Neuroimaging

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4 ROI coordinates of Craddock's template
By Lily Wu · University of Queensland

Lily Wu · University of Queensland

Thank you for your suggestion! I'll discuss this with my colleagues. Thanks very much , again!

Thank you for your suggestion! I'll discuss this with my colleagues. Thanks very much , again!

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6 Is it possible to modify a phosphoprotein with a fluorescent protein/fluorescent dye in a way that it emits light based on its phosphorylation state?
By Lena Robra · National Centre for Biological Sciences

Narayanan Parthasarathy

Hi Lena, You can use luciferin and luciferase enzyme reaction for the phosphorylation reaction. You can also quantify the reaction. Dr.N.Parthasarathy... [more]

Hi Lena, You can use luciferin and luciferase enzyme reaction for the phosphorylation reaction. You can also quantify the reaction. Dr.N.Parthasarathy.

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15 Has anyone tried the new CLARITY technique out of the Deisseroth lab in Stanford?
By William Adler · Beth Israel Deaconess Medical Center

William Adler · Beth Israel Deaconess Medical Center

If anyone else in the US is having trouble buying FocusClear from CelExplorer labs (or wants to avoid the shipping charge), you can buy it from their ... [more]

If anyone else in the US is having trouble buying FocusClear from CelExplorer labs (or wants to avoid the shipping charge), you can buy it from their US distributor, Cedarlane Labs. https://www.cedarlanelabs.com/Products/Search?lob=All+Products&searchby=Description&supplier=CELLEXP&text=&x=51&y=3

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8 Problems with long storage of brain material in 4% paraformaldehyde
By Irina Makarenko · Russian Academy of Sciences

Irina Makarenko · Russian Academy of Sciences

You are wright for IHC (I always did short time fixation for it) but I am working with DII labeling and long storage in PFA is very good for it.

You are wright for IHC (I always did short time fixation for it) but I am working with DII labeling and long storage in PFA is very good for it.

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7 What are the most important ethical concerns related to the use of “lie-detection methods” for forensic or security purposes?
By Ahmed Karim · Eberhard-Karls-Universität Tübingen

Ahmed Karim · Eberhard-Karls-Universität Tübingen

Hi everybody, I would appreciate if any researcher viewing our question would share with us his/ her opinion and join or “brain-storming”: ***Wh... [more]

Hi everybody, I would appreciate if any researcher viewing our question would share with us his/ her opinion and join or “brain-storming”: ***What are the most important ethical concerns related to the use of “lie-detection methods” for forensic or security purposes?*** Let me point here to some highly controversial issues: Opponents of lie-detection methods usually criticize the lack of reliability and the possibility to manipulate the outcome by countermeasures. However, metaanalyses show that the “Control Question Test (CQT)” is indeed lacking reliability (Iacono & Lykken, 1997, J Applied Psychology; Lykken, 1998, A tremor in the blood), whereas the Guilty-Knowledge-Test (GKT) has an average hitrate for innocent subjects of 95,9 % (SD= 6,96%) and a hitrate of 80,6% (SD= 14,01%) for guilty subjects (Elaad, 1998, Expert Evidence). In the same time, several studies have emphasized the lacking reliability of witness reports (a variety of factors influence witness reports such as the skin colour or the degree of childlikeness in the face of the suspect ) and that witness testimonies can even be manipulated by the way a question is formulated. Nevertheless, witness reports have always been admitted for forensic purposes in contrast to lie-detection methods. I would be interested in the different views regarding this controversial topic.

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11 JMRUI software
By Katarzyna Bieńkowska · University of Technology Munich

Durgesh Kumar Dwivedi · All India Institute of Medical Sciences

Dear Katarzyna, I want to measure Lipid (1.3ppm), cholestrol (~5.4ppm) and Choline (3.2ppm)... I have acquired spectra with and without water suppres... [more]

Dear Katarzyna, I want to measure Lipid (1.3ppm), cholestrol (~5.4ppm) and Choline (3.2ppm)... I have acquired spectra with and without water suppression. Now I want to quantitate above mentioned metabolites.

