MR Protocols - Revision history

Huawu: /* T1 map + PD map */

2026-03-18T20:47:28Z

T1 map + PD map

← Older revision		Revision as of 20:47, 18 March 2026
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	* IR EPI TI=50(400/1200/2400) (1:15 X 4): Gradient echo IR EPI, 1.875 x 1.875 x 4mm^3 voxel size, 2x in-plane acceleration. The first scan should be run with Auto Prescan + Scan, and the following three should be run using Manual Prescan (do not change any parameters) + Scan.		* IR EPI TI=50(400/1200/2400) (1:15 X 4): Gradient echo IR EPI, 1.875 x 1.875 x 4mm^3 voxel size, 2x in-plane acceleration. The first scan should be run with Auto Prescan + Scan, and the following three should be run using Manual Prescan (do not change any parameters) + Scan.

	Note that you could also choose to use only the four IR EPI scans to get a quantitative T1 map at a lower resolution. The working principle and model fitting procedure is explained [~~http~~://~~www-mrsrl.stanford~~.~~edu~~/~~~jbarral~~/~~t1map.html~~ here].		Note that you could also choose to use only the four IR EPI scans to get a quantitative T1 map at a lower resolution. The working principle and model fitting procedure is explained [https://github.com/mathieuboudreau/Gold-Standard-Inversion-Recovery-T1-Mapping here].

	== Arterial-Spin Labeling (ASL) ==		== Arterial-Spin Labeling (ASL) ==

Huawu: /* Technical Notes */

2026-03-18T20:44:07Z

Technical Notes

← Older revision		Revision as of 20:44, 18 March 2026
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	H.DW_scheme(s, 2) = M(2,0)d[0] + M(2,1)d[1] - M(2,2)*d[2];		H.DW_scheme(s, 2) = M(2,0)d[0] + M(2,1)d[1] - M(2,2)*d[2];

	If you get the data from the CNI Neurobiological Image Management System (NIMS), then the b-values and b-vectors have already been extracted for you and are provided along with the NIFTI file containing your data. These three files (the NIFTI, bvals, and bvecs files) can be send directly into most diffusion data analysis packages, such as the Stanford Vita Lab [[~~http~~://vistalab~~.stanford.edu~~/~~newlm~~/~~index.php~~/~~MrDiffusion~~ mrDiffusion]] or FSL's [[http://www.fmrib.ox.ac.uk/fsl/fdt/index.html FDT]]. The b-values file contains a set of numbers (one for each acquired volume) that describe the b-value of the corresponding volume. The b-vecs file contains a triplet of numbers for each acquired volume, describing the diffusion-weighting direction for the corresponding volume. E.g., if you run our 60-direction scan, you will get 6 non-DW volumes followed by 60-DW volumes. Thus, you nifti file will contain 66 volumes. The b-vals file will contain 66 numbers (six 0's, fllowed by 60 1000's) and the b-vecs files will contain 66 triplets describing the DW directions for each volume (the triplets for the first 6 non-DW volumes are meaningless and can be ignored).		If you get the data from the CNI Neurobiological Image Management System (NIMS), then the b-values and b-vectors have already been extracted for you and are provided along with the NIFTI file containing your data. These three files (the NIFTI, bvals, and bvecs files) can be send directly into most diffusion data analysis packages, such as the Stanford Vita Lab [[https://github.com/vistalab/vistasoft/wiki/Diffusion-weighted-MRI mrDiffusion]] or FSL's [[http://www.fmrib.ox.ac.uk/fsl/fdt/index.html FDT]]. The b-values file contains a set of numbers (one for each acquired volume) that describe the b-value of the corresponding volume. The b-vecs file contains a triplet of numbers for each acquired volume, describing the diffusion-weighting direction for the corresponding volume. E.g., if you run our 60-direction scan, you will get 6 non-DW volumes followed by 60-DW volumes. Thus, you nifti file will contain 66 volumes. The b-vals file will contain 66 numbers (six 0's, fllowed by 60 1000's) and the b-vecs files will contain 66 triplets describing the DW directions for each volume (the triplets for the first 6 non-DW volumes are meaningless and can be ignored).

