• Jenn Olejarczyk asked a question:
    Any suggestions on neuroimaging of oculomotor cognitive control tasks? I want something similar to antisaccade task, like IOR maybe?

    The antisaccade task has been a well-studied paradigm to assess executive functioning. People are asked to look in the opposite direction of a salient peripheral stimulus. I am wondering if there are similar tasks out there that use eye movements, other than the antisaccade task, to measure executive functioning or cognitive control. Inhibition of return (IOR) could be similar to the antisaccade task and there is also the gap effect. Any suggestions on particular paradigms or authors would be a huge help. Thanks!

  • Yves Miaux added an answer:
    What is the definition of the intensity time curves for perfusion MRI Data?

    What is the definition of the intensity time curves for perfusion MRI Data?

    You can find some excellent information in an interesting review paper recently published by Nelson on the different imaging modalities that can be used in the "Assessment of therapeutic response and treatment planning for brain tumors using metabolic and physiological MRI" (Nelson S. NMR Biomed. 2011; 24: 734–749). You will find some excellent references in this paper.

  • David Reese Mckay added an answer:
    Can anyone point me to an article(s) that specifically studies the influence of methodological/analytic choice in neuroimaging?

    Can anyone point me to an article(s) that specifically studies the influence of methodological/analytic choice in neuroimaging?  The rational and science behind neutral cue subtraction seems justified for the majority of physiological and neuroimaging studies.  However, when it comes to the frontal lobe, I'm not convinced that neutral cue subtraction is appropriate.  Of course, baseline correction is critical.  However, if passive viewing of geometric shapes elicit change in the PFC, why would we want to subtract a neutral cue?  Consider the variety of stimuli in IAPS neutral cues (books, household objects, etc).  These items will likely produce unique results in the PFC.  Any pub recommendations or thoughts would be greatly appreciated.

    David Reese Mckay · Yale University School of Medicine

    I think the PET guys that spent a lot of time on progressive subtraction of paradigms might have good perspective on this. Marcus Raichle wrote about differences between resting state data when passively viewing a cross hair vs eyes closed.

    The brain does so much covert processing, your answer will ultimately depend on the level of inference you wish to draw.  You could always test it like Raichle et al. did.

    Raichle M et al. A default mode of brain function (2001) PNAS 98(2) 676-682.

    See the last two paragraphs of results section; they say more details to be published separately, but I never saw anything. I'd be interested if you track down further details.

    Hope this helps,


  • Kevin Mandrick added an answer:
    Non-contact EEG sensors
    I need some practical suggestions for designing a data acquisition subsystem to a BCI.
    I am interested in sensors that do not require contact with the brain.
    I've read something about Photrodes. Are there other options?
    Kevin Mandrick · Institut Supérieur de l'Aéronautique et de l'Espace (ISAE)

    There is a few solutions on the market for non-invasive optical brain imaging (fNIRS devices). Personnaly, I could suggest one. It exists some companies like Rogue, Artenis, Shimadzu, Hamamatsu, Nirx, Techen, Gowerlabs, Hitachi, Cortech, ISS, Hemophotonics, MRRA just to cite commercial entities...

  • Greg Murray added an answer:
    You brain people are kidding me right? Is it true that the literature is unclear about whether the OFC is the same thing as the vmPFC?

    Writing a review of the chronobiology of reward,  and just conclusing that the neuroimaging evidence is stronger for chronobiological influence on vmPFC than the OFC.    Then I just happen to read something saying vmPFC and OFC are sometimes considered synonymous!

    Greg Murray · Swinburne University of Technology

    not sure if you got my thanks you yesterday...Anyway,  thanks Dominik!  Super useful expert answer!

  • Arnold Trehub added an answer:
    What are the advantages and what are the problems of the hypothesis about “retinoid system”?
    Is the hypothesis about “retinoid system” (by Professor Arnold Trehub), as described in “Consciousness and Cognition” 16 (2007) 310–330 and in the other works of Professor Trehub, a plausible hypothesis? What are its advantages and what are its problems?

    Professor Trehub describes it in the following words:
    “Activation of the brainʼs putative retinoid system has been proposed as the
    neuronal substrate for our basic sense of being centered within a volumetric
    surround –- our minimal phenomenal consciousness (Trehub 2007). Here, the
    assumed properties of the self-locus within the retinoid model are shown to
    explain recent experimental findings relating to the out-of-body-experience. In
    addition, selective excursion of the heuristic self-locus is able to explain many
    important functions of consciousness, including the effective internal
    representation of a 3D space on the basis of 2D perspective depictions. Our
    sense of self-agency is shown to be a natural product of the role of the heuristic self-locus in the retinoid mechanism.” (Abstract, from: Where am I? Redux.)

