- Ali Gordjinejad added an answer:JMRUI softwareI 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?
I have a question regarding loading CSI files with jMRUI: I tried to load the files as .IMA but it doesn't work. I thought it would maybe work if I save my data on the Trio Siemens scanner as spectroscopy DICOM files. But it still doesn't work? I tried on jMRUI: Siemens Raw Data (NUM 4), DICOM,.......it just reports: "mrui.plugin.conversion: Invalid Siemens Raw Data files: incorrect header." Can anybody help me? Thanks.Following
- Mohammad Javad Amoshahy 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 http://www.ncbi.nlm.nih.gov/pubmed/16685825 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.
Please give a download link for best MRI images database of a brain tumor with ground truth.Following
- Chanukya Krishna Chama added an answer:What is the easiest/fastest way to convert nifti files to img/hdr?-
I find following tools for easiest/fastest conversion
http://imagej.nih.gov/ij/ <-- ImageJ
http://fiji.sc/Fiji <-- Fiji (ImageJ2)Following
- Annabelle Tully 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?
I have done passive clearing on rodent brain slices, 2-3mm thick. Works like a charm. Electeophoresis induced too much damage, I found. I tried electrophoresis on a half hemisphere, and it just looked like a yellow loogie in the end, despite temperature and voltage being low (~35C and 20V respectively). I also did passive clearing on a larger chunk (about 2cm^3), and a half hemisphere, but at a 4% bis-acrylamide concentration it took almost 4 months. However, it was not at 37C most of the time, and I somewhat neglected it. No damage, looks great, just slow. The slices took about 3 weeks at 37C if it was below 3% (closer to 4-5 weeks for 3-4%), and it worked beautifully (Without changing the clearing solution at all). I do antibody staining for about 4 days on the slices.
I tried a 0.5% concentration on entire half hemispheres passively, but its not really clearing, just slowly disintegrating..
So far the passive approach on thick slices is a clear winner for me.Following
- 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.
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.Following
- 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.
I wasn't sure but now with these references and your experience I've decided not to use faces. Thank you!Following
- Dorian Pustina 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.
In my opinion the best software for tractography now is a combination ExploreDTI/MRtrix, using CSD and probabilistic algorithm. As you mentioned yourself, ExploreDTI does not offer great probabilistic algorithms, yet is the software I use to manage the preprocessing, MRtrix cannot do preprocessing at all. Using them in combination with HARDI, I have been able to obtain difficult tracts such as the optic radiations, also getting similar results to dissection studies and other tractography papers. So ExploreDTI could be the best preprocessing software, MRtrix the best CSD tractography software.
StarTrack did not yield good tractography for me, streamlines were more noisy with more erroneous directions. This is despite using HARDI. But I think Flavio was working on integrating a probabilistic algorithm as this option was greyed out when I used it.
- Eugene F Kislyakov 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:
Three (number) is simpler, than carrot, Bernd.Following
- James Bjork added an answer:What do negative beta weights in ROI analyses mean?
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!
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.Following
- 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.
Thank you for all your suggestions, we ended up going with the freely available n-back task from the Human Connectome Project.Following
- 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.
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.Following
- 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!
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 knowledgeFollowing
- 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?
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.Following
- 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?
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.Following
- Kevin Mandrick added an answer:Non-contact EEG sensorsI 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?
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...Following
- 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.
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. firstname.lastname@example.orgFollowing
- 