# PRESS Data Collection on Siemens XA30 System

## Placing the Reference and Metabolite Voxels

* After collecting your anatomical scan (MPRAGE), drag the small gray head icon from the scan to the viewing windows. All three planes should show up automatically. If not, go to the MR View & GO tab and drag over the axial and coronal images.

<figure><img src="/files/Xe3aeWptIe4h40QCHiXy" alt="A view of the Siemens console while scanning a participant. After the T1 anatomical scan is collected, drag the small head to the right of the scan name over to the first image window. The image of the scout/localizer will be replaced with the T1 scan."><figcaption><p>Drag the MPRAGE into the left viewing window. Watch to see if the middle and right windows autofill with the reconstructed axial and coronal MPRAGE images.</p></figcaption></figure>

<figure><img src="/files/A0HzIdgj8nqMaEb6O46f" alt="If the coronal transverse planes do not automatically populate the viewing window, you can manually place them. First, go to the MR View &#x26; Go tab on the top of the Siemens console. On the right side of the screen are the reconstructed T1 anatomical scans (They will have the suffix “_Cor” and “_Tra”. One at a time, click the scans and drag them up to hover over the Patient Window tab. The Patient window tab will open, and you can drag the scans to the middle and right viewing windows, respectively."><figcaption><p>If the axial and coronal reconstructions do not autofill, go to the MR View &#x26; Go tab and find the images on the right panel. Drag the coronal reconstruction from the right panel up to the Patient Window (the other available tab). That tab should open and you can then drag the run to the middle viewing window. Repeat those steps to drag the axial (Tra) reconstruction to the right window.</p></figcaption></figure>

* Drag over the water reference scan to be executed by the scanner and open the sequence.
* A red dot will appear on your sagittal image. This dot is NOT your voxel. It is used to convert the images to non-distortion-corrected images. On the sagittal image, place the dot in the general area your voxel will be. Then click “Convert images.”

<figure><img src="/files/BSjPoLgtEK4RumvII6sE" alt="Opening up the spectroscopy run in the Siemens console will allow the user to place a red dot over the anatomical brain region that they wish to put their MRS voxel. Once the dot is placed (this does not need to be precise), press “Convert Images”."><figcaption><p>In this example, we placed the voxel in the ACC. Because of that, we placed the red dot in the same area, then selected "Convert Images"</p></figcaption></figure>

{% hint style="info" %}
Tips on voxel placement:

* Unlike the previous versions of Siemen's console software, XA30 does not have a "scroll nearest" function. It simultaneously updates the position in the other two planes as you move it in one plane.
* The dotted lines on your voxel mean it is not in view.
* You will need to manually move the crosshairs on the screen to ensure your voxel is placed correctly. To see the crosshairs, press the “H” key.
* You can scroll through your slices by right clicking the mouse and scrolling up and down.
  {% endhint %}

<figure><img src="/files/wKdRkbpnMfTfbI8OX6P6" alt="View of the Siemens console, where a spectroscopy voxel is manually placed over the ACC of the brain."><figcaption><p>Voxel placement in the ACC. The red box highlights the routine tab (where to find the parameters)</p></figcaption></figure>

* Once you are satisfied with the placement, click the orange “Go” button.
* The full width half maximum (FWHM) measurement will pop up after the scanner shims. The goal is to have a FWHM measurement <20.

<figure><img src="/files/psPVyFljTjv0LNKISFXH" alt="The &#x22;Confirm Frequency Adjustment&#x22; pop up window will appear after you place the spectroscopy voxel and press &#x22;Go&#x22;. The FWHM of the scan is listed in the top right corner of the window."><figcaption><p>The FWHM can be found in the upper right of the pop up window, depicted here in the red box. Since the FWHM is below 20, the window can be closed by hitting "Continue"</p></figcaption></figure>

<details>

<summary>How to manually adjust the FWHM if it is higher than 20</summary>

* If you are unhappy with the FWHM value (>20) during your water reference scan, you can manually adjust it by clicking “cancel” rather than “continue” on the pop-up screen.

<figure><img src="/files/bvqumOrRnpG4D0IdyFvA" alt="A &#x22;Confirm Frequency Adjustment&#x22; pop up window where the FWHM is over 20. In that case, users should select the &#x22;cancel&#x22; button, located on the bottom of the window."><figcaption><p>A high FWHM, measured here at 22.1. Rather than clicking 'Continue", select "Cancel" and complete the following steps.</p></figcaption></figure>

* Double click the water reference sequence to open it and go into the “Details View” tab.
* Click “System”, “Adjustments", and then click “Manual Adjustments”.