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12 How to study the neural code?
By Davide Viggiano · Università degli Studi del Molise

Hassan Nasser · Institut National de Recherche en Informatique et en Automatique

Thank you Milan ... Looking forward to hear from you.

Thank you Milan ... Looking forward to hear from you.

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Question:
Open neurons on Aclar sheets
I want to grow neurons on Aclar sheets. I know that we can grow cells but for neuronal cells there is a specific protocol. Can any body give me sugges... [more]

I want to grow neurons on Aclar sheets. I know that we can grow cells but for neuronal cells there is a specific protocol. Can any body give me suggestion for coating the aclar sheets before seeding neurons? or how to grow neurons on Aclar sheet? I would be best if one has already an experience with it but all suggestions are very much required.

By Sneha Pant · University of Warsaw

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6 What is the best technique to quantify Choline acetyltransferase labeled cells in the medial septum of the mouse?
By Steven Lowrance · Central Michigan University

Susan Hendricks Tappan · MBF Bioscience

Stereology does not assume homogeneity of your population - in fact it is free from that bias. It makes no assumptions of size, shape, orientation, o... [more]

Stereology does not assume homogeneity of your population - in fact it is free from that bias. It makes no assumptions of size, shape, orientation, or distribution of your object (in this case, cell population) to be estimated. Stereology achieves unbiased quantification by providing rules to ensure that each cell has an equal opportunity to be counted once and only once. Each cell is represented by a unique point – a feature that can only occur in the cell once (like the cell top). When you are only examining a single 2D image of a 3D specimen, you cannot identify the unique point, only the number of profiles or cell pieces in the image [which will lead to an overestimation of the number of cells]. In addition, stereology uses a 3D disector or counting frame to ensure that each cell in the section thickness is counted only in the area of the section thickness that is not damaged. Without proper adherence to both of these principles, the “equal opportunity to be counted once and only once” is not achieved. The aspect of quantification is only one part of the equation however. We need to consider the sampling too -- in order to obtain a measure that relates to your hypothesis, you need to sample accordingly. Meaning, that examining a single (or even three) "representative" section(s) tells you what was occurring only where you looked --- it's dangerous to extrapolate to the whole organ/region on the basis of that small amount of sampling. What if there are differential effects on the periphery? Or a concomitant volume loss due to your manipulation? You'd miss key results by limiting your analysis to such a small portion of your region. Thus, stereology instead guides you to systematically sample through your region -- you're not analyzing your entire region, but your entire region must be available for sampling. When your cell population is not homogenously distributed within your tissue (more rostral than caudal for example), you adjust your sampling parameters so that you are sampling at a density sufficient to pick up that difference. It is best to determine this during a pilot study using one animal from each group - like Xilu Jiao does. Check out this review for a perspective: http://www.ncbi.nlm.nih.gov/pubmed/15652981

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Question:
Open How is body integrity identity formed?
Sensory information from our limbs (touch and proprioception) reaches somatosensory I cortex (SI) by making two synapses (one at cuneate nucleus (medu... [more]

Sensory information from our limbs (touch and proprioception) reaches somatosensory I cortex (SI) by making two synapses (one at cuneate nucleus (medula) and one at VPN of thalamus). I wonder how this information is used to build a body integrity identity. What are the other pathways between SI, SII and other cortical regions that have role in body integrity identity? I want to note that I found lots of cognitive studies, but I mostly wonder about the basic physiology of body integrity identiy.

By İsmail Devecioğlu · Bogazici University

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1 What software packages are particularly good for PET analysis?
By David Groppe · The Feinstein Institute for Medical Research

Mark Ahlman · National Institutes of Health

Based on your topics of interest that you have listed, I assume you're looking at PET activity in the brain. I'll try to answer for that organ, specif... [more]