    For the publications of Professor Trehub see:

    The question has been already discussed on the folowing thread:
    Arnold Trehub · University of Massachusetts Amherst

    Here is recent evidence that excitation of neurons in the parahippocampal place area (medial fusiform gyrus) of the human brain can evoke activity in a neuronal network that generates a hallucination of a world scene from an egocentric perspective:

    Seeing Scenes: Topographic Visual Hallucinations Evoked by Direct Electrical Stimulation of the Parahippocampal Place Area

    Pierre Megevand et al

    The Journal of Neuroscience, 2014, p. 5403

    Direct electrical stimulation of house-selective visual areas elicits topographic visual hallucinations The locations and effects of electrical stimulation are summarized in Figure 1B–D and detailed in Table 1. Stimulation of DTIp2-1, in the medial fusiform gyrus, an area that was houseselective according to both fMRI and iEEG, caused the patient to experience a complex, topographic visual hallucination: he reported seeing a train station in the neighborhood where he lives. When questioned, the patient reported seeing the scene as if it was in front of him.

    This suggests that neurons in the parahippocampal area are an integral part of the extended retinoid system.

  • Esat Adiguzel added an answer:
    Can anyone help with a problem with extracting hippocampal volume using VBM and WFU-pickatlas?


    Sorry I am new to VBM and I want to compare hippocampous volume by using two different method (manual tracing and atlas-based method ) .I have two kind of samples patient with MTLE and normal ones. I used a script “ get_totals.m” by Ged Ridgway and WFU-pickatlas but the results were odd and very small. There is also an article “ Age-related changes in regional brain volume evaluated by atlas-based method “ Wataru Gonoi 2010 springer , that used nearly the same method using WFU-pickatlas and SPM5.
    I checked SPM mail archive there were same titles but unfortunately I got confused there were no clear answers and now I am not sure whether this method is correct and reliable .

    I would be very appreciated if anyone could help me.

    Best regard


    Esat Adiguzel · Pamukkale University

    I understand that you need to check the reliability of software. You can use stereological methods to measure real volumes. But you should have the thickness of the MRI slices. After this procedure, same volume should be measured using by the software. I can send you the references and more knowledge about stereological methods.

  • Leonard F Koziol added an answer:
    Are there any white matter (WM) tracts that can be implicated to affect sexual functioning in patients with MTBI?

    Alteration of sexual functioning in patients with traumatic brain injury is a phenomenon that has been widely studied. However, these studies are predominantly limited to self reported symptoms and hypothalamic-pituitary dysfunction (assessed through hormonal workouts mostly. Detailed imaging studies of this phenomenon are extremely scarce, if not unheard of.

    What are your thoughts on possible influence of deep white matter tracts on sexual functioning in TBI, and MTBI specifically?


  • Irina G Makarenko added an answer:
    Problems with long storage of brain material in 4% paraformaldehyde
    After long storage of brain material with DiI insertions in 4% PAF, some tissue looks very good, but several specimens are covered by white crystals on the surface and inside the tissue.

    After cutting on the vibratome the last ones do not provide good pictures. Do you know if it is possible to restore such material? How to do this?
    Irina G Makarenko · Russian Academy of Sciences

    Thanks for your answer. Evrything is clear.  But it looks strange that I newer read about formaldehyde as a fixator for the DiI tracing!

    Long storage is a result of our Russian specificity : when I had grant and animals (rats) I worked on the fetuses. Sometimes they were very numerous and I prepared not only planned material but some additional training applications according my ideas.  Later if I had students I gave them this material or use it myself.  So sometimes storage was rather long.  Really I prefere long stroage for the developmental studies, because in this case I am sure that the absence of studied connections is not the result of short exposition. Additionally dendritic tree is better

    Yes we have fluorescent and confocal microscopes with such filters, but now I have no my own grant and do not perform new experiments as I have previously prepared material.   Additionally I am not sure that it will be possible to send a chemical reagent to Russia although it is interesting to try....    You mention that DiD is better - what is the difference with DiI

  • Olaf Dietrich added an answer:
    How much SNR difference can we expect for brain imaging if we compare a Philips Ingenia 70 cm bore to a Siemens Prisma 60 cm bore?

    I realize the 60 cm is better in general, but I wonder if the Ingenia would reduce this difference somewhat?  We're compromising needs for extremity/MRS users and brain/MRI users.  At the same time we don't want to sacrifice the quality of the fMRI studies.  What data is available to help us motivate our decision?

