how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.		The following set of slides remind you about how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.

imported>Wandell at 19:41, 5 May 2017

2017-05-05T19:41:40Z

← Older revision		Revision as of 19:41, 5 May 2017
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	=~~Basic Scanning on the GE Scanner - How to Guide~~=		=Screenshots: Setting up protocols =
	~~For those new to MRI scanning here is a "How to Guide" for basic scanning.~~		The following set of slides remind you about how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.
	The following set of slides ~~shows~~ how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.

	[[Image:Slide02.png\|thumb\|200px\|none\|Subject Data Entry]]		[[Image:Slide02.png\|thumb\|200px\|none\|Subject Data Entry]]

imported>Wandell: /* Spectroscopy */

2017-05-05T19:40:20Z

Spectroscopy

← Older revision		Revision as of 19:40, 5 May 2017
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	== ~~Spectroscopy ==~~		=Basic Scanning on the GE Scanner - How to Guide=
	~~Spectroscopy~~ protocols for ~~GABA~~ are described [[~~GABA spectro~~ \| in the ~~GABA spectroscopy page~~]].		For those new to MRI scanning here is a "How to Guide" for basic scanning.
			The following set of slides shows how to start a scanning session with entering subject information, entering information correctly into the "Patient ID" field for automatic data transfer to NIMS, continuing on by running a protocol with both anatomical and fMRI sequences, and ending the scanning session.

			[[Image:Slide02.png\|thumb\|200px\|none\|Subject Data Entry]]
			'''Subject Data Entry'''
			When you first arrive at the scanner, you will see the interface shown in this slide. This is the subject information data entry form. In order to enter information the cells must be white. If they are not, clicking the icon in the upper left hand corner (circled in red) will turn them into enterable fields.


			[[Image:Slide03.png\|thumb\|200px\|none\|Subject Data Entry]]
			'''Subject Data Entry'''
			Key data fields that must be entered include: Subject Name, Subject Weight, Subject Date of Birth, and Operator Name
			The subject’s weigh must be included in the weight field for SAR calculations otherwise the scanner will not run.
			For data retrieval and archiving please make sure that your data is stored in the your correct lab folder.
			The format requirements for the "Patient ID" field are as follows (and are also posted by the GE console):[SUNet ID of faculty PI] [slash] [description] (all lower case, no spaces, alphanumeric only)
			Examples are:
			gross/study1,
			wandell/abc,
			kalanit/xyz754.
			Click on Start Exam (circled in red) to proceed to protocol list.

			[[Image:Slide04.png\|thumb\|200px\|none\|Protocol Retrieval]]
			'''Protocol Retrieval'''
			Click on the protocol you wish to run (highlighted protocol will appear in yellow). To move it into the “protocol basket” click on the arrow to the right of the protocol list (circled in red). By double clicking on the protocol you can view all the sequences in the protocol., You can also move individual sequences to the ‘protocol basket” from other protocols.

			[[Image:Slide05.png\|thumb\|200px\|none\|Protocol Retrieval]]
			'''Protocol Retrieval'''
			Once you have collected a protocol, click accept (circled in red) to move to the next display.

			[[Image:Slide06.png\|thumb\|200px\|none\|Choosing dB/dt and SAR Limits]]
			'''Choosing dB/dt and SAR Limits'''
			You will need to choose either Normal Mode or First Level before proceeding further. To accept First Level click accept (circled in red) or you can choose Normal Mode by clicking that box.

			[[Image:Slide07.png\|thumb\|200px\|none\|The Localizer]]
			'''The Localizer'''
			Every protocol will have a localizer as its first sequence. The purpose of the localizer is to verify the land marking of the subject and to provide coronal, sagittal, and axial images onto which prescription geometries can be determined for subsequent sequences in the protocol. The designation ”InRx” (circled in red) to the left of the sequence name indicates that either the parameters and/or geometry must be checked by the user for the sequence to be executable. In the case of the localizer there are no parameter adjustments needed. In order to run the sequence the “Save Rx” (circled in red) must be clicked. This will turn the “InRx” to “ACT”. The localizer can now be run by clicking on the “Scan” button (circled in red, above the “Save Rx” button), which now will be highlighted.

