• John Broussard added an answer:
    What is the best technique for clearing the brain while preserving endogenously expressed GFP?

    I have looked at CLARITY, SeeDB, 3DISCO, in the literature and they almost always require immunolabeling. Which technique preserves GFP (or YFP) the best, without additional immuno?

    John Broussard · Baylor College of Medicine

    Thank you Nicolas

  • Annerine Roos 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?
    Annerine Roos · Stellenbosch University

    Dear Paul

    It makes sense what you are saying about FWE etc. Do you have a reference to support your notions, that could be used in a manuscript?

  • Bernhard Dohmen added an answer:
    Does anybody have knowledge of validated radio tracer in PET for Parkinson's disease imaging?

    other than FDG.

    Bernhard Dohmen · Agaplesion Diakonieklinikum Rotenburg

    For clinical imaging in PD DATScan (SPECT-Tracer) imaging dopamintransporters is the only (but EMEA licenced) Tracer. As far a I know Prof. Tatsch (Karlsruhe/Germany) is preparing a normal database together with international colleagues.

    For differential diagnosis of atypically PD postsynaptic imaging using I-123-IBZM (as far as I know licenced in UK and NL) sometimes is done. Sometimes FDG-PET is used in such setting.

    For Research puposes various Tracers are used depending on the binding site Research is targeted. Affinity of the tracers useable is sometimes a matter as well. 

  • Jason Seeho Chan added an answer:
    Is there anyone who is performing real time fmri with AFNI??

    Dear All, 

    I have a question related to how can I use of AFNI for real time fmri because of the data format

    I'm receiving data from the scanner in the form of Par/Rec and I don't know which format should I use for AFNI real time ??
    as I saw from the demo of AFNI data were in the form of BRIK/HEAD.

    so I was wondering is it the only accepted format ?? or what are other formats that can be used for realtime AFNI ??

    also if not then what can I do to change the format of each volume from par/rec to BRIK/HEAD??


    Jason Seeho Chan · Goethe-Universität Frankfurt am Main

    The PAR/REC format is proprietary to Philips, however, I know that this is also possible to tell the system to output nii.  

  • Marcia Ratner added an answer:
    Can someone help me to understand the role of PET in motor and NMS complications in Parkinson's Disease?

    I am focusing on the neuroimaging role in PD research. How can I differentiate a PD from a variety of atypical PD disorders? 

    Marcia Ratner · Boston University School of Medicine

    Radio-labled F-DOPA PET scans show reduced uptake in the striatum reflecting a loss of DA neurons and a compensatory down regulation of the DAT.  

    By contrast patients with manganese induced Parkinsonism show relatively normal uptake in the striatum reflecting the different neuropathology.  

    In general, parkinsonism can be differentiated from idiopathic PD by uptake of F-DOPA in the striatum; the exception to this rule would be the parkinsonism induced by MPTP since this neurotoxicant causes a profound loss of DA neurons projecting to the striatum similar to that seen in idiopathic PD.

  • Bernd Merkel added an answer:
    What can I measure with an MRI pASL sequence with one timepoint ? Can I derive arterial transit times ?

    Hi all ! I have 100 patients with a pASL sequence and would like to get some information about the CBF. Is this actually possible with just one TI ? Can I somehow calculate an arterial transit time ? Because if I just measure at one time-point, I do not know whether the bolus has already passed or not arrived yet, right ? Is it only useful for grey matter or also white matter ?

    Thanks for any help !

    Bernd Merkel · University of Melbourne

    Thank you Marco and Wanyong for your answers !

  • Renaud La Joie added an answer:
    Can anyone suggest how to set a maximum pixel cluster size as a threshold in REST toolbox for RS fMRI seed based analysis?

    Resting state fMRI - detection DMN with seed in hippocampus:

    I would like to set a maximum pixel cluster size as threshold to compare seed based analysis results of data sets made on different scanners and with different head coils. This is not possible with the REST toolbox. Any other suggestions? Thanks in advance.

    Renaud La Joie · Claude Bernard University Lyon 1

    Hi Stephanie,

    The statistical thresholding of rs-fMRI data is always a bit tricky: there are multiple ways to do it, and no clear consensus. To determine a minimal cluster size, I used the AFNI toolbox, and especially their 3dClustSim program; it uses Monte Carlo simulations to determine a minimal cluster size which leads to a global alpha value you can specify (usually 0.05), based on the voxel-level statistical threshold (p-value) you use. Attached is the link to the detailed program description.

    ex: with a p<0.001 threshold at the voxel level, you'll need clusters > 120 voxels; with a p<0.005, threshold at the voxel level, you'll need clusters > 205 voxels...

    Does that help? Is that what you wanted?

  • Pauline Roca asked a question:
    What is the best freely available software in order to study aneurysm growth based on Magnetic Resonance Time of Flight images ?

    I want to study aneurysm growth (in volume) in a set of subjects, based on Time of Flight images (MR) images at two time points.

    For each subject, I want to do a rigid registration between time of flight images as well as a segmentation of the cerebral vascular system. And then, I want to compare the two registered segmentation volumes in order to quantify the aneurysm growth.

    For doing this, some teams used in-house registration tools (not distributed as far as I know, AnToNIA for ex) and the registration is performed using a volume of interest around the aneurysm sac (and not using the whole brain).

    I currently know free registration tools not specific to aneurysms (FLIRT of FSL for exemple: Additional question: Do you think these kind of methods is appropriate to do "aneurysms registration" ? 

    Thanks in advance,

  • Lizzie Shephard added an answer:
    How do I best identify and remove resting tremor from EEG data?

    Hi all, I'm currently trying to analyse resting state EEG data from a group of PDD patients. This was a fairly trivial task in the controls, but for some of the patients their low frequency patterns do not conform to what is expected. From their notes it would seem that this was resting tremor. I was wondering if anybody else had experienced this and knew of a good way to clean it. My main aims are to avoid rejecting too much data, and to ensure that the alpha and high theta bands are no longer contaminated.


    Lizzie Shephard · King's College London

    Hi Nik. This sounds like a really interesting (if difficult) problem! I agree with you re notch filters; fine for removing electrical line noise but a bit quick and dirty for more complex oscillatory patterns. I'd be interested to hear your solution to the tremor/neuronal activity issue. In terms of classifying the motor artefacts, I found that I had to do this on a participant-by-participant basis because the movements varied a lot between subjects. I don't know if that would be the same for your tremor patients. 

  • 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

    Thanksyou so much Jerome is great help

  • Andreas Johnen added an answer:
    How can I find the difference between grey matter density maps at 2 time points at the subject level?

    I am working on a longitudinal VBM analysis using SPM. Essentially, I have grey matter density whole-brain map for each subject at 2 time points.

    I would like to find out how I can perform the following in SPM:

    (1) Obtain a grey matter density "difference" map (for the whole brain) between time 1 and time 2 for each subject
    (2) Correlate the time 1 and time 2 whole-brain maps

    Any help will be greatly appreciated. Thanks!

    Best regards,

    Andreas Johnen · Universitätsklinikum Münster

    No worries. Also check out this manual which I found very useful, even if you do VBM without the VBM toolbox.

    It has some handy information on VBM and longitudinal data!

  • 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.

  • 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.

  • 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.


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