NwebScope.mri Help
To get help on a specific control function or parameter, go to the sample page and click on that parameter.

New users of the NwebScope remote instrument controller interfaced to the NmrScope may wish to read through the rest of this document. There are four parts:

  • an overview of the web control system;
  • an "FAQ" - answers to "frequently asked questions";
  • a brief discussion of the pulse sequence; and
  • detailed explanations of the various commands and parameters. These explanations can also be accessed directly from the sample page.

Click here to connect to the MRI instrument (authorization required).


There are basically two different types of web pages you will use: the control page, and the database pages.

The Control Page (click here to see a sample) has three parts:

1) Image section.

This shows the most recent image, with a filename containing a serial number. It also provides hot links to the other parts of the web page, and to this help file. The "Redisplay" function simply loads the latest image without requesting a new acquisition. Use this button if you are monitoring someone else's session, rather than the RELOAD button of your browser.

Some messages may appear in this area as well. At the top are messages from the system operator. Below the picture are optional descriptions (if someone has provided the text files).

2) Predefined commands section.

This provides a series of "macro"-type commands to change the NMR acquisition. Each button changes the appropriate parameters, and does a new acquisition and display. These functions are common to all pulse sequences, although they may not actually be implemented in some cases (clicking just repeats the previous acquisition, in this case).

3) Detailed parameter list.
If you are an experienced MRI user, you can change almost anything in the pulse sequence by editing the appropriate field here. After making changes, click the "submit" button to carry out a new acquisition.

The contents of this list are extracted from the pulse sequence in use, and thus may change from one session to the next. Each line shows a parameter name (defined by the author of the pulse sequence), the current value, in a box you can edit, and the upper and lower limits that are acceptable to the pulse sequence software.

Unless otherwise noted, most times are in milliseconds, distances are in millimeters, and frequencies are in Hertz. Variables ending in "_10" are typically 10x the actual value, thus allowing for adjustments in fractions of a unit. (E.g. te_10 = 95 means an echo time of 9.5 msec). Other parameters may be chosen by number from a list. Contact the on-site staff for details of the various choices.

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The Database Pages .
The database is accessible at all times, even if the MRI system is not available for remote users. There are several different pages to access the database. The best is to go through the MRI Database Home Page, which in turn gives access to the following pages:

To review previously acquired images from the current session, choose Session Review (click here to try it now).

To review and compare images from multiple sessions (the entire database), choose the MRI Database page (click here to try it now).

To choose multiple images from a table showing some of the acquisition parameters, choose the MRI Database Parameter page (click here to try it now.)

To print the table, or choose single images from a table showing some of the acquisition parameters, choose the MRI Database Table page (click here to try it now.)

You may wish to make Bookmarks in your web browser for quick access to these features.

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Frequently Asked Questions

Q: How can I save the images for future use?

A: With Netscape, hold the mouse button down on the image to get a menu of options. Choose "save this image" from the menu. This will save the image in "JPEG" format - you'll need a JPEG viewer program to use it, such as JpegView (Mac) or LView (Windows).
An alternate approach is to choose "copy this image" from the menu. That puts the image on your "clipboard" after which you can "paste" it into some other program (NIH Image, Lview, Photoshop, WordPerfect, etc.). Then save the file in the format of the receiving program.

Q: I want to modify the image display (contrast, brightness, annotation). How can I accomplish this ?

A: You'll have to transfer the image to another program which provides these features. See the previous question.

Q: The instrument doesn't seem to respond to my parameter changes - I get different results than I expect. Why ?

A: This could be because the images are being "cached" by yourweb browser - stored locally on your desktop, and redisplayed from there. Consult the web browser (Netscape, Mosaic, Navigator, etc.) documentation for information on how to prevent this. Often, simply pressing "reload" will help (although this may also trigger a new acquisition). Also, quitting and restarting the browser software may fix the problem. (Don't worry - this won't crash the system).

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The Pulse Sequence.

At present, most of the work with NwebScope is done using a 2D gradient echo sequence (GE2D_N.PPL). This sequence has a 1msec sinc rf pulse (4 kHz bandwidth). The matrix and receiver bandwidth are selectable, but not via the Web interface (contact the on-site experimenters for setups). The echo time is adjustable in 0.1 msec increments. No checking for invalid entries is made. Users should be aware of the limitations of the SMIS pulse programmer when dealing with integer values.

Common problems with invalid entries (and their consequences) include:

* te or t_acq longer than tr (crashes the system).
* slice offset frequency larger than 32000 Hz (with narrow slice and large offset, for example).(wraps around to the other side of sample).
* te too short (crashes the system!).

Plans are in the works to address most of these faults.

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Command Explanations

Message from the Operator

The system operator (who is actually at the magnet site) can post messages here. Please follow any directions.