Based on your topics of interest that you have listed, I assume you're looking at PET activity in the brain. I'll try to answer for that organ, specifically, but comment on general whole body use as well. For the brain, I found that NeuroQ by Syntermed was uses robust means for internal normalization of activity and I believe it is FDA approved for cognitive and epilepsy applications with FDG. You can use the choice to normalize to the whole brain or the cerebellum and it uses T or Z scores that differ from a normal database. The GUI is one of the best for QC of your images and for accurate registration. For research it's great because it spits out a nice excel table with the raw and relative uptake values. Outside the brain, the heart has many software packages available to it which also have normal database comparisons used clinically and in research. Corridor4DM, QPS to name a few. For the whole body, I'm not aware of a suite that is able to automatically normalize by tissue type. Segmentation of the organs for this task is a work in progress and is something we do here at the NIH. What most people do is measure regions of interest in the blood or the liver as a background ROI. They then measure their target of interest to create a target to background ratio. It stands to reason that a computer could help out with this sort of thing, but I don't think it's available yet. Best regards,

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33 If you could buy any 3T human MRI right now, what would you get? Why would you choose that system?
By Mark Bolding · University of Alabama at Birmingham

Douraied Ben Salem · Centre Hospitalier Universitaire de Brest

If the diffusion and the ASL images have a poor quality with this machine, then I dont buy it. WHY the images are bad this is not my problem, you sh... [more]

If the diffusion and the ASL images have a poor quality with this machine, then I dont buy it. WHY the images are bad this is not my problem, you should ask directly Siemens. Prof. Ben Salem D.

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5 Would you think that the ICC(2,1) model is appropriate to assess across-day test-retest reliability for a given structural MRI parameter, such as FA?
By Susan Mérillat (-Koeneke) · University of Zurich

Prasath Jayakaran · University of Otago

Thank you for initiating this interesting discussion. It was one of those areas where I had difficulty in deciding an appropriate model and I suppose ... [more]

Thank you for initiating this interesting discussion. It was one of those areas where I had difficulty in deciding an appropriate model and I suppose it is worth taking a step backwards to look at the theoretical back ground of the ICC models. I am not sure what type of variability you are expecting from your design and measures. But if you are expecting a variability in the measurement/estimation procedure only, for example error from the MRI equipment/technique it might be 3,n and if you are expecting variability from more than one source say subjects and the MRI technique you would be looking at 2,n model. Have a look at “Shrout,P.E, Fleiss,J.L. Intraclass correlations: Uses in assessing rater reliability; Psychological Bulletin, 1979, 86, 2, 420-428” you perhaps have already come across this material. According to this article, you won’t be erroneously using a model if an appropriate error term is unavailable, but the other way round you are more likely to be. This is my understanding of the ICC models but I may not be right and am open for discussion.

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Open New database of recent work done with fNIRS.
For those of you who are interested in fNIRS, we have created a database of recent work done with this emerging new technique, in order to provide sta... [more]

For those of you who are interested in fNIRS, we have created a database of recent work done with this emerging new technique, in order to provide standards within the community and hope that this will eventually improve data acquisition and facilitate comparison among studies. The article is free to download and we'd appreciate feedback on the suggested guidelines.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058906 ×
PLOS ONE: An Online Database of Infant Functional Near InfraRed Spectroscopy Studies: A Community-Augmented Systematic Review

PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

By Manu Schuetze · Max-Planck-Institut für Psycholinguistik

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3 Should we consider cerebral white matter hyperintensities as irreversible in nature?
By Simon Hjerrild · Aarhus Universitetshospital

Sushmita Purkayastha · Harvard University

Thanks for continuing discussion on this topic. Here is a longitudinal study which just came out relating the FLAIR and DTI as independent predictors ... [more]

Thanks for continuing discussion on this topic. Here is a longitudinal study which just came out relating the FLAIR and DTI as independent predictors of WMH in elderly population. http://www.ajnr.org/content/34/1/54.full.pdf+html

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3 What do you think the role of neuroimaging, such as functional MRI, might be in defence research over the next decade?
By Catherine Davey · Defence Science and Technology Organisation (DSTO)

Matthew Wall · University College London

fMRI is getting some attention as a potential technology for interrogation/lie-detection/intelligence gathering.

fMRI is getting some attention as a potential technology for interrogation/lie-detection/intelligence gathering.

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Open Is there an efficient way to detect tauopathies in patients?
Tauopathy (micro-lesions) or tangles differ across disorders. Is there any means by which to detect them utilising technological advances?