	=Simultaneous Multi-Slice (SMS)=		=Simultaneous Multi-Slice (SMS)=

Huawu: /* Technical notes */

2026-02-11T21:28:20Z

Technical notes

← Older revision		Revision as of 21:28, 11 February 2026
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	== Technical notes ==		== Technical notes ==
	* [[Data_Processing\|Some old notes]] from the former CNI staff/users on data processing and resources.		* [[Data_Processing\|Some old notes]] from the former CNI staff/users on data processing and resources
	* [[media:Bob_spatialRes_111216.pdf\|Slides on spatial resolution]] from CNI tutorial		* [[media:Bob_spatialRes_111216.pdf\|Slides on spatial resolution]] from CNI tutorial
	* [[MR Signal Equations]]		* [[MR Signal Equations]]

Huawu: /* Technical notes */

2026-02-11T21:27:53Z

Technical notes

← Older revision		Revision as of 21:27, 11 February 2026
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	== Technical notes ==		== Technical notes ==
			* [[Data_Processing\|Some old notes]] from the former CNI staff/users on data processing and resources.
	* [[media:Bob_spatialRes_111216.pdf\|Slides on spatial resolution]] from CNI tutorial		* [[media:Bob_spatialRes_111216.pdf\|Slides on spatial resolution]] from CNI tutorial
	* [[MR Signal Equations]]		* [[MR Signal Equations]]

Huawu at 21:21, 11 February 2026

2026-02-11T21:21:44Z

@@ Line 92: / Line 92: @@
 == Technical Notes ==
 If your protocol has multiple long-duration functional scans, you may consider doing additional field map measurements between the functional scans to access any field drift. See the [[Improving EPI]] page for information on fixing some common image problems with EPI images.
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 Note that you could also choose to use only the four IR EPI scans to get a quantitative T1 map at a lower resolution. The working principle and model fitting procedure is explained [http://www-mrsrl.stanford.edu/~jbarral/t1map.html here].
-== Spectroscopy ==
+== Arterial-Spin Labeling (ASL) ==
 The newest ASL sequence from GE is a pseudo-continuous sequence called 3DASL. By default it is set to create a Cerebral Bloodflow (CBF) volume as a post-processing task (reported in ml/100gm/min). Separate from post-processing, the sequence produces 2 volumes, a perfusion-weighted (PW) volume and a PD volume. The PW volume is created from subtracting the tagged volume from the control volume during the scan sequence.
@@ Line 275: / Line 268: @@
 Alternatively, you can quantify CBF yourself from the PW volume if you'd like to use different parameters or would like to perform additional spatial/intensity corrections before CBF quantification.
-=== Additional ===
+== Spectroscopy ==
 * [[media:Bob_spatialRes_111216.pdf|Slides on spatial resolution]] from CNI tutorial
 * [[MR Signal Equations]]

Huawu at 21:16, 11 February 2026

2026-02-11T21:16:24Z

← Older revision		Revision as of 21:16, 11 February 2026
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	* The Lucas center has its own instance of Flywheel [http://lucascenter.flywheel.io lucascenter.flywheel.io]. '''Prior to scanning at Lucas, please be sure to coordinate with Tom Brosnan, or [mailto:lmperry@stanford.edu Michael Perry], to have your group’s accounts and projects configured.''' Michael can help you make sure your projects have the correct gear rules configured to process your data, which is an important consideration to maintain consistency across the two sites. As a good first approximation you can map existing project gear rules at CNI to your new projects at Lucas. Our goal is to make the same gears available at Lucas as are available at CNI. This is a work in progress.		* The Lucas center has its own instance of Flywheel [http://lucascenter.flywheel.io lucascenter.flywheel.io]. '''Prior to scanning at Lucas, please be sure to coordinate with Tom Brosnan, or [mailto:lmperry@stanford.edu Michael Perry], to have your group’s accounts and projects configured.''' Michael can help you make sure your projects have the correct gear rules configured to process your data, which is an important consideration to maintain consistency across the two sites. As a good first approximation you can map existing project gear rules at CNI to your new projects at Lucas. Our goal is to make the same gears available at Lucas as are available at CNI. This is a work in progress.

	= ~~Conventional~~ imaging =		= Anatomical imaging =

	~~== Anatomical imaging ==~~		==T1 weighted ==

	===T1 weighted ===
	All the suggested T1-weighted scans use GE's "BRAVO" sequence. It is an IR-prep, fast SPGR sequence with parameters tuned to optimize brain tissue contrast. Unless you have good reason to do so, you probably don't want to play with any parameters other than slice orientation, voxel size, and bandwidth. And for those, most users just pick one of the suggested configurations:		All the suggested T1-weighted scans use GE's "BRAVO" sequence. It is an IR-prep, fast SPGR sequence with parameters tuned to optimize brain tissue contrast. Unless you have good reason to do so, you probably don't want to play with any parameters other than slice orientation, voxel size, and bandwidth. And for those, most users just pick one of the suggested configurations:

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	* T1w 0.7mm sag (5:41 X 3): T1-weighted, 0.7mm^3 voxels, 3D Bravo, sagittal slices. 3-4 scans (averaged in post-processing) are advised for good signal-to-noise quality. If you can afford the time, and make use of high-quality anatomical images, this is the sequence to use.		* T1w 0.7mm sag (5:41 X 3): T1-weighted, 0.7mm^3 voxels, 3D Bravo, sagittal slices. 3-4 scans (averaged in post-processing) are advised for good signal-to-noise quality. If you can afford the time, and make use of high-quality anatomical images, this is the sequence to use.

