mrVista WorkFlow

Presently, the Heeger lab does these scans at the 1.5T. At the 1.5T, there is a choice of two coils: one large and one small. The smaller head coil gets ~50% signal-to-noise. However, not everyone's head fits inside this coil. The large head coil is a GE coil and it is encased in light-colored plastic. The small head coil is encased in dark gray/black plastic. If you choose this coil, you must make a change in the protocol to accomodate for it (See scanning instructions ). The Wandell lab (and Gary) prefer anatomy collection at the 3T. This uses the copper-covered 'helmet head' coil. The Wandell lab collects these with the protocol: wand-23plane. Gary recommends using his code to correct for intensity fall-off around the periphery of the images.

No bite bar is used for these scans. Instead, the subject's head is stabilized inside the coil with foam pads.

Like the functional scans, it is necessary to know the subject's weight and birthday.

1.    Enter scanner mode: click scanner icon in upper-leftcorner of display.
2.    If exam is in progress, select End Exam in Rx Manager and Confirm .
3.    Click New Patient .
4.    In Patient Position area:
       a.    Patient ID: dheeger xxx ( xxx are your initials).
       b.    Patient Name: subject’s full name.
       c.    Weight: subject’s weight.
       d.    Exam description: brain dob mm/dd/yyyy (date of subject’s birth)
5.    Put subject in scanner. Landmark subject.
6.    Protocol Selection (schematic representation of human body)
       a.    Protocol set to Site (not GE).
       b.    Click the head of the body schematic (protocols will appear).
       c.    Select heeger-vAnatomy protocol .
      d.    Ifyou've opted to use the smaller dark-gray head coil, change coil type fromhead to surface . Select 'smhead' asthe name of the coil.
       e.    Accept .

1.    Select localizer series.
Localizers in this case are coronal slices. Protocol selection should automatically select and download the localizer scan. If this is the case, the ScannerStatus area on the left-hand sideof the display should indicate that series1 has been downloaded.
If localizer scan was not automatically downloaded with protocol selection:
           a.    Select Localizer seriesin Rx Manager .
           b.    Select View/Edit (displaysINRX status).

2.    If you've opted to use the small coil, once again change coil type fromhead to surface . Select 'smhead' asthe name of the coil.
3.    Save Series
4.    Prepare to Scan
5.    Alert subject that localizers are coming.
6.    Select Scan in Scanner Control area. Scanner willautomatically run a “prep”for about 30 seconds followed by thelocalizer scan.
7.    When scanner stops, images should be displayed in miniviewer in upper-right of display. If localizer images aren’t displayed,select     Update to load them.
8.    Maximize to enlarge display. Use scroll bar on the right-hand side of theviewer.
9.    Adjust brightness and contrast.
Press middle mouse button .Drag target up/down to increase/decrease brightness. Drag target left/right to increase/decrease contrast.
10. Scroll through localizer images. Note slice number ofwidest slice.

As of 8/6/01 two addition test anatomy series have been added. Bothdo a rapid sampling of the entire brain.
They are: '3D anatomy 2 min' and '3D anatomy 4 min.' Both cover the entire FOV of the actual 3D anatomy,
as opposed to '3D test anatomy,' which samples a subjection of the slices with good image quality in ~3 min,
but sample it rapidly to produce images of the entire FOV at poor image quality so that scanner operator can
be sure to both include entire skull and avoid aliasing.

1.    Hi-light 3D test anatomy (or 3Danatomy 2 min/4 min) series in Rx Manager.
Anatomies, in this case, are sagittal slices.This scan is ~3 min. and is used to determineadequacy of the field of view (FOV)--that the head is in the proper position.
2.    View/Edit
3.    If the coil was changed to 'smhead' above, change to 'smhead' again for this series.
4.    Select Graphic Rx in Scan Parameters.
5.    Scroll through and select chosen Localizer image using Image Number Slider on the left-hand side of display. Adjust brightness and contrast, if necessary
6.    Turn-off/deselect Auto W/L .
7.    Prescribe slices: These are 3D inplanes and are prescribed as such.
       a.     Drop ‘slab’ by clicking mouse left-button.
       b.     Orient slab to include top of skull.
8.    Set Fallback to R0 .
9.    Accept
10.    Make sure Freq DIR in Acquisition Timing section below Autoview window is not set to R/L. May be set to either A/P or S/I dependingonslice orientation.
11. Save Series
12. Prepare to Scan (wait while inplanes download).
13. Scanner control display (small monitor to the right of scannerinterface)should show timing for the new series.
14. Alert subject that he/she will move.
15. Move to Scan
16. Alert subject scan is coming.
18. Scan - Prep will run for 30 seconds, followed by Inplane scan.
19. Check to see that subject's nose doesn't wrap around and appear in the back of subject's head (this is known as 'aliasing'). If this occurs, remove padding below subject's head so that the center of their head sits lowerdown in the coil. Check adequacy of FOV in both x and y directions (see 3D Anatomy, 6b). If FOV is inadequate, you'll need to make adjustments in the prescription of the 3D Anatomy series.

