Beauchamp:Subjects

Beauchamp Lab

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Lab Location

The lab is located in the Core for Advanced MRI at Baylor College of Medicine (CAMRI). CAMRI is located on the first floor of the Smith Research Wing of Baylor College of Medicine. Here is a map of Baylor College of Medicine showing the location of the Smith Research Wing:

 https://www.bcm.edu/map#!BCMS

Visitors to CAMRI can enter BCM at one of two entrances. The first, the main entrance to BCM, is located at 1 Baylor Plaza, Houston, TX. This entrance is most convenient for those walking, being dropped off, or taking public transit. The second is the entrance to BCM from Garage 6, and is most convenient for those driving. Texas Medical Center Garage 6, 1300 Moursund St, Houston, TX 77030. After parking, take the elevator to the ground floor. More information on parking at TMC is available at

 http://www.texasmedicalcenter.org/parking/visitors/

To enter Baylor College of Medicine, non-employees must have a government-issued ID and obtain a temporary badge at a security desk. Visitors must be approved by a BCM employee. To obtain approval, call CAMRI reception at 713-798-4214, or call (713)798-3175 (Dr. Beauchamp direct line) or (713)798-1838 (lab phone) or (301)768-8758 (Dr. Beauchamp cell phone) if you need help.

Link to consent form that must be signed by all subjects

Subjects who are interested but who have not been studied are in the file

 open /Volumes/data2/interestedsubjects.txt

A handy website for scheduling subjects is

 http://www.signupgenius.com/

The username is beauchamplab@gmail.com; ask MSB for the password.

The web site for human subjects education is http://www.citiprogram.org

All subjects for ALL experiments MUST be entered into the ExperimentSummary spreadsheet on the server, including all demographic data.

All subjects must be entered on the PaymentForm2011 file on Data2. Subjects are color coded based on whether or not we have already received cash from Summer. We are now keeping the payment forms from each subject, and will send the spreadsheet via encrypted e-mail to Summer when we need to replace cash to pay subjects.

Forms: Before scanning, please click on each form in order to download the form to your computer. Then, print the form out, fill it in, and take to the scanner.

Form #1A: UT MR Procedure Screening (as of Jan 2010)

Form #1B: BCM HNL MR Procedure Screening (as of 2014)

Form #2: Subject payment form for adults and children

Form #2: Subject Payment Form

Form #3: Examination Order Form (as of 12/21/10)

The experimenter must fill out an Experiment Sheet (here's one specific for Yoshor experiments)

If there are any questions about findings on the structural MRIs ("incidentalomas") ask Vips to push the anatomies to the second floor reading room. Then, call the neuroradiologist (currently Gayle ) at x7589. Go up to the reading room and read the scan with her.

Scanning at BCM Ask for the password of the experiment computer. Instructions for accessing the BCM scanner calendar are on the Beauchamp Lab Google Docs page. The phone number in the control from for 3T-5 is 713-798-9041

(The Inter-Departmental Transfer Voucher Form shouldn't need to be filled out once a month, but it's here just in case)

Scanning Documents: After the experiment, all forms must be scanned in and placed in the subject's experiment directory. The scanner scans both sides of every page automatically, so please use the back of the experiment sheet and print the consent form two-sided.

An e-mail that could be used for subject recruitment is

 UTfmri@gmail.com

Coordinator for Dr. Yoshor's patients: Pam Wilson

Scheduling: Make sure to tell Leticia that this is a Yoshor subject (to ensure the correct account is charged). Pam will work with Audrey to determine available dates for patient scanning. She will schedule the scans at UT (typically within 2 weeks prior to implantation). Make sure patients are able to wear contact lenses and have decongestants/allergy medication with them!

Consents: Pam will mail them the consent forms in advance. Audrey will collect Mike and Daniel's consent forms. She will put a PDF copy of the consent forms on the server and send a copy to Ping (who can slip it into the patient binder). A hard copy of the consent forms should be given to Daniel in a folder as well.

Payment: Day before the scan, give Susan Papalexandris an IOU form and pick up the money (call her first @ 5606). The subject is paid at the time of the scan, and fills out a Subject Payment Form (above). Make it clear to the subject that the payment is for the fMRI study (and not for any electrophys experiments later). This can be exchanged by the experimenter with Susan for reimbursement.

Day of scan: Pam will coordinate escorts with Audrey (since the patient will be getting their presurgical workup done as well as their structural and functional research scans). Pam will handle lunch and parking reimbursement. Give payment and sign forms. Go over the tasks with the patient on the laptop and explain instructions. For Yoshor patients ONLY, a CD with *ONE* T1 scan in DICOM format (.DCM files) must be created by Vips and then given to Yoshor or a representative. Call Pam afterwards and find out where to send the patient. Update the pt info spreadsheet, scan in documents, copy Beauchamp consent for Daniel. Copy over Presentation files into "behavioral data" folder on the server. Return payment receipt to Susan.

MRI processing: In the days between the scan and implantation, Audrey will make a cortical surface model. Make functional maps if time permits.

CT scan: Once post-implantation CT is acquired, Daniel will contact Audrey regarding where to pick it up. When she comes to pick up the CT, she will load both the structural MR and CT images onto Stealth. This will be used for anatomical orientation in case the CT-MRI merge by AFNI is not done in time for experiments. She will pick up the electrode assignments from Lisa in St. Luke's (22nd floor) and scan in the drawings.

CT-afni merge: Open OsiriX. Import DICOM folder from post-implantation CT. Export to data9 surface folder (hierarchical, decompress). Cd to the StealthBrain folder. Open to3d window (to3d IM-*), select x, y and z boxes, give prefix a name and save as {$ec}_CT. Quit to3d. Copy {$ec}_CT files into subject's afni folder. View {$ec}_CT in afni, make sure somewhat aligned. Use 3dAllineate to align CT to T1.

Tagging electrodes: In afni, set underlay to the anatomical (either T1 or SurfVol), overlay to aligned CT. Define Datamode- Plugins- Edit Tagset. Set dataset to be a +orig file (not .nii) of anatomy (T1 or surface). Tagfile = {$ec}electrodes.tag, then set each tag label to however the drawings are labelled by entering in "Tag Label" and then pressing "Relabel". For each electrode of note from Lisa's drawings, find densest view of electrode, make sure it's centered in other views. Zoom in to make sure it's centered. Press "set". Do this for all electrodes. When done, press "Write" to write the data file. Make another copy of {$ec}electrodes.tag as {$ec}electrodes.1D for surface nodes. Edit the file so that it only has the 3 columns of x,y,z. First line #spheres. Open up SUMA, set the overlay with functional maps. Then, press ctrl-command-s and select {$ec}electrodes.1D. Now the electrode spheres should appear on the fMRI activation map. Take snapshots of electrodes on interesting functional activations.

Items to put in patient binder: Printed snapshots, DVD labeled with both Mike and Daniel's codes that includes the relevant AFNI data to view (on the mac in Y2230) the electrodes and functional activations on the cortical surfaces, printout of the pt info spreadsheet.