  • Ekaterina V. Pechenkova added an answer:
    Does anyone have experience with fMRI on Siemens Spectra (3T) or Siemens Aera (1.5T)?

    It maybe looks like a strange question, because none of these scanners is probably your system of choice for neuroimaging research, but I would appreciate any sharing of experience.

    Ekaterina V. Pechenkova · Institute of Practical Psychology and Psychoanalysis

    Thank you! Yes, I would prefer Trio as well :) So far it seems to be the best research scanner. But other Siemens scanners can be used for fMRI as well.

  • Kenneth Sung Lai Yuen added an answer:
    Can we bridge the Gap between stimuli space and activiy space using neuroimaging techniques?

    In brain decoding encoding methods we are dealing with features at the stimuli side (image, videos, etc.) these features includes shape,  color, texture etc. In the brain activity side we have for example fMRI time series data related to the some stimuli, and we extract features from this signals. The question is can we map between two types of aforementioned features?

    Kenneth Sung Lai Yuen · Universitätsmedizin der Johannes Gutenberg-Universität Mainz

    You could refer to the following two seminal papers that propose a method in attempted to map the two different spaces (perceptual vs stimulus):

    Kriegeskorte N, Mur M, Bandettini P (2008), “Representational similarity analysis - connecting the branches of systems neuroscience.” Front Syst Neurosci 2:4

    Kriegeskorte N, Mur M, Ruff DA, Kiani R, Bodurka J, Esteky H, Tanaka K, Bandettini PA (2008), “Matching categorical object representations in inferior temporal cortex of man and monkey.” Neuron 60(6):1126-41

    And in the lab of Jack Gallant they've done a lot to build forward models to predict individual's percept from moltivoxel fMRI BOLD signal:

  • Cinnamon Welland added an answer:
    Does anyone know of any innovative articles about disorders of consciousness treatments?
    I´m looking for some new updates in the treatment of DOC in order to improve neurorehabilitation programms
    Cinnamon Welland · George Washington University

    I attended a lecture last week at the Kennedy Krieger Institute given by Dr. Joseph Giacino.  His program at Spaulding Hospital may be of interest to you.  Here is a recent publication about his work...

    Giacino, J., Carter, C., Charney, C., Ambrosi, D., Doiron, M., Herman, S., & Young, T. (2014). A Systematic and Evidence-Based Approach to Clinical Management of Patients with Disorders of Consciousness. In M. Sherer & A. M. Sander (Eds.), Handbook on the Neuropsychology of Traumatic Brain Injury (pp. 139-156): Springer New York.

  • Ahreum Lee asked a question:
    Is there anyone using the Spectratech OEG-16 (NIRS) and some other tool to analyze brain activation areas?


    I used the NIRS, which is Spectratech OEG-16, and am trying to find the best adaptable software to analyze it (especially for activation map).

    I tried to use the NIRS-SPM though it had some error messages and I could not deal with these.

    If there is anyone who has tried to analyze the Spectratech OEG-16 to get the 3D images, I'd appreciate some comments :)


  • James G Smirniotopoulos added an answer:
    What are the best methods to compare the similarity of two medical images?
    When searching for a method to compare two medical images, e.g. to determine how similar they are or how much and where they differ, I came across several proposals. A simple subtraction image + width of histogram or entropy, crosscorrelation or joint histograms to name some of them. Nevertheless, I wonder if there is something like a standard method? And if not, it might be worth to discuss what could be a sensible approach.
    James G Smirniotopoulos · Uniformed Services University of the Health Sciences


    Thanks for providing a copy of the article!


  • Cynthia O'Rourke added an answer:
    Has anyone seen CLARITY tissue clearing with no electrophoresis?
    I just posted this in the CLARITY resource center forum, but posting it here too. We found this hydrogel perfused/embedded right hemisphere of a rat cortex to be nearly completely clear after sitting in clearing solution in 37 degree incubator for ~5 weeks completely unattended. Next to zero tissue damage and it looks by far better than any brain that we have run through our ETC chamber. Has anyone else seen this?
    Cynthia O'Rourke · Reed College

    Please keep us updated, Gregory! We're trying the passive approach here, and I'm sure the researcher in charge of the project would love to know if the tubes need as much baby-sitting as they're giving them. 

  • Bruno Quendera added an answer:
    What are the currently available best systems for color calibration in the MR environment?
    Most systems are not MR compatible.
    Bruno Quendera · University of Coimbra

    It's possible to measure the color conditions in bore if magnetic field is turned down (it a risky procedure rarely made in maintenance and with an high possibility of quench) in the same conditions as during experiments but without damaging the spectrophotometer.

