Spectro - Revision history

Laimab: /* 1.4.1 High Order Shimming for MRSI */

2026-06-26T01:57:00Z

1.4.1 High Order Shimming for MRSI

← Older revision		Revision as of 01:57, 26 June 2026
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	~~Higher~~ Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.		High Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.

	Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures		Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures

Laimab: /* 1.4.1 High Order shimming for MRSI */

2026-06-26T01:56:37Z

1.4.1 High Order shimming for MRSI

← Older revision		Revision as of 01:56, 26 June 2026
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	==='''1.4.1 High Order ~~shimming~~ for MRSI'''===		==='''1.4.1 High Order Shimming for MRSI'''===

Laimab: /* 1.3.2 sLaser Prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI) */

2026-06-26T01:55:28Z

1.3.2 sLaser Prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)

← Older revision		Revision as of 01:55, 26 June 2026
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	[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.		[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.

	==='''1.3.2 sLaser ~~Prototocol~~ examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===		==='''1.3.2 sLaser prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===

Laimab: /* 1.4.1 High Order shimming for MRSI */

2026-06-26T01:53:25Z

1.4.1 High Order shimming for MRSI

← Older revision		Revision as of 01:53, 26 June 2026
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	Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.		Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.

	Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures		Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures
	[[File:Testcsi52_HOSpatch_Details.png\|none\|1000px]]		[[File:Testcsi52_HOSpatch_Details.png\|none\|1000px]]
	Shimming-1		Shimming-1

Laimab: /* 1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI) */

2026-06-26T01:52:11Z

1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)

← Older revision		Revision as of 01:52, 26 June 2026
Line 233:		Line 233:
	[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.		[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.

	==='''1.3.2 sLaser Prototocol ~~Examples~~ on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===		==='''1.3.2 sLaser Prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===

Laimab: /* 1.3.1 Current CNI spectroscopy protocols */

2026-06-26T01:51:45Z

1.3.1 Current CNI spectroscopy protocols

← Older revision		Revision as of 01:51, 26 June 2026
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	=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==		=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==

	==='''1.3.1 Current CNI spectroscopy ~~protocols~~'''===		==='''1.3.1 Current CNI spectroscopy sequences'''===

	'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''		'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''

Laimab: /* 1.4.3 Extracting voxel prescription information retrospectively */

2026-06-26T01:48:36Z

1.4.3 Extracting voxel prescription information retrospectively

← Older revision		Revision as of 01:48, 26 June 2026
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	[[File:Spectro_voxel_size.png\|none\|1000px]]		[[File:Spectro_voxel_size.png\|none\|1000px]]

	===1.4.3 Extracting voxel prescription information retrospectively===		==='''1.4.3 Extracting voxel prescription information retrospectively'''===
	The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm.		The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm.

Laimab: /* 2. Miscellaneous Historical Information */

2026-06-26T01:46:21Z

2. Miscellaneous Historical Information

← Older revision		Revision as of 01:46, 26 June 2026
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	\|}		\|}

	= 2. Miscellaneous Historical Information =		= '''2. Miscellaneous Historical Information''' =

	[[Historical Information]]		[[Historical Information]]

Laimab: /* 1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences */

2026-06-26T01:45:41Z

1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences

← Older revision		Revision as of 01:45, 26 June 2026
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	[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698		[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698

	==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==		=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==

Laimab: /* 1.6 Legacy and Other Spectroscopy Sequences */

2026-06-26T01:45:19Z

1.6 Legacy and Other Spectroscopy Sequences

← Older revision		Revision as of 01:45, 26 June 2026
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	Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).		Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).

	==1.6 Legacy and Other Spectroscopy Sequences==		=='''1.6 Legacy and Other Spectroscopy Sequences'''==

	Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.		Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.