Brain Core: Difference between revisions

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[[File:Core.png|thumb|500px]]
[[File:Core.png|thumb|500px]]
CINL Brain Core is an arm of the Civitan International Neuroimaging Laboratory. The original "Visual Brain Core" was made possible by a generous grant from UAB's HSF/GEF grant program. Given that our resources ended up being used by a broader base of users than just vision researchers, we've dropped the "visual" from our name. Also, we're continuing our work in collaboration with UAB's Civitan International Neuroimaging Lab, and so we're officially the CINL Brain Core now.
CINL Brain Core is an arm of the [https://www.uab.edu/medicine/cinl Civitan International Neuroimaging Laboratory]. The original "Visual Brain Core" was made possible by a generous grant from UAB's HSF/GEF grant program. Given that our resources ended up being used by a broader base of users than just vision researchers, we've dropped the "visual" from our name. Also, we're continuing our work in collaboration with UAB's Civitan International Neuroimaging Lab, and so we're officially the CINL Brain Core now.


==CINL Brain Core Mission==
==CINL Brain Core Mission==
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===CINL Brain Core Personnel and Office Hours===
===CINL Brain Core Personnel and Office Hours===


**'''Office Hours:
**'''Monday, 10:00 am - noon, Civitan International Research Center, Second floor outside room 210.'''
*Ravi Tripathi, MS: Computer Systems Specialist.  Consultation on high performance computing and algorithm issues.  
*Ravi Tripathi, MS: Computer Systems Specialist.  Consultation on high performance computing and algorithm issues.  
**'''Office Hours:
** '''Thursday, 10:00 am - noon, Edge of Chaos in Lister Hill Library.'''
**'''Monday, 10:00 am - 1:00 pm, Civitan International Research Center, Second floor lobby or room 235C.'''
*Mark Bolding, Ph.D. will discuss MR physics related questions.  Ravi Tripathi, MS: Computer Systems Specialist.  Consultation on high performance computing and algorithm issues.
** '''Thursday, 10:00 am - 1:00 pm, Civitan International Research Center, Room 235C.'''


===CINL Brain Core Seminar Series and Neuroimaging Journal Club===
===CINL Brain Core Seminar Series and Neuroimaging Journal Club===
Brain Core seminar series includes high level speakers usually from outside UAB.  Every third Friday at noon in CIRC 120.   
Brain Core seminar series includes high level speakers usually from outside UAB.  Every second Friday at noon in CIRC 120.   
We will discuss new ideas and techniques in brain imaging.  
We will discuss new ideas and techniques in brain imaging.  During other fridays at noon in CIRC 120, we have Neuroimaging Journal Club.
The Neuroimaging journal club is for UAB and Auburn researchers to share their work, or journal articles of their interest with our neuroimaging community.
Information about this colloquium is here: [https://www.uab.edu/medicine/cinl/seminars CINL page ].


The Neuroimaging journal club is for UAB and Auburn researchers to share their work, or journal articles of their interest with our neuroimaging community. 
 
[[https://docs.uabgrid.uab.edu/wiki/List_of_speakers_in_Visual_Brain_Core_Seminar_Series List of speakers in Brain Core Seminar Series]]
[[https://docs.uabgrid.uab.edu/wiki/List_of_speakers_in_Visual_Brain_Core_Seminar_Series Older website for speakers]]


===For Use in Grant Proposals:===
===For Use in Grant Proposals:===
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===Mailing List:===
===Mailing List:===
To subscribe to the VBC mailing list, click [mailto:sympa@vo.uabgrid.uab.edu?subject=none&body=subscribe%20vbc here] (and send the email without any changes) '''''or''''' send an email to [mailto:sympa@vo.uabgrid.uab.edu sympa@vo.uabgrid.uab.edu] with the following text in the body of the email '''subscribe vbc'''
Please follow these instructions to subscribe to the ‘CINL-NOTICE’  listserv:
Click here, or alternatively, send an email to listserv@listserv.uab.edu with the email body as sub cinl-notice.
After which you’ll receive an email to confirm your email address.
After confirming your email address, you would start receiving cancellation emails from others on the list as well as be able to send your own notifications .