  • Cainositas Cainosito added an answer:
    What is the meaning of "synaptic puncta"?
    Could you tell me what does the "Synaptic puncta" mean?

    Is it a synonym for synaptic surface?

  • Jamie Lars Hanson added an answer:
    Are there many published papers using PPI (Psycho-Physiological Interaction) that more fully graph the main effect and interaction terms?
    Most PPI papers often report statistics of an interaction (but that seem challenging to interpret since the main effects of that brain regions aren't necessarily discussed/graphed).
    Jamie Lars Hanson · Duke University

    Thank you for the thoughtful response! And for the paper suggestions! Since asking the question, I also found a few papers that graphed the interaction (but it still seems as though the preponderance of publications do not include such graphics, sadly).

    I will check out those papers! Thanks again!

  • Mark Charles DeLano added an answer:
    If you could buy any 3T human MRI right now, what would you get? Why would you choose that system?
    Ingenia, Achieva, Skyra, Verio, Discovery, which one is best for fMRI, for DTI, for MRS? How about a Trio with the new Tim 4G electronics? Or maybe you want a Fonar...
    Mark Charles DeLano · Michigan State University

    Though my previous post some time ago favored GE, after serious consideration I went with the Prisma.  Parallel transmit reduces B1 issues, better gradients reduce distortions on EPI and should give better echo spacing on everything, better coils facilitate better acceleration factors, and better software/multi-band and zoom it  for our DTI/DSI and fMRI work tipped the scales.  The scanner is impressively quiet.  We go live clinically soon--ran into a snag with a flood in the room of the new building it is going into.  The 64 channel head coil is 40 head/24 neck elements and there are 12 anterior and 12 posterior elements.   Haven't had the opportunity to use it and will repost after a bit of experience.

  • Vigneswaran Veeramuthu added an answer:
    Negative correlation between fractional anisotropy and neuropsychological performance scores at admission for patients with mild TBI - any thoughts?

    Literatures are generally equivocal about negative correlation found in diffusion tensor imaging (DTI) of mTBI patients, especially when the inverse correlations are found at the initial admission DTI and neuropsychological testing. Some associate the negative correlation with cytotoxic edema (thus the increased FA vs poorer neurocognitive performance). How do you justify both positive correlation and negative correlation with poorer cognitive performance at admission?

    Vigneswaran Veeramuthu · University of Malaya

    Thank you so much for your suggestions Dorian Pustina. I will definitely take your suggestion into account. Truly appreciate your kind gesture in lending your expertise in this area.

  • Silvia Alemany added an answer:
    Does anybody know about any study relating olfactory cortex volume or function and childhood maltreatment?
    Croy and colleagues (2010; see attached) mentioned "Due to the reported volume
    reduction and functional peculiarities in parts of the central
    olfactory processing system in patients with child maltreatment and PTSD we
    expected an altered activation, as detected by fMRI, in these areas
    in response to olfactory stimuli"; however I have not yet found any neuroimaging study specificcally linking olfactory cortex to exposure to early stress.
    Silvia Alemany · CREAL Center for Research in Environmental Epidemiology

    Thank you very much for your responses! :)


  • Danilo Maziero added an answer:
    Does anyone have experience with ICA using BV?
    I scanned 20 subjects during 6 min resting state. now, I would like to apply ICA (using BV). I know that in FSL one can calculate the optimal number of components (for each subjects). Can BV do the same? I tried to use 30 components to all subjects, however looking at the "networks", I think I should use different number of components to each subjects.
    Danilo Maziero · University of São Paulo
    Well, I have been working with ICA in BV for a while, basically in epilepsy patients data, always doing individual analysis. In epilepsy patients data I had found from 25 to 200 components (a lot of noise, motion and also RSN split in different components).

    You are right, even for health subjects we can have a large range of components to be found (from 20 to 60).

    There are some strategies for estimating the "ideal" number of ICs to be found, one of them is the RAICAR (Ranking and Averaging Independent Component Analysis by Reproducibility).
    Particularly, I have always applied the PCA from FSL and them used that number in BV (It sounds not usual to apply FSL at the beginning and then BV, but I have always preferred to see my results in BV, once we have the license).

    I hope this is helpful
  • Erik A. Martens added an answer:
    Has anyone tried the new CLARITY technique out of the Deisseroth lab in Stanford?
    We are about to get the necessary materials to do CLARITY with rat brains, and wonder if anyone else here has given it a shot. I figured this might be a good place to share any pitfalls we might come across, etc. I don't anticipate any problems at the moment, as the protocol is very clear and detailed. Very excited to be trying CLARITY out.