1.    Hi-light 3D Anatomy series in Rx Manager.
       This scan is ~24 min.
2.    View/Edit
3.    If the coil was changed to'smhead'above, change to 'smhead' again for this series.
4.    Select Graphic Rx in Scan Parameters.
5.    Scroll through and select chosen Localizer image using Image Number Slider on the left-hand side of display.
       Adjust brightness and contrast, if necessary
5.    Turn-off/deselect Auto W/L .
6.    Prescribe slices:
These are 3D inplanes and are prescribed as such.
       a.     Drop ‘slab’ by clicking mouse left-button.
       b.     Orient slab to accomodate for any necessary changes as reflected by the images from the test anatomy scan.
Slab may be dropped higher or lower than in the test scan.
If the skull doesn't fit inside the slab, adjust FOV:
Erase all (in Graphic Rx)
Accept

Adjust as necesary:
FOV in Scanning Range adjusts the FOV along the coronal and axial directions (the y-direction in Graphic Rx view).
Slice Thickness in Scanning Range adjusts the FOV along the sagittal directions (the x-direction in Graphic Rx view).
Increase slice thickness in increments of 1/10 (i.e. 1.2 -> 1.3).

Return to Graphic Rx. Select chosen slice.
Drop and orient slab again with one left-click of the mouse.
Slab should appear wider now

7.    Set Fallback to R0 .
8.    Accept
9.    Make sure Freq DIR in Acquisition Timing section below Autoview window is not set to R/L.
May be set to either A/P or S/I dependingonslice orientation.
10. Save Series
11. Prepare to Scan (wait while inplanes download).
13. Scanner control display (small monitor to the right of scannerinterface)should show timing for the new series.
14. Alert subject that he/she will move.
15. Move to Scan
16. Alert subject scan is coming.
18. Scan
Prep will run for 30 seconds, followed by Inplane scan.

1. Click browser icon in upper-left.
2. Within image-view window, click browser left-hand side.
3. Select current patient in left-hand window.
4. Select Localizer series in right-hand window.
5. Select chosen slice in bottom-window.
6. Viewer
7. With image slider, select chosen image.
8. In blank area at lower-left of screen, type xr s#
    (# = inplane series number, '3' in this case)
9. Save Screen Data Management : preparing and anatomies and moving them to local drives 1.    Session Initialization andtransferringanatomies
           a.    From Tools window, open shell, login to lucas:

>> rloginlucas -l heeger
Password:
>> v1->mt
>> cd /local/heeger

b. Run script:

If the volume anatomy was collected at 1.5T, run:
>> anattrans.sh
If the volume anatomy was collected at the 3T, run:

>> anattrans3.sh
You will be promted with the following:
Subject:
>> subjectsLastName
Localizer series #:
>> 1
Inplane series #:
>> 3
Screen save series #:
>> 99

a. Tar andFTP in separate steps:

Tar anatomies
>>tar cvf subjectsLastName.tar subjectsLastName
Login to maroon:
>> ssh maroon -l userName
>> cd /maroon/a1/anatomy
FTP anatomiesto maroon from lucas
From your maroon login:
>> ftp lucas
Username:
>> heeger
Password:
>> v1->mt
>> cd /local/heeger
>> bin
>> get subjectsLastName.tar
>> bye
Un-tar files:
>> tar xvf subjectsLastName.tar

b. David Ress's one-step method, no tar required:

From destination location on maroon (see Login to maroon 17 linesabove), type:
>> scp -r heeger@lucas:/local/heeger/subjectsLastName .
Enter 'yes' at warning.
Enter password at prompt:
>> v1->mt

Volume Anatomy Scanning - Set up