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Redisplay (no acq)

This command will display the most recent image, without starting a new acquisition. Use it if you are following a colleague's work, to see his latest results. It's like looking over the operator's shoulder.

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This command will acquire a new image using the same parameters as the ones for the currently displayed image. This is an easy way to get back to a known setup in case you got lost.

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Image number

The image file name is shown under the image for reference, along with information about the source of the image (who acquired it, and when). The number (such as 00015) also appears in the title as Frame 15. You can use this number to retrieve this image and parameters later, either from the image database or from the menu of your Web Browser (e.g. Go in NetScape).

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If one of the collaborators has provided an appropriate text file, it will appear here. The text file can contain HTML codes, such as links to images.

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Predefined Command List

Detailed Parameter List

You can control the MRI system by choosing either a predefined command, which sets some of the parameters automatically, and then acquires a new image, or by changing the individual detailed parameters yourself and then clicking Submit. You cannot do both at once - predefined commands will ignore any changes to the detailed parameters. (The links here are simply a shortcut to get you to the desired part of the page.)

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Session Review

This link takes you to the image database, from which you can select any image or group of images. From the displayed group of images, you can click on an individual image to see the complete control page with parameters. You can then Submit those parameters to repeat the experiment with the same settings. Click here to try it now.

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Slice Forward - predefined command

Slice Backward - predefined command

Slice Offset (mm) - detailed parameter

The slice position, or offset, is the distance from the center of the magnet (the origin of the coordinate system) to the center of the slice. Moving forward makes the offset more positive (by 2 millimeters), while backward makes it more negative by 2 mm. You can enter any specific offset (such as -23 mm) directly In the detailed parameter list, up to 7 times the slice thickness.

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Thickness Increase - predefined command

Thickness Decrease - predefined command

Slice (mm) - detailed parameter

The slice thickness, in millimeters, can be increased or decreased in steps of 1 mm, or can be entered directly in the detailed parameter list. Thinner slices will make "noisier" images, with "snow" or "graininess". Thicker slices may obscure details.

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FOV increase - predefined command

FOV decrease - predefined command

FOV (mm) - detailed parameter

The Field of View (FOV) is the size of the MRI window into the object, in millimeters. For most purposes, the FOV is square. Since the displayed image is always the same size on the screen, decreasing the FOV will magnify the object, while increasing it will do the opposite. The predefined commands change by 10%. You can also enter any specific size in the detailed parameter list.

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Side (View sagittal) - predefined command

Front (View axial) - predefined command

Top (View coronal) - predefined command

Orientation - detailed parameter

You can choose from 6 different views of the sample. These orientations are numbered 0 through 5, and may be entered directly in the detailed parameter list. However, only 3 of the 6 views are unique (the others are merely rotated by 90 degrees, for most purposes). These are the views looking down each of the three principal axes (X, Y, Z). These are designated sagittal (X - looking at the side), axial (Z - looking at the end), and coronal (Y - looking down from the top), although the terms are completely arbitrary for most samples. Whenever one of the predefined commands is used, the slice position is reset to the center of the magnet (0 mm).

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T1 Contrast - predefined command

T2 Contrast - predefined command

Tr - detailed parameter

Te (x10) - detailed parameter

Flip Angle - detailed parameter

Contrast is the difference in brightness between different areas of the image which enables us to see things. The contrast results from differences in the physical or chemical properties of the various parts of the sample. The MRI system can be adjusted to change the contrast - sort of like changing the color of light used to illuminate an object.

T2 contrast tends to enhance the brightness of liquids such as water. T1 contrast enhances fats, and sometimes more viscous substances. Solid tissues tend to be dark in both contrast types. These two predefined commands automatically change the three parameters, Tr (repetition time), Te (echo time, multiplied by 10), and Flip Angle. Experienced users may wish to change the individual parameters as well.

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Signal Averaging - predefined command

Reset Averaging - predefined command

When images are "noisy" or "grainy" (e.g. When the slice is too thin or the field of view too small), you can sometimes improve the appearance by averaging several acquisitions. After changing parameters you must reset averaging to avoid averaging two different views !

When signal averaging is in effect, the true signals add up, while the random noise ("snow") tends to average to zero. The image thus gets clearer (unless there is movement, or some other problem).

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Limits - detailed parameter list

There are limits on the values of some parameters. These are shown in brackets next to the parameter field. For example [20, 32767] in the Tr field means the value must be between 20msec and 32.767 sec. Values outside this range will be ignored.

NOTE: Not all "legal" combinations may be physically acceptable (for example, Tr cannot be less than Te, although the parameter page may allow you to enter such a combination). Legal, but invalid, combinations may cause the MRI system to hang up. The details depend on the pulse sequence in use.

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C.D.Gregory: April 12, 1996

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