• Douraied Ben Salem added an answer:
    What are the causes of negative CSF cytology in the presence of ependymal metastases for a case hypothalamic germinoma?

    Any further role for the radiologist in this case?

    Douraied Ben Salem · Centre Hospitalier Universitaire de Brest

    If a new CSF cytology is performed  few weeks later, it may turn positive.

  • Manu Singla added an answer:
    How can we flip image in left right direction in FSL?

    I have a volume  of MRI which is left hemisphere of brain and I want to flip it in left right direction to perform symmetric analysis with right hemisphere.

    Can anyone suggest me how can it be done.

    Manu Singla · BITS Pilani, Hyderabad

    Thanks all for your suggestions...

  • Patrik Pluchino added an answer:
    Has anyone used Matlab/E-Prime to present experimental stimuli recording the EEG with the Mobita TMSi portable amplifier (Wireless sync)?

    I was encountering issues related Matlab (related to Visual Studio) and for this reason I have decided to switch to E-Prime in order to present the experimental stimuli.

    But I do not know how to write in the E-Prime code a inline in order to send triggers to the Wireless Sync that could later appear in the Polybench Software in the EEG signal. 

    Moreover I'm using E-Prime to control also a RED 500 SMI eye tracker through an ethernet cable. 

    For this reason I would like that E-Prime could send simultaneoulsy to both devices the triggers.

    Patrik Pluchino · University of Padova

    Dear All,

                  thank You all for the answers. I'll have a look to all the advices.

    Best regards,

    Patrik Pluchino

  • Floyd Thompson added an answer:
    What parameters would be important to extract from movement-related cortical potentials other than Time and amplitude of peak negativity?

    We want to identify the differences in MRCP's and ERD's during dynamic wrist and hand movement. What parameters would be important to investigate when the differences will serve to the development of a platform for BCI- (neurofeedback) rehabilitation? We are already extractiong the time and amplitude of Peak negativity and could look at the rebound rate. What else would you recommend?

    Floyd Thompson · North Florida and South Georgia Veterans Health System

    It would be interesting to quantitate the cortical potentials to wrist flexion torque, wrist extension torque, with prescribe torque objectives, in regard to velocity of torque development, amplitude of torque generated. Then compare rhythmic patterns with  alternation of flexion and extensor movement responding to movement cueing in regard to direction, velocity, and force.

  • Roya Kheyrkhah added an answer:
    Are there any EEG data from 7-12 years old children that are perfect and don't have any specific seizures and where can I find them?

    The most of data are related to disorders and disabilities, i want the perfect one of them. can any one help me? thanks.

    Roya Kheyrkhah · University of Tehran

    your welcome Elizaveta and thanks for your attachments.

  • Francesco Sammartino added an answer:
    Asymmetry voxel based morphometry?

    I'm struggling with calculating the asymmetry index in SPM: Can anyone provide a reference on how to do it? I found very confusing the concept of averaging each hemisphere with its flipped version. Thank you a lot.

    Francesco Sammartino · Toronto Western Hospital

    Thank you!

  • Brianne Jeffrey added an answer:
    Can we reliably measure dopamine in response to game stimuli in humans?

    The "dopamine argument" is one of the most enduring claims in texts about the effects of games and gamification.

    The popular idea simplifies the functions of dopamine in the organism, by presenting it as a  "reward molecule". As scientists we are aware that this is a gross simplification. Yet it is a highly persistent claim, which we'd like to test in order to address the central claims in the popular discourse head on.

    I am aware that the dopaminergic system can be monitored using e.g. PET, and I have found several references on the web about measuring it in blood samples, but are these viable ways of testing responses to e.g. game experiences?

    The setup would be a factorial design or a RCT with game-elements as the 'treatment', and measures of game behavior plus subjectives experience as supportive DVs in addition to dopamine levels.

    How could something like this be achieved? And is the idea realistic?

    Brianne Jeffrey · University of Pennsylvania

    I have recently heard of a group doing fast-scan cyclic voltammetry for sub-second dopamine detection in human patients. However, these patients are already undergoing surgery for deep brain stimulation. This clearly limits the population you would be working with.

