Difference between revisions of "Beauchamp:Subjects"

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'''Forms''': Before scanning, please click on each form in order to download the form to your computer.
The web site for human subjects education is  
Then, print the form out, fill it in, and bring with you to your appointment.
[[Media:MRScreeningFormJan2010.pdf|Form #1: MR Procedure Screening (as of Jan 2010)]]
[[Media:BeauchampConsentForm.pdf|Form #2: Informed Consent (as of 4/19/10)]]
[http://www.openwetware.org/images/3/32/Subject_payment_form.pdf Form #3: Subject Payment Form]
[[Media:ExaminationOrderForm_Mar10.pdf‎|Form #4: Examination Order Form (as of 3/10/10)]]  (here's one specific for [[Media:Yoshor_ExamOrderForm.pdf|Yoshor experiments]])
The experimenter must fill out an [[Media:BeauchampLabExperimentSheet_Aug2008.doc|Experiment Sheet]] (here's one specific for [[Media:YoshorExptSheet.doc|Yoshor experiments]])
(The [[Media:voucher.pdf|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.
'''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 [[Media:paymentIOU.doc|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 [http://www.openwetware.org/images/3/32/Subject_payment_form.pdf 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.

Revision as of 08:44, 6 May 2010

Brain picture
Beauchamp Lab

Thank you for your interest in becoming a volunteer in one of our experiments. For more information or to schedule an appointment, please send an e-mail to


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