    Here is a link to the CLARITY protocol:

    Chung, K., J. Wallace, S.-Y. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, and K. Deisseroth. 2013. Structural and molecular interrogation of intact biological systems. Nature advance online publication (April).
    Erik A. Martens · University of Copenhagen
    Most clarification methods such as Clarity, seeDB, Scale, are preceeded by an incubation period in 4% PFA of the sample before it is clarified. The length of incubation is typically 12h - can longer incubation times impact the clarification so it fails?
  • Valia Rodriguez added an answer:
    Can anyone advise me in search of software for EEG sources?
    I'm doing source analysis. Does anyone know a software for source analysis like FD VARETA?
    Valia Rodriguez · Cuban Neuroscience Center
    Look in here
  • Umeo Ito added an answer:
    Is there an international need for manual structural volume analysis in MRI studies?
    In my research I have analysed structural volumes in MRI scans by manual tracing measures and correlated against automated measures, with particular interest in subcortical grey matter structures. As I am still a student it is interesting to gauge the overall need for the skill in the international community, either as a diagnostic tool or as an inter-rater reliability measure.
    Umeo Ito · Tokyo Medical and Dental University. Tokyo Metropolitan Institute of Medical Science,
    For neurosurgical use, the manual segmentation is too time consuming prior to emergency operation. Practically, estimation of the size of lesions seeing the three horizontal, coronal and sagittal view is sufficient. For animal experiment, planimetry of HE stained sections of constant thickness enlarged on the papers by CP scanner is more practical.
  • Asaid Khateb added an answer:
    Can someone suggest a good, short duration fMRI activation task?
    I am looking for a good fMRI task which shows strong activation, but is approximately 6 minutes or less in duration. This task is to be used with older people. A memory paradigm would be preferable, but suggestions for attentional tasks would also be helpful.
    Asaid Khateb · University of Haifa
    The semantic categorization task we developed in Geneva for pre surgical purposes is a good, short (4 minutes duration) and reliable, easy to perform by old people. It had been used in more than 100 patients including epilepsy, aphasia , tumors etc..
    see references
    1. Seghier M, Lazeyras F, Momjian S, Annoni J-M, de Tribolet N, Khateb A. Language representation in a patient with a dominant right hemisphere: fMRI evidence for an intrahemispheric reorganisation. NeuroReport 2001;12:2785-2790.
    2. Khateb A, Martory MD, Annoni JM, Lazeyras F, de Tribolet N, Pegna AJ, Mayer E, Michel CM, Seghier ML. Transient crossed aphasia evidenced by functional brain imagery. Neuroreport 2004;15:785-790.
    4. Seghier ML, Lazeyras F, Pegna AJ, Annoni JM, Zimine I, Mayer E, Michel CM, Khateb A. Variability of fMRI activation during a phonological and semantic language task in healthy subjects. Hum Brain Mapp 2004;23:140-155.
    5. Seghier ML, Lazeyras F, Pegna AJ, Annoni JM, Khateb A. Group analysis and the subject factor in functional magnetic resonance imaging: Analysis of fifty right-handed healthy subjects in a semantic language task. Hum Brain Mapp 2008;29:461-477.
  • Brian Andrew Gordon added an answer:
    Does anyone have an opinion about the use of nuisance covariate regression in fMRI local connectivity measures?
    Nuisance covariate regression (head motion, CSF and WM signal, global signal) in local connectivity measures (like Regional Homogeneity (ReHo), Amplitude of Low Frequency Fluctuations (ALFF and fALFF), Degree Centrality and Voxel-Mirrored Homotopic Connectivity (VMHC)) is still a matter of debate. What is your opinion? Is nuisance regression more effective before or after bandpass filtering?
    Brian Andrew Gordon · Washington University in St. Louis
    There is some merit in throwing out volumes with high motion rather than simply regressing out motion covariates. There have been a number of papers on this topic lately. Here are just a couple.

    As far as regressing the global signal, most lab tends towards removing it. This article is worth a read on that topic.
  • Matthew B Wall added an answer:
    Can the suprachiasmatic nucleus be a 'seed region' in a resting state fMRI investigation?
    We are designing a neuroimaging study to test hypothesised circadian moderation of reward function in humans. Seems like our hypothesis is best tested using resting state methods, ideally with the hypothalamic suprachiasmatic nucleus as a 'seed region' to investigate correlations with brain reward centres (particularly ventral striatum).

    I understand that small, deep brain centres are difficult to image.
    Matthew B Wall · Imanova
    No problem, and best of luck with the project, it sounds really interesting.


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