Tauopathy (micro-lesions) or tangles differ across disorders. Is there any means by which to detect them utilising technological advances?

By Cheryl Johnston · Independent Researcher

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5 Has anyone written an article about the possibility of redefining the point of 'death' in PVS patients with neuroimaging?
By Fiona Brittle · University of Kent

Carl Erik Fisher · Columbia University

Hi Fiona - here's an article I wrote discussing the specific legal implications in U.S. statutory law. I'd be very interested to hear more about the ... [more]

Hi Fiona - here's an article I wrote discussing the specific legal implications in U.S. statutory law. I'd be very interested to hear more about the UK perspective. Please message me if you'd like to discuss further. Best of luck.

Diagnosing consciousness: neuroimaging, law, and the vegetative state. × Carl E Fisher, Paul S Appelbaum

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4 Which optimization best suits the demon's method in combination with SSD (sum of squared intensity difference).
By Madiha Azam · University of Engineering and Technology, Taxila

Madiha Azam · University of Engineering and Technology, Taxila

Ok thanx Daniel for this valuable suggestion.

Ok thanx Daniel for this valuable suggestion.

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1 What does Floating Light mean in FLAMES?
By Ashish Gupta · Amity University

Kristy Conn · Stony Brook University

The "Floating Light" part of FLAMES refers to the fact that the device uses an infrared light beam to stimulate the target neurons. This approach allo... [more]

The "Floating Light" part of FLAMES refers to the fact that the device uses an infrared light beam to stimulate the target neurons. This approach allows one to avoid mechanical stress and trauma sometimes associated with stimulating electrodes in direct physical contact with neurons.

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Question:
Open Has anyone used the [35S] GTPyS assay on brain sections of rats to assess DOPr activation?
I know it has been used successfully with MOPrs but I have had issues with DOPr and wondered if anyone had used this method in their lab?

I know it has been used successfully with MOPrs but I have had issues with DOPr and wondered if anyone had used this method in their lab?

By Pamela Farshim · University of Surrey

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32 Best stimulus delivery software for fMRI experiments?
By Alexander Lebedev · University of Bergen

Gerit Pfuhl · Norwegian University of Science and Technology (NTNU)

nope, unfortunately. One has to rewrite the E-prime code for Presentation. But the overall logic stays the same. So it is feasible within a few days t... [more]

nope, unfortunately. One has to rewrite the E-prime code for Presentation. But the overall logic stays the same. So it is feasible within a few days to "translate" E-Prime paradigms into Presentation ...

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3 Does anybody know a good 3D depiction of the hippocampus?
By Martin Pyka · Ruhr-Universität Bochum

Kevin Black · Washington University in St. Louis

A German group published some very pretty pictures in a journal article some time ago--sorry, that's not much help, but may be nice. Also search for h... [more]

A German group published some very pretty pictures in a journal article some time ago--sorry, that's not much help, but may be nice. Also search for hippocampus publications by Lei Wang (formerly at Washington Univ. in St. Louis, now at Northwestern)--one should have a nice picture.

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1 Can anyone tell me the steps for thinplate spline transformation on an MRI brain image to register it with target image?
By Madiha Azam · University of Engineering and Technology, Taxila

Amine Larhmam · Université de Mons

Hi, maybe this can help you : http://www.cs.wayne.edu/~jinghua/publication/miccai-07.pdf There is also a code source of the Thin Plate Spline algorit... [more]

Hi, maybe this can help you : http://www.cs.wayne.edu/~jinghua/publication/miccai-07.pdf There is also a code source of the Thin Plate Spline algorithm here : http://elonen.iki.fi/code/tpsdemo/index.html

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5 How is fMRi scanning of children different from adults?
By Michael Silverman · Mount Sinai School of Medicine

P Cédric Koolschijn · Universiteit van Amsterdam

Jasper already covered some important aspects. In my experience, it is best to make the visit comfortable and a fun experience so that they leave hap... [more]