  • Adriana Bucur added an answer:
    JMRUI software
    I am planning to run some metabolic analysis with JMRUI software (for magnetic resonance spectroscopy) and I find it hard to analyse the data with it (finding an appropiate tutorial etc). Did somebody use it and could give me some support?
    Adriana Bucur · The University of Manchester

    Dear Ali, 

    Have you tried "Dicom", "Siemens DICOM Import (MPI Leipzig)", or "Siemens Format (NUM3)"?

    Dear German, 

    If your FID is sufficiently/completely decreased in your first 1024 points, you can truncate the last 1024 points from "Preprocessing" menu -> "Truncate". This gives you the option of truncating as many points as you wish from either the beginning or the end of your FID or a combination of first and last points. 

    Conversely, for going from 1024 to 2048, you probably know you can use the "Zero filling" option from the "Preprocessing" menu.

    I hope this helps.

    Best wishes, 


  • Which is the most efficient neuroimaging technique?

    In cognitive state detection and analysis. we analyze spatio-temporal brain data from MEG, fmri, PET, EEG and so one. to detect the brain cognitive states. we need to which one of these neuroimaging  techniques give us more information. if there is a Convincing evidence on choosing one of neuroimaging techniques. fmri, MEG, PET, EEG, or what

    Gabriel Gonzalez-Escamilla · Universidad Pablo de Olavide

    Well it will depend on your research question, there are several data repositories, some of them dedicated to specific research questions (eg. resting-state, mental disorders: Pain, AD, PD), some of the most used data repositories:

    also, the adni database contains many other biomarkes for AD

    some useful tools:

    But there are a few more.


  • S. E. Robinson added an answer:
    Is there any algorithm useful for magnetic source imaging of human palm?

    We have used biomagnetometer with 248 axial gradiometers (3600WH, 4D Neuroimaging, San Diego, CA) to measure the pattern of bioelectromagnetic field on human palm but our software is only for MEG. We need a different algorithm for source localization on human palm/hand. Thanks

    S. E. Robinson · National Institutes of Health

    You can use the dipole in a homogeneous conducting sphere forward model as an approximation -- if you set the origin far below the center of the palm. This would be equivalent to a dipole in a half-space model. There will be some error due to the return currents being constrained to the palm, which does not extend past you origin. Nonetheless, you should be able to obtain a useful dipole fit.

  • 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 an essay that is relevant to our discussion about the retinoid theory of consciousness:

  • Arnaud Attyé added an answer:
    How do you do high-level tractography?

    I'm looking to perform tractography with high resolution DTI data; at 64 gradient directions, voxel sizes of 2x2x2, b-value = 1500, 3T images.

    I've been reading around and found that the fODF (like CSD based, Jeurissen et al., 2011) algorithms could be an improvement over the dODFs (DSI and q-ball) and of course over the tensor-based algorithms, but there are still so many different fODF algorithms and I would like to know how to choose one or two.

    I'm also interested in quantification of the streamlines from tractography, and I would like to know which are the most useful metrics derived from tractography (i.e. fiber leght, number of fibers, etc), and if a reliable way to obtain such measurements exists.

    Arnaud Attyé · Centre Hospitalier Universitaire de Grenoble

    I agree with previous comments for MRtrix that is a wonderful software for post-processing, especially when using Track-weighted imaging. TWI maps bring new insights in brain anatomical pathways as well as for studying peripheral nerves. Yet, quantitative microstructural analysis remains difficult except for basic DTI derived parameters such as FA or MD.

  • Iza sazanita Isa added an answer:
    Can anyone suggest a MRI images database of a brain tumor with ground truth?
    I want to evaluate the efficiency of a MRI segmentation method. To do so, I need a database of MRI images of the brain with tumors (glioblastoma or any other type of tumors), but with a Ground truth (GT). Most of the time, the GT corresponds to manual segmentation done by a radiologist.