===[[BrainhackUAB]]===
===[[BrainhackUAB]]===
 
<!-- this link does not have  much in it
===[[Other information]]===
===[[Other information]]===
-->


==Neuroimaging at UAB==
==Neuroimaging at UAB==


===UAB Neuroimaging Facilities===
===UAB Neuroimaging Facilities===
 
<!-- need to add good links to here -->
 
[http://www.alabamaadvancedimaging.org/ Alabama Advanced Imaging Consortium
[[Civitan International Neuroimaging Laboratory]]
[https://www.uab.edu/medicine/cinl Civitan International Neuroimaging Laboratory ]  


[[UAB-HSF MEG Laboratory]]
[[UAB-HSF MEG Laboratory]]


[[Small Animal Imaging Shared Facility]]
[[Small Animal Imaging Shared Facility]]
 
<!-- the following is outdated and could be improved
Equipment for collecting behavioral data during Neuroimaging
Equipment for collecting behavioral data during Neuroimaging


*[http://www.sr-research.com/EL_1000.html Eye Tracker]
*[http://www.sr-research.com/EL_1000.html Eye Tracker] -->


===Neuroimaging and Systems Neuroscience Labs at UAB===
===Neuroimaging and Systems Neuroscience Labs at UAB===
*[http://www.markbolding.com/ Bolding Lab]
*[http://www.uab.edu/engineering/home/component/contact/contact/82-be/19-allan-c-dobbins?Itemid=999/ Dobbins Lab]
*[https://www.uab.edu/medicine/ophthalmology/faculty/gamlin/ Gamlin Lab]
*[https://www.uab.edu/optometry/home/faculty-staff/faculty-directory/29-facultystaff/facultybio/111-gawnetimothy/ Gawne Lab]
*[http://www.uab.edu/medicine/psychiatry/71-merida-m-grant/ Grant Lab]
*[http://www.uab.edu/cbra/ Kana Lab/Cognition, Brain, and Autism Laboratory]
*[http://www.uab.edu/medicine/radiology/directory/neuro-imaging/24-directory/neuro-imaging/470-rkessler Kessler Lab]
*[http://www.uab.edu/cas/psychology/psy-fac/33-primary-faculty/48-dr-david-knight Knight Lab]
*[http://labs.uab.edu/kwon/ Kwon Lab]
*[http://www.uab.edu/medicine/psychiatry/faculty/faculty-bios/78-adrienne-c-lahti Lahti Lab]
*[http://www.mcconathylab.com/ McConathy Lab]
*[http://www.uab.edu/medicine/neurology/faculty/by-specialty/skidmore/ Skidmore Lab]
*[http://www.uab.edu/medicine/neurology/faculty/a-z/szaflarski Szaflarski Lab]
*[http://visscher.neurobiology.uab.edu/Home.html Visscher Lab ]
*[http://www.uab.edu/medicine/neurology/faculty/by-specialty/walker Walker Lab]


*[http://www.psy.uab.edu/younger/ Younger Lab/Neuroinflammation, Pain and Fatigue Laboratory]
*[https://www.uab.edu/medicine/cinl/about/researchers a partial list of researchers who use the CINL]


(UAB folks, please let us know if your lab should be included on this list, or add more information about it!)
(UAB folks, please let us know if your lab should be included on this list, or add more information about it!)
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'''[http://www.eng.auburn.edu/research/centers/mri/equipment/siemens-magnetom-7t.html Siemens Magnetom 7T]'''
'''[http://www.eng.auburn.edu/research/centers/mri/equipment/siemens-magnetom-7t.html Siemens Magnetom 7T]'''


'''UAB & Auburn Neuroimaging Journal Club'''
'''UAB & Auburn Neuroimaging Colloquium'''


*Neuroimaging journal Club. Every other Friday at noon, second floor CIRC. Contact Adrienne Lahti to get on the mailing list alahti at uab.edu
*Neuroimaging journal Club. Shared across campuses via GoToMeeting.
To get on our mailing list, [https://docs.google.com/forms/d/e/1FAIpQLSdNi8bGzhQleGUg5h3hLZtXTDL-vAJMyf-n5W6i_ohdedISbw/viewform click here]


'''[[UAB & Auburn Neuroimaging Retreat]]'''
'''[[UAB & Auburn Neuroimaging Retreat]]'''
[[Photos]]


==How To...==
==How To...==
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[[Psychtoolbox]]
[[Psychtoolbox]]
[[Coding Help]]


[[https://docs.uabgrid.uab.edu/wiki/Box.com_bulk_transfer Saving Data in Box]]
[[https://docs.uabgrid.uab.edu/wiki/Box.com_bulk_transfer Saving Data in Box]]


*[[Unix shortcuts]]
*[[Unix shortcuts]]
*[[Eye Tracker]]