	===T2 weighted ===		== T2 weighted ==

	* 3D T2 (5:03): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. A single scan gives good signal-to-noise quality.		* 3D T2 (5:03): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. A single scan gives good signal-to-noise quality.
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	* 3D T2 PROMO (5:42): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. PROMO (PROspective MOtion correction) adjusts the scan parameters during the scan to prospectively correct for patient motion and thus reducing the image artifacts.		* 3D T2 PROMO (5:42): T2-weighted, 0.8mm^3 voxel size, 3D Cube T2, sagittal slices. PROMO (PROspective MOtion correction) adjusts the scan parameters during the scan to prospectively correct for patient motion and thus reducing the image artifacts.

	=== T2w/PDw ===		== T2w/PDw ==

	2D T2w/PDw FSE (4:25): A standard 2D T2-weighted scan. You also get a bonus proton-density scan. Note that the two datasets will be interleaved; you'll want to separate them in post-processing.		2D T2w/PDw FSE (4:25): A standard 2D T2-weighted scan. You also get a bonus proton-density scan. Note that the two datasets will be interleaved; you'll want to separate them in post-processing.

	=== Technical Notes ===		== Technical Notes ==

	In general, using a higher pixel bandwidth can help reduce chemical shift effects that push the fat signal from the scalp into the brain.		In general, using a higher pixel bandwidth can help reduce chemical shift effects that push the fat signal from the scalp into the brain.
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	The 3D Geometry Correction option uses a 3D correction for gradient non-linearity, over the 2D correction that is performed when the option is not checked. By including the slice direction in the correction, the resulting images are closer to geometric truth. The model used to represent gradient nonlinearity is the same as the 2D correction ("gradwarp") and it uses the same cubic interpolation function as the 2D correction.		The 3D Geometry Correction option uses a 3D correction for gradient non-linearity, over the 2D correction that is performed when the option is not checked. By including the slice direction in the correction, the resulting images are closer to geometric truth. The model used to represent gradient nonlinearity is the same as the 2D correction ("gradwarp") and it uses the same cubic interpolation function as the 2D correction.

	== Functional imaging ==		= Functional imaging =

	=== BOLD EPI (Full brain) ===		== BOLD EPI (Full brain) ==

	BOLD EPI 2.9mm 2sec: gradient echo EPI, 2.9mm^3 voxel size, 45 slices (~13 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you full coverage of the brain. The 2x in-plane acceleration reduces the EPI distortion. This is a standard sequence for fMRI scans.		BOLD EPI 2.9mm 2sec: gradient echo EPI, 2.9mm^3 voxel size, 45 slices (~13 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you full coverage of the brain. The 2x in-plane acceleration reduces the EPI distortion. This is a standard sequence for fMRI scans.

	=== BOLD EPI (High resolution, partial brain) ===		== BOLD EPI (High resolution, partial brain) ==

	BOLD EPI 1.8mm 2sec (partial coverage): gradient echo EPI, 1.8mm^3 voxel size, 25 slices (~4.5 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you partial coverage of the brain at a higher resolution. It is a good choice if you are interested in a particular part of the brain.		BOLD EPI 1.8mm 2sec (partial coverage): gradient echo EPI, 1.8mm^3 voxel size, 25 slices (~4.5 cm), TR/TE 2s/30ms, 2x in-plane acceleration. This sequence gives you partial coverage of the brain at a higher resolution. It is a good choice if you are interested in a particular part of the brain.

	===Technical Notes ===		== Technical Notes ==
	If your protocol has multiple long-duration functional scans, you may consider doing additional field map measurements between the functional scans to access any field drift. See the [[Improving EPI]] page for information on fixing some common image problems with EPI images.		If your protocol has multiple long-duration functional scans, you may consider doing additional field map measurements between the functional scans to access any field drift. See the [[Improving EPI]] page for information on fixing some common image problems with EPI images.

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	\|}		\|}

	== Diffusion weighted imaging ==		= Diffusion weighted imaging =

	=== DTI ===		== DTI ==
	* DTI 2mm b1000 60dir (9:21): 2mm^2 voxel size, 60-70 axial slices, b-value 1000, 60 diffusion directions.		* DTI 2mm b1000 60dir (9:21): 2mm^2 voxel size, 60-70 axial slices, b-value 1000, 60 diffusion directions.