    I have found an alternative solution : the use of synthetic ground truth. Some formulas are given in this article :
    Synthetic ground truth for validation of brain tumor MRI segmentation but I don't have the code source and the article is not very well detailed.

    As attachment, an example of a ground truth (green) segmentation done by a physicist.
    Iza sazanita Isa · Universiti Teknologi MARA

    Anyone please suggest me an MRI white matter database. 

  • Kevin R. Urstadt 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?
    Kevin R. Urstadt · University of Michigan

    The Clarity Wiki implies that omission of bis-acrylamide (using only acrylamide) in the hydrogel polymerization process allows the tissue to be more porous. Perhaps that hastens clearing time?

    Yang et al. (Cell, 2014) did this acrylamide-only hydrogel prep for tissue that had been pre-fixed, and their brains were cleared in substantially less time, on the order of days instead of weeks. They did use a little more SDS in their clearing solution, however (8% instead of the original protocol's 4%).
    Link to extended PDF:

    Additionally, Poguzhelskaya et al. (Molecular Neurodegeneration, 2014) did this in 1-1.5 mm thick coronal mouse brain sections as Annabelle had mentioned, having first perfused mice with the hydrogel solution. Their clearance time was 7-10 days.

    I'm also just starting this passive clearing approach, so I'm only beginning to try these approaches. Best of luck to those also starting up this useful technique in their labs.

  • Xiao-Song He added an answer:
    Is FWE correction too conservative for whole-brain analyses?
    I'm doing a whole brain analysis on my dataset in SPM. There is hardly any result left after the FWE correction. I found a couple of papers that conducted the whole-brain analysis reported either FWE uncorrected results or just indicated regions reached significance (p<0.001, uncorrected) didn't survive FWE correction. However, for those studies doing ROI analyses, most reported positive result after FWE correction. So if FWE correction is too conservative for whole-brain analyses but not for ROI analyses?
    Xiao-Song He · Thomas Jefferson University

    Pretty nice discussion! Thank you all! 

  • Martin Pyka added an answer:
    Can anybody share raw-data of the rat-hippocampus obtained with the CLARITY-method with me?

    For a computational model of the rat-hippocampus I would like to better understand how the projections from the entorhinal cortex to the hippocampus looks like. I think, data obtained with CLARITY-method would be the best for my needs. Does anybody have volumetric data of the rat hippocampus and adjacent regions that he could share with me?

    Martin Pyka · Ruhr-Universität Bochum

    Sorry, but I don't get it. Where can I find the data?

  • Dorian Pustina added an answer:
    Does anyone know of an brain atlas of arterial territories that is registered to MNI or talaraich or some common space?

    I need a file that I can download use for data analysis (basically automatically determining what vascular distribution a stroke has occurred in).

    Dorian Pustina · University of Pennsylvania

    Same here, would be really interested to have a probabilistic digital atlas of territories. Will look at the papers Pascal and Christian suggested, but if someone has a link to a probabilistic blood supply map, that would be awesome.


  • Bernd Merkel added an answer:
    I'm looking for a journal in Neuroimaging which explicitly allows 2 senior co-authors. Any suggestions/ideas ?

    Usually a paper has one last (=senior) author. In my case, I have 2 senior (last) co-authors. Is there a paper that explicitly makes this visible ?

    Bernd Merkel · University of Melbourne

    Thanks Rebecca !

  • Chanukya Krishna Chama added an answer:
    What is the easiest/fastest way to convert nifti files to img/hdr?
    Chanukya Krishna Chama · IIT Kharagpur

    I find following tools for easiest/fastest conversion   <-- ImageJ

    (or)  <-- Fiji (ImageJ2)

  • Darren Jian Sheng Yeo added an answer:
    In resting-state fMRI analysis, is the cerebellum removed?

    I am doing a seed-based correlation analysis, and would be including the time courses from white matter, ventricles, global signal, and motion parameters as regressors. Is the cerebellum usually removed for such analyses?

    I would also like to clarify if a whole brain mask including the cerebellum is used to derive the global signal.


