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CSI (3D) Multi-Voxel Spectroscopy - Post-processing (A-E-Line)

This Job Aid provides workflow steps on how to post-process a CSI 3D Multi-Voxel Spectroscopy dataset on E-Line software. 

CSI (3D) Multi-Voxel MR Spectroscopy Postprocessing (A to E-line) Evaluation of Spectroscopy data results in spectra from the voxels of interest in the CSI slice. The spectra provide information regarding the existence, distribution, and ratio of diagnostically relevant metabolites in the examination region. Spectroscopy evaluation also allows creating spectral maps for an overview of spectra of interest as well as displaying the CSI data as colored metabolite images. 1. From the Patient Bowser > select 2D CSI Raw Data Icon a. Select Applications > Spectroscopy Applications Transfer Patient Applications Signal Image Protocols Post-processing System Options Help : Integral GM_CHD PEDI SPEC Report Open 9 RAW 1 TE 135 4/12/2005 Exam Report Tools 0.477 csi se 135 Mosaic 0.10 - 3D :0315 ₡0.300 Viewing Argus 0.05_ Bre Vis 1: 0 247 BOLD Filming BOLD Evaluation Soft Tissue (MR) Composing Mean Curve Perfusion (MR) 3D Spectroscopy Neuro 3D (MR) Spectroscopy Tissue 4D (MR) Vessel View Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 SIEMENS Master Template: EFF Date 22 Aug 17 | HOOD/HILS HOOD05162002647849 Healthineers Jobaid: Effective Date:03/10/2020 | HOOD05162003069923 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 2. Save Enlarged Spectrum and Reference Images a. Select Save Data Icon b. Click Selected Result (e.g. spectrum) and 3 reference images c. Select OK Save Data Please choose which item(s) you want to save in database: O Selected result (e.g. spectrum) and 3 reference images O Selected result (e.g. spectrum) O Selected reference image OK ancel Help 3. Save additional Enlarged Spectrum a. Select New VOI on Axial CSI reference image b. Select Save Data Icon Save Data c. Select Selected Result (e.g. spectrum) Please choose which item(s) you want to save in database: i. Repeat to save additional enlarged Selected result (e.g. spectrum) and 3 reference images spectrums O Selected result (e.g spectrum) d. Select OK O Selected reference image 4. Select Single Dataset Mode icon OK Cancel Help 5. Create Spectral Map a. Select Spectral Map Icon b. Select Empty Segment c. Spectral Map Window > Inside VOI i. Calculation Region > Select Inside VOI ii. Spectrum calculation > Select Only if needed iii. Select OK iv. Zoom/Pan Spectral Map (as needed) Inside VOI Spectral Map Spectral Map X AH Calculation region: Spectrum calculation: · Inside VOI . Only if needed All Enforce in any case @User defined Ignore errors OK Cancel Help Sciml Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 2 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 d. Spectral Map Window > User Defined i. Calculation Region > Select User defined (Optional) ii. Select (+) > Depress Left mouse & Ctrl keys > draw around voxels of interest 1. Hint: draw around entire voxel to include in results 2. Delete drawing > select X icon iii. Spectrum calculation > Select Only if needed iv. Select OK v. Zoom/Pan Spectral Map User Defined Spectral Map pectral Map x AH AH Calculation region: Spectrum calculation: - Inside VOI · Only if needed All Enforce in any case · User defined + Ignore errors OK Cancel Help e. Save Spectral Map i. Select Save Data Icon ii. Click Selected Result (e.g., spectral Map) iii. Select OK Save Data Please choose which item(s) you want to save in database: O Selected result (e.g. spectrum) and 3 reference images O Selected result (e .g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 3 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 6. Create Metabolite Image a. Select Single Dataset Mode Icon b. Select Empty Segment c. Select Metabolite Image Icon d. Metabolite Image window > Inside VOI i. Calculation Region > Select Inside VOI ii. Spectrum calculation > Select Only if needed iii. Metabolite > choose metabolite dropdown options iv. Intensity range > Enter 0 and 100% v. Select OK – metabolite image superimposed on reference image vi. Zoom/Pan Metabolite Image Metabolite Image AH Calculation region: Spectrum calculation: Cho · Inside VOI Only if needed @ All Enforce in any case @ User defined Il Ignore errors 100% Metabolite Cho Ratio of metabolites Metabolite image RHP Overlap reference image Peak info map Intensity range: 0 100 0% Color table: Interpolate OK Cancel Help e. Save Metabolite Image i. Select Save Data Icon ii. Click Selected Result (e.g., spectral Map) iii. Select OK Save Data Please choose which item(s) you want to save in database: Selected result (e.g. spectrum) and 3 reference images Selected result (e.g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 4 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 7. Create Ratio of Metabolite Images a. Select Single Dataset Mode Icon b. Select Empty Segment c. Select Metabolite Image Icon d. Metabolite Image window > Inside VOI (or) User Defined (e.g., If User Defined is selected follow instructions provided above) i. Calculation Region > Select Inside VOI ii. Spectrum calculation > Select Only if needed iii. Check Box > Ratio of Metabolites iv. Metabolites > choose metabolites dropdown options v. Intensity range > Enter 0 and 100% vi. Select OK – metabolite image superimposed on reference image vii. Zoom/Pan Ratio of Metabolite Image Metabolite Image X Calculation region: Spectrum calculation: Cho / Cr · Inside VOI . Only if needed @ All @ Enforce in any case User defined Ignore errors 1.58 Metabolite Cho / Cr Ratio of metabolites Metabolite image HP Overlap reference image Peak info map Intensity range 0 100 5am Color table: Interpolate OK Cancel Help a. Save Ratio of Metabolite Image viii. Select Save Data Icon ix. Click Selected Result (e.g., spectral Map) x. Select OK Save Data Please choose which item(s) you want to save in database: O Selected result (e.g. spectrum) and 3 reference images Selected result (e.g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 5 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 8. Create Peak Info Map Image (only) a. Select Single Dataset Mode Icon b. Select Empty Segment c. Select Metabolite Image Icon d. Metabolite Image window > Inside VOI (or) User Defined (e.g., If User Defined is selected follow instructions provided above) i. Calculation Region > Select Inside VOI ii. Spectrum calculation > Select Only if needed iii. Uncheck Box > Metabolite Image iv. Check Box > Peak Info Map v. Intensity range > Enter 0 and 100% vi. Select OK vii. Zoom/Pan Peak Info Map Image Metabolite Image X AH Calculation region: Spectrum calculation: Cho · Inside VOI . Only if needed @ Enforce in any case @User defined I Ignore errors 0.30 0.36 0.34 0.31 0.33 0.32 0.30 0.33 0.32 0,29 0.31 0.31 Metabolite Cho 01.27 0:32 0.31 0:32 0128 Ratio of metabolites Metabolite image RHP Overlap reference image Peak info map 0.31 0 36 0.26 0:27 0:32 0:23 Intensity range: 0 100 0.34 0.30 0 22 0.24 0,25 0:23 0.25 0 23 0,22 0.20 0.21 0,25 OK Cancel Help b. Save Peak Info Map Image viii. Select Save Data Icon ix. Click Selected Result (e.g., spectral Map) x. Select OK Save Data Please choose which item(s) you want to save in database: O Selected result (e.g. spectrum) and 3 reference images Selected result (e.g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 6 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 9. Create Peak Info Map Image overlaid on Metabolite Image a. Select Single Dataset Mode Icon b. Select Empty Segment c. Select Metabolite Image Icon d. Metabolite Image window > Inside VOI (or) User Defined (e.g., If User Defined is selected follow instructions provided above) i. Calculation Region > Select Inside VOI ii. Spectrum calculation > Select Only if needed iii. Check Box > Metabolite Image iv. Check Box > Peak Info Map v. Intensity range > Enter 0 and 100% vi. Zoom/Pan Peak Info Map overlaid on Metabolite Image vii. Select OK Metabolite Image X AH Calculation region: Spectrum calculation: Cho Inside VOI . Only if needed All Enforce in any case User defined Il Ignore errors 0.30 0 36 0.31 0,33 0.32 0,30 0 33 0.32 0.31 0,31 Metabolite: Cho 0.27 0.31 0.32 0.31 0.32 0: 28 RHP Ratio of metabolites Metabolite image 0.31 0.30 0.26 0.27 0.32 0.29 Overlap reference image Peak info map 0.34 0.30 0:22 0.24 0.25 0:29 Intensity range: 0 100 0.25 0.23 0.22 0.20 0.21 0.25 5cm Color table: Interpolate OK Cancel Help c. Save Peak Info Map overlaid on Metabolite Image viii. Select Save Data Icon ix. Click Selected Result (e.g., spectral Map) x. Select OK Save Data Please choose which item(s) you want to save in database: O Selected result (e.g. spectrum) and 3 reference images Selected result (e.g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 7 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 10. Create a Result Table a. Select Single Dataset Mode Icon b. Select Empty Segment c. Select Signal > Result Table Signal Image Protocols Post-p Display Parameters ... Undo Last Change Ctrl+Z Peak Information ... CSI Parameters ... Fit to Segment Spectrum Annotate Spectrum Result Table. Multiple Dataset Mode Single Dataset Mode d. Result Table Of Current Spectrum window i. Select Reference Metabolite ii. Select OK Result Table Of Current Spectrum X Metabolite Pos./ppm Integral Ratio NAA 2.02 0.38 1.00 Cr 3.04 0.24 0.63 Cho 3.22 0.27 0.71 Cr2 3.93 0.21 0.56 Metabolite os. /ppm Integral Ratio 2.02 0.48 1.00 3.04 0.30 0.63 Cho 9 3.22 0.31 0.66 cr2 3.93 0.25 0.52 Show hidden metabolites Store in text file OK Cancel Combine Help e. Save CSI Result Table Spectrum i. Select Save Data Icon ii. Click Selected Result (e.g., spectral Map) iii. Select OK Save Data Please choose which item(s) you want to save in database: Selected result (e.g. spectrum) and 3 reference images Selected result (e .g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 8 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 11. Add Spectra – displays calculated spectra of the anatomical region of interest that covers several voxels as a sum spectra Post-processing Syste Arrange Steps ... a. Select Single Dataset Mode Icon Interactive ... b. Select Empty Segment Spectral Map. c. Select Post-processing > Add Spectra Metabolite Image .. Metabolite Movie Add Spectra ... d. Add Spectra window Modify CSI-FT ... 3D CSI Selection. i. Calculation Region > Select User defined (e.g., adds region of interest to computation range) i. Select (+) > Depress Left mouse & Ctrl keys > draw around voxels of interest 1. Hint: draw around entire voxel to include in results 2. Delete drawing > select X icon ii. Spectrum calculation > Select Only if needed iii. Select OK (e.g., generates sum spectrum) Add Spectra 1: Integral Calculation region: Spectrum calculation: - Inside VOI · Only if needed 0.15- All Enforce in any case O User defined + - Il Ignore errors 0.10 - 1 0.590 OK Cancel Help NAA 1; 0.362 0.05 -6.213 0.00 e. Save Add Spectrum i. Select Save Data Icon ii. Click Selected Result (e.g., spectral Map) iii. Select OK Save Data Please choose which item(s) you want to save in database: O Selected result (e.g spectrum) and 3 reference images Selected result (e.g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 9 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 12. Change 3D CSI Slice (optional) Post-processing Systen a. Select Single Dataset Mode Icon b. Select Empty Segment Arrange Steps ... c. Select Post-processing > Modify 3D CSI Selection Interactive ... d. 3D CSI Selection window Spectral Map ... i. Plane number – set plane number for 3D Metabolite Image ... slice (e.g., spectrum in active segment re- Metabolite Movie calculated) Add Spectra ... 1. Note: Moves to next slice plane that intersects VOI Modify CSLET ii. Select Close 3D CSI Selection 3D CSI Selection Main orientation: Transverse Plane number: Close Help e. Save new 3D CSI Slice Results i. Select Save Data Icon ii. Click Selected Result (e.g., spectral Map) iii. Select OK Save Data Please choose which item(s) you want to save in database Selected result (e.g spectrum) and 3 reference images Selected result (e.g. spectrum) O Selected reference image OK Cancel Help Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 10 of 11 Job Aid | CSI (3D) Multi-Voxel Spectroscopy A-E-line Post-processing Effective Date: 03/10/2020 | HOOD05162003069923 Please note that the learning material is for training purposes only! For the proper use of the software or hardware, please always use the Operator Manual or Instructions for Use (herein- after collectively “Operator Manual”) issued by Siemens Healthineers. This material is to be used as training material only and shall by no means substitute the Operator Manual. Any material used in this training will not be updated on a regular basis and does not necessarily reflect the latest version of the software and hardware available at the time of the training. The Operator's Manual shall be used as your main reference, in particular for relevant safety information like warnings and cautions. Note: Some functions shown in this material are optional and might not be part of your system. Certain products, product related claims or functionalities (hereinafter collectively “Functionality”) may not (yet) be commercially available in your country. Due to regulatory requirements, the future availability of said Functionalities in any specific country is not guaranteed. Please contact your local Siemens Healthineers sales representative for the most current information. The reproduction, transmission or distribution of this training or its contents is not permitted without express written authority. Offenders will be liable for damages. All names and data of patients, parameters and configuration dependent designations are fictional and examples only. All rights, including rights created by patent grant or registration of a utility model or design, are reserved. Copyright © Siemens Healthcare GmbH 2018 ………………………………………………………… Siemens Healthineers Headquarters Siemens Healthcare GmbH Henkestr. 127 91052 Erlangen, Germany Telephone: +49 9131 84-0 siemens.com/healthineers Published by Siemens Healthcare GmbH © Siemens Healthcare GmbH, 2018 Page 11 of 11