Jasper already covered some important aspects. In my experience, it is best to make the visit comfortable and a fun experience so that they leave happy and even want to come back for follow-up studies if necessary. Definitely do mock scanner training, and let them hear scanner sounds beforehand. This has proven to reduce movement: http://www.ncbi.nlm.nih.gov/pubmed/20040825 and http://www.ncbi.nlm.nih.gov/pubmed/20225122. Two additional approaches to reduce head movements: 1) use metaphors. A. in your introduction use an example of a camera as a metaphor of a MRI scanner. i.e. if you move while taking a picture the image is ruined, similar to try to get a sharp image of a moving object. B. explain the sequence of your scanning procedure, and after performing their tasks they'll have their own private cinema for a movie. 2) you can use a bit of masking tape loosely attached to the forehead and the headcoil just as a reminder. It doesn't irritate, but withholds them from moving. Pay good attention and talk to them between runs and scans. You'll find out quickly if they're OK, or if they need a small break. Show a move during the structural scans (T1, DTI, MTR). We used finding nemo and various ice age movies (no sounds, but with subtitles). Make sure the movies are not too funny, you don't want them laughing. With respect to analyzing procedures. There are some papers on this topic: http://www.ncbi.nlm.nih.gov/pubmed/12781724 ; http://www.ncbi.nlm.nih.gov/pubmed/12482076. Reduce post-testing time. Especially for the younger kids, 8-10yrs, it's quite an experience, if your post-testing time is too long you end up measuring fatigue in stead of performance. If you have any further questions, feel free to contact me.

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6 How is the minimisation of contributions from other sources accomplished in linear spatial filtering ("beamforming")?
By Julian Keil · Charité Universitätsmedizin Berlin

Jürgen Dammers · Forschungszentrum Jülich

Dear Julian, it is difficult to explain the minization procedure within a few lines, but have a look at the following (open access) book http://www.i... [more]

Dear Julian, it is difficult to explain the minization procedure within a few lines, but have a look at the following (open access) book http://www.intechopen.com/books/magnetoencephalography In particular chapter 4 nicely leeds you through the beamformer technique including the different minimization procedures used in the community. http://www.intechopen.com/books/magnetoencephalography/characterization-of-brain-dynamics-using-beamformer-techniques-advantages-and-limitations

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3 Computed tomography (CT) angiography in rats.
By Francesco Blasi · Massachusetts General Hospital

Damian Mcleod · University of Newcastle

For angiography you can use the femoral vein to administer the contrast. You may just need a larger volume of contrast that is constantly infused.

For angiography you can use the femoral vein to administer the contrast. You may just need a larger volume of contrast that is constantly infused.

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Open Looking For traumatic brain injury subjects/collaborators for NIH Tau molecular probe Funding opportunity.
NIH Funding Opportunity Announcement RFA-NS-13-00: http://grants.nih.gov/grants/guide/rfa-files/RFA-NS-13-008.html research topics states as o... [more]

NIH Funding Opportunity Announcement RFA-NS-13-00: http://grants.nih.gov/grants/guide/rfa-files/RFA-NS-13-008.html research topics states as one objective "•Development of in vivo molecular imaging probes and/or methods with potential applications in humans relevant to TBI detection and risk assessment for the development of subsequent neurological diseases and disorders after TBI.” UCLA recently published a pilot study using F[18]FDDNP-PET showing increased Tau protein deposits in retired professional athletes. -http://www.espn.go.com/pdf/2013/0122/espn_otl_CTELiving.pdf We are investigating applying for funding to be involved in the study. The FOA states " This FOA will be used to support a multicenter team in the USA to conduct a prospective, observational, hypothesis-driven study(s) on 3,000 – 4,000 children and adults with TBI and control subjects." We have the facilities to synthesize and image F[18]FDDNP-PET studies in humans. We are seeking a local population of TBI patients to participate. We would consider negotiating shares of any successful grant application with potential collaborators.

RFA-NS-13-008 International Traumatic Brain Injury Research Initiative NIH Cooperative Program for Comparative Effectiveness of Clinical Tools and Therapies (U01).mht ×

By Michael Meal · University at Buffalo, The State University of New York

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Neuroimaging

PLOS ONE: An Online Database of Infant Functional Near InfraRed Spectroscopy Studies: A Community-Augmented Systematic Review

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