    Darren Jian Sheng Yeo · Vanderbilt University

    Thank you so much for all the advice, Dr. Cocozza, Dr. Hernandez-Castillo, and Dr. Ashtari! Thanks for the paper too, Dr. Di! Yes, I gathered that I should not remove the cerebellum in my analysis. That question came up because the removal of cerebellum was part of a segmentation procedure, and I realized that I can also define the white matter and ventricles without using the segmentation procedure.

    I am still undecided about including global signal regression though.

  • Maria Carmen Martín-Buro added an answer:
    Are the images of faces problematic stimuli in neuroimaging?

    In a memory experiment, what is preferable to use: images of faces or objects? Some people say that faces are problematic because they are relevant stimuli that are not processed like the rest of stimuli and it could introduce non-memory-related  activations in neuroimaging data. We are not interested in exploring emotion or social cognition. 

    Maria Carmen Martín-Buro · Universidad Politécnica de Madrid

    I wasn't sure but now with these references and your experience I've decided not to use faces. Thank you!

  • James Bjork added an answer:
    What do negative beta weights in ROI analyses mean?

    Hi all,

    I am currently analysing data from an fMRI study, with a 2x2 between-within design. Patients vs controls reflect the between factor, and congruent and incongruent trials reflect the within factor (this is a Stroop task).

    After seeing an interaction effect between the two factors in several brain clusters, I wanted to extract the beta-weights from these clusters to explore the underlying effects.

    I used Marsbar to extract the raw beta-weights from congruent and incongruent trials, separately (so no contrast between conditions performed), and plotted the results for my two groups.

    Many of the resulting beta-weights are negative, and I wonder what this means? Does it reflect a sort of 'deactivation'?  

    Any input will be highly appreciated!

    James Bjork · Virginia Commonwealth University

    I always do a VOI analysis of a contrast-activated voxel, to characterize what is driving the A-B contrast.  Is it that there is activation during event A or deactivation during B, or some combination of the two?  Because I use event-related designs with trials every several seconds, I can use AFNI with mapfiles that enable trial-averaged dumpouts of the whole hemodynamic response averaged across all trials of that type (c.f. PMID 18672069 ).  That gives a graphical answer right there.  IMO one shouldn't just plug and chug contrasts using turnkey software without knowing what's going on in the trial-type-averaged BOLD signal volume by volume.

  • Helen Macpherson 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.
    Helen Macpherson · Swinburne University of Technology

    Thank you for all your suggestions, we ended up going with the freely available n-back task from the Human Connectome Project. 

  • Jared P Dempsey 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.

    Jared P Dempsey · Addiction Recovery Research Institute (Lubbock, TX)

    Thanks, all.  I ended up conducting analyses both ways.  Hopefully someone will specifically investigate the neutral cue impact soon.  Some food for thought:

    -Neutral cue response is modulated during pharmacological treatment

    Outhred T, Das P, Felmingham KL, Bryant RA, Nathan PJ, Malhi GS, Kemp AH. Impact of acute administration of escitalopram on the processing of emotional and neutral images: a randomized crossover fMRI study of healthy women. Journal Of Psychiatry & Neuroscience: JPN 2014;39 (4), 267-275.

  • Ivan Bodis-Wollner added an answer:
    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!

    Ivan Bodis-Wollner · State University of New York Downstate Medical Center

    Voluntary saccades to imagined target features in complete darkness. There are some fMRI studies on saccades in the dark .. worth reviewing them, but the one I am bringing to your attention has not been explored to the best of my knowledge

  • Bruno Costa 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?
    Bruno Costa · Federal University of Rio de Janeiro

    Does any one know if it is possible to do the Anova estatistics on the software sLORETA? I think the software doesn`t have this option but some articles say that they did it as the file here.

  • Gioele Santucci 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?

    Gioele Santucci · University of Bologna

    For Example, when you are studing brain tumors and you use a DCE- T2*Weighted imagind SSH, it is better to use a preinjection of 2cc of intravenous paramagnetic contrast and waiting period of 8-10 minutes: this is usefull for having an intensity time curve with a more  accurate subtraction and provides information about the function of the blood-brain barrier. 

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