			[[Image:Slide08.png\|thumb\|200px\|none\|Asset Calibration]]
			'''Asset Calibration'''
			All imaging sequences include parallel imaging techniques to speed up data acquisition. GE sequences use either ARC or ASSET. All sequences in your protocol that use ASSET need to use data from the ASSET calibration sequence. It a good practice to run this sequence after the localizer. Proceed as follows:
			Highlight the sequence with a single mouse click. By clicking Setup (circled in red) The designation “InRx” will appear to the left of the sequence name. Clicking in the left upper window (circled in red). will result in a grid appearing. Position the grid as shown in the screen shot to the right, making sure that the grid covers the image and also covers space outside the image as shown in the screen shot. As with the localizer first click “SaveRx” and click “Scan” to run the sequence.

			[[Image:Slide09.png\|thumb\|200px\|none\|3D Anatomical Sequences]]
			'''3D Anatomical Sequences'''
			Depending on your method of data analysis, you will have at least one anatomical sequence in addition to the fMRI sequences as part of your protocol. These sequences can be either 2D or 3D. 3D Anatomical sequences are prescribed with slabs, shown in this slide rather than slice grids as seen with the localizer and Asset calibration, and are manipulated the same way. In the “Setup” mode parameters can be adjusted. The full parameter tab can be viewed by using the toggle button (circled in red) to display the full parameter page or the axial image views. Depending on the study it is sometimes preferable to run a 3D T1 weighted sequence first, which will then allow prescribing of the functional MRI sequences. After the geometry has been prescribed in this 3D anatomical sequence clicking “SaveRx” and “Scan” allow the sequence to run.

			[[Image:Slide10.png\|thumb\|200px\|none\|fMRI Sequences]]
			'''fMRI Sequences'''
			fMRI sequences can be set up and run similarly to other sequences previously described by using the “Setup”, “SaveRx”, and “Scan”(circled in red)
			The screen shot on the right shows where a geometry has been prescribed by clicking first on the upper left image. You can then move the grid by using the mouse and can rotate it by placing the mouse on either of the two dots on the grid. Parameters can be adjusted also and they can be viewed by clicking on the pointer (circled in red) to hide the third image window.

			[[Image:Slide11.png\|thumb\|200px\|none\|fMRI Sequences]]
			'''fMRI Sequences'''
			Parameters may be adjusted on each of the available tabs (circled in red): Details, Multi-Phase, Acceleration, Advanced.

			[[Image:Slide12.png\|thumb\|200px\|none\|fMRI Sequences]]
			'''fMRI Sequences'''
			The parameter in the Multi-Phase tab “Phases per Location”( circled in red) can be used to change the length of time fMIR sequence is run to match the length of the paradigm.

			[[Image:Slide13.png\|thumb\|200px\|none\|fMRI Sequences]]
			'''fMRI Sequences'''
			The parameter “ Start Scan Trigger” (circled in red) determines how the fMRI sequence is triggered relative to the paradigm.
			Prior to running the fMRI sequence it is important to adjust the high order shims. There is a dedicated sequence to do this and shown In the next slide. Is is also important to remember that the shimming program will use the last sequence prescribed for high order shimming.

			[[Image:Slide14.png\|thumb\|200px\|none\|High Order Shims (HOS)]]
			'''High Order Shims (HOS)'''
			There are no parameters that need to be adjusted in the HOS sequence. The sequence is run by clicking on “SaveRx” and “Scan” and following the pop-up window choices. Clicking “Calculate Shims” and “Done” in the pop-up shim window allows the optimized shim values to be entered into the system.

			After the completing the shim program. The fMRI sequence is run. Multiple copies of the sequence can be obtained by using the cutting and pasting options via the right mouse button when used over the sequence list.

			[[Image:Slide15.png\|thumb\|200px\|none\|Ending the Exam]]
			'''Ending the Exam'''
			Exams are ended following the drop down window choices after clicking on “End” (circled in red)

imported>Wandell: Created page with "== Spectroscopy == Spectroscopy protocols for GABA are described in the GABA spectroscopy page."

2017-05-05T19:39:33Z

Created page with "== Spectroscopy == Spectroscopy protocols for GABA are described in the GABA spectroscopy page."

New page

== Spectroscopy ==
Spectroscopy protocols for GABA are described [[GABA spectro | in the GABA spectroscopy page]].