	=== HARDI ===		== HARDI ==
	* DTI 2mm b2500 96dir (16:58): 2mm^2 voxel size, 60-70 axial slices, b-value 2500, 96 diffusion directions.		* DTI 2mm b2500 96dir (16:58): 2mm^2 voxel size, 60-70 axial slices, b-value 2500, 96 diffusion directions.
	If you are pressed for time, you can drop the b-value to 2000 and/or reduce the number of directions to 80:		If you are pressed for time, you can drop the b-value to 2000 and/or reduce the number of directions to 80:
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	* DTI 2mm b2000 80dir (12:37): 2mm^2 voxel size, 60-70 axial slices, b-value 2000, 80 diffusion directions.		* DTI 2mm b2000 80dir (12:37): 2mm^2 voxel size, 60-70 axial slices, b-value 2000, 80 diffusion directions.

	=== Technical Notes ===		== Technical Notes ==
	Diffusion imaging at the CNI uses a modified version of GE's DW-EPI sequence. The sequence was modified so that for dual-spin-echo scans, the polarity of the second 180 degree pulse is inverted relative to the first 180. This causes off-resonance signal from fat to get defocused and thus help reduce fat-shift artifacts (See Sarlls et. al. Robust fat suppression at 3T in		Diffusion imaging at the CNI uses a modified version of GE's DW-EPI sequence. The sequence was modified so that for dual-spin-echo scans, the polarity of the second 180 degree pulse is inverted relative to the first 180. This causes off-resonance signal from fat to get defocused and thus help reduce fat-shift artifacts (See Sarlls et. al. Robust fat suppression at 3T in
	high-resolution diffusion-weighted single-shot echo-planar imaging of human brain. MRM 2011, PubMed PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21604298 21604298] and Reese et. al. Reduction of eddy-current-induced distortion in diffusion MRI using a twice-refocused spin echo. MRM 2003, PubMed PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12509835 12509835]).		high-resolution diffusion-weighted single-shot echo-planar imaging of human brain. MRM 2011, PubMed PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21604298 21604298] and Reese et. al. Reduction of eddy-current-induced distortion in diffusion MRI using a twice-refocused spin echo. MRM 2003, PubMed PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12509835 12509835]).

Huawu: /* Technical notes */

2026-02-11T21:13:09Z

Technical notes

@@ Line 242: / Line 242: @@
 == Technical notes ==
 * [[media:Bob_spatialRes_111216.pdf|Slides on spatial resolution]] from CNI tutorial
 * [[MR Signal Equations]]

Huawu: /* Technical notes */

2026-02-11T21:08:44Z

Technical notes

← Older revision		Revision as of 21:08, 11 February 2026
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	== Technical notes ==		== Technical notes ==
	* [[media:~~bob_spatialRes_111216~~.pdf\|Slides on spatial resolution]] from CNI tutorial		* [[media:Bob_spatialRes_111216.pdf\|Slides on spatial resolution]] from CNI tutorial
	* [[MR Signal Equations]]		* [[MR Signal Equations]]

Huawu: /* Additional information (deprecated) */

2026-02-11T21:04:40Z

Additional information (deprecated)

← Older revision		Revision as of 21:04, 11 February 2026
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	In-vivo spectroscopy sequences and analysis methods available and used at CNI are described [[GABA spectro \| on this CNI spectroscopy page]].		In-vivo spectroscopy sequences and analysis methods available and used at CNI are described [[GABA spectro \| on this CNI spectroscopy page]].

	= Additional information ~~(deprecated)~~ =		= Additional information =
	== Device specific processing ==		== Device specific processing ==
	The [[GE Processing \| GE processing]] includes various steps that can influence the signal-to-noise of your data. We explain what we have learned about this and how to control it in this page.		The [[GE Processing \| GE processing]] includes various steps that can influence the signal-to-noise of your data. We explain what we have learned about this and how to control it in this page.

Huawu: /* Device specific processing */

2026-02-04T22:19:35Z

Device specific processing

← Older revision		Revision as of 22:19, 4 February 2026
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	= Additional information (deprecated) =		= Additional information (deprecated) =
	== Device specific processing ==		== Device specific processing ==
	The [[GE Processing \| ~~General Electric~~ processing]] includes various steps that can influence the signal-to-noise of your data. We explain what we have learned about this and how to control it in ~~the [[GE Processing]]~~ page.		The [[GE Processing \| GE processing]] includes various steps that can influence the signal-to-noise of your data. We explain what we have learned about this and how to control it in this page.

	== Technical notes ==		== Technical notes ==