===fMRI related how-to's and important links===
===fMRI related how-to's and important links===
[[General Information]]


[[Tools]]
[[Tools]]
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[[Cool Websites for Beginners]]
[[Cool Websites for Beginners]]


[[fMRI statistics]]


===UAB Neuroimaging Tools and How-To's (requires blazer id)===
===UAB Neuroimaging Tools and How-To's (some require blazer id)===


[[Imaging Protocols]]
[[Imaging Protocols]]
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[[Institutional Review Board]]
[[Institutional Review Board]]
[[https://uab.box.com/s/1wtg1qbk9st1pekui2dtjksvt2os9els blah]]

Latest revision as of 21:10, 13 March 2019

Core.png

CINL Brain Core is an arm of the Civitan International Neuroimaging Laboratory. The original "Visual Brain Core" was made possible by a generous grant from UAB's HSF/GEF grant program. Given that our resources ended up being used by a broader base of users than just vision researchers, we've dropped the "visual" from our name. Also, we're continuing our work in collaboration with UAB's Civitan International Neuroimaging Lab, and so we're officially the CINL Brain Core now.

CINL Brain Core Mission

Our mission is to help produce high quality, cutting edge research examining the visual brain. To achieve this, we will help investigators overcome some common barriers to performing high quality vision research, and provide forums to discuss new ideas and research techniques.

The 5 aims of the Brain Core

Visual Brain Core Poster

Information For CINL Brain Core

CINL Brain Core Personnel and Office Hours

    • Office Hours:
    • Monday, 10:00 am - noon, Civitan International Research Center, Second floor outside room 210.
  • Ravi Tripathi, MS: Computer Systems Specialist. Consultation on high performance computing and algorithm issues.
    • Thursday, 10:00 am - noon, Edge of Chaos in Lister Hill Library.
  • Mark Bolding, Ph.D. will discuss MR physics related questions. Ravi Tripathi, MS: Computer Systems Specialist. Consultation on high performance computing and algorithm issues.

CINL Brain Core Seminar Series and Neuroimaging Journal Club

Brain Core seminar series includes high level speakers usually from outside UAB. Every second Friday at noon in CIRC 120. We will discuss new ideas and techniques in brain imaging. During other fridays at noon in CIRC 120, we have Neuroimaging Journal Club. The Neuroimaging journal club is for UAB and Auburn researchers to share their work, or journal articles of their interest with our neuroimaging community. Information about this colloquium is here: CINL page .


[Older website for speakers]

For Use in Grant Proposals:

The CINL Brain Core is supported by users. For this reason, we ask that you include use of the Brain Core resources in the budget of your upcoming grants. Quotations from previous proposals are provided here: Grant Proposal Language.

Mailing List:

Please follow these instructions to subscribe to the ‘CINL-NOTICE’ listserv:

Click here, or alternatively, send an email to listserv@listserv.uab.edu with the email body as sub cinl-notice. After which you’ll receive an email to confirm your email address.

After confirming your email address, you would start receiving cancellation emails from others on the list as well as be able to send your own notifications .

BrainhackUAB

Neuroimaging at UAB

UAB Neuroimaging Facilities

[http://www.alabamaadvancedimaging.org/ Alabama Advanced Imaging Consortium Civitan International Neuroimaging Laboratory

UAB-HSF MEG Laboratory

Small Animal Imaging Shared Facility

Neuroimaging and Systems Neuroscience Labs at UAB

(UAB folks, please let us know if your lab should be included on this list, or add more information about it!)

Here is a partial list of manuscripts that have resulted from CINL and Visual Brain Core resources.

Cluster Computing Environment at UAB: Cheaha

  • Cheaha_GettingStarted - information on getting an account and learning about how to use the cluster
  • Cheaha - background information on the cluster useful for grants and publications

UAB-Auburn University Collaboration for Neuroimaging

Auburn University MRI Research Center Siemens Magnetom 7T

UAB & Auburn Neuroimaging Colloquium

  • Neuroimaging journal Club. Shared across campuses via GoToMeeting.

To get on our mailing list, click here

UAB & Auburn Neuroimaging Retreat

How To...

Computer and coding related how-to's

Using Linux

Matlab

Psychtoolbox

[Saving Data in Box]

fMRI related how-to's and important links

Tools

Brain atlases

Cool Websites for Beginners


UAB Neuroimaging Tools and How-To's (some require blazer id)

Imaging Protocols

Analysis Scripts

Behavioral data analysis techniques

Institutional Review Board