<figure><img src="/files/B1kQuuO4dj2lBcgGwCrA" alt="Instructions on how to perform a manual shim on the Siemens console. First, click on the “Details View” tab, then click “System”, “Adjustments”, and “Manual Adjustments”."><figcaption></figcaption></figure>

* Go to the left hand side and click “Interactive Shim” then follow the same process as the one used on the prior version of the scanner.
  * For this system, A11 is X, B11 is Y, and A10 is Z. When you have adjusted the system to a FWHM you like, click “Stop”, "Load Best", and then “Apply.”
  * It is important to remember that the FWHM number presented on the screen won’t update after you do this step, so be sure to write it down once you get your value.

<figure><img src="/files/CwpgE3Kj7rAWXUW5quKu" alt="The “Manual Adjustments” pop up window. To perform an interactive shim, press “Inter. Shim” on the left panel of the window. Then, adjust parameters by pressing the up or down arrows next to “A11”, “B11”, and “A10”. The top of the window will auto populate the FWHM value as it changes. Once it is acceptable, press “Stop”, “Load Best”, and “Close”."><figcaption><p>The Interactive Shim Page</p></figcaption></figure>

</details>

* Next, drag over the metabolite scan to be executed by the scanner and open the sequence. While the metabolite scan is open, right click on the water reference scan and select “copy parameters”, then “measurement parameters”, and then “apply.” Now, your voxel should be in the same position as that of the reference scan. Press the orange “Go” button to initiate the sequence.

<figure><img src="/files/DhO81kz0NGJFNAT9U8L8" alt="&#x22;Measurement parameters&#x22; is listed as an option in the &#x22;Copy Parameters&#x22; window."><figcaption></figcaption></figure>

* Drag and drop over the “Auto Start MR Spectro” sequence after collecting your metabolite data. Be sure to press the “Go” button. This step is necessary for extracting your RDA files! Only do it after ALL spectroscopy sequences are run.

<figure><img src="/files/1WKQoO5nEP5YchnNogSj" alt="The “Auto Start MR Spectro” sequence is shown in the list of runs on the Siemens console. After dragging it over, open it by double clicking and press “Go”."><figcaption><p>Running "Auto Start MR Spectro" is a necessary step to create RDA files. Run this sequence at the end of your MRS acquisition.</p></figcaption></figure>

## Exporting the Data (RDA and twix files)

* To export the RDA files, go into the files tab and select both the water reference file and metabolite file. Right click on them and select the “MR Spectro” option.

{% hint style="info" %}
If you are having issues exporting the data in MR Spectro, try reopening it by first selecting "View as Read-Only with".
{% endhint %}

<figure><img src="/files/dGZuPGf5f9NvxjEJyFbr" alt="The Patient Browser is where users select their MRI session and open their spectroscopy runs with “MR Spectro”."><figcaption></figcaption></figure>

* Go under the MR Spectro Analysis gray box on the left hand side of the screen and click “Export Selected Raw” and click “Export All.”
* Select your drive ([scannershare](/bnc-user-manual/mrf-guides/exporting-data-via-scannershare.md)) and both files will be saved there.
  * You can no longer name the RDA files. They will be manually named by the MRI console and can be identified by both timestamp and sequence number.

<figure><img src="/files/WDdUY0nFSYGR9dAh0F9E" alt="The MR Spectro Analysis panel on the left hand side of the MR Spectro tab. This is where users can export RDA files by clicking “Export Selected Raw” and “Export All.”"><figcaption></figcaption></figure>

* To export the twix files, you need to be in Med Admin mode. Click Med Admin in the upper righthand corner and enter in the username and password.
* Now, press the “Windows” key on the keyboard for the start menu. If the Windows key doesn’t work, press “tab,” “delete,” and "\[->".
* Go to the command prompt option on the start menu and type in “twix”.

<figure><img src="/files/nt7opSQZTKze2K9BdcNU" alt="The &#x22;Command Prompt&#x22; terminal."><figcaption><p>This terminal can be found by pressing the Windows key, and selecting "Command Prompt". The twix command will open a popup and allow you to select your files.</p></figcaption></figure>

* A window should pop up. Select your water reference and metabolite files and export them to [scannershare](/bnc-user-manual/mrf-guides/exporting-data-via-scannershare.md) by right clicking and selecting "Copy total raid file".

{% hint style="info" %}
IMPORTANT: XNAT does NOT automatically receive your RDA or twix files! You need to [follow these steps](/bnc-user-manual/xnat/uploading-data/uploading-raw-spectroscopy-data.md) to transfer your raw MRS data from scannershare to XNAT.
{% endhint %}

<figure><img src="/files/TKaiPDHdDSPGhrQ3TM4k" alt="The pop up window where users can export twix files."><figcaption><p>Select the files, right click, and export to drive via "Copy total raid file".</p></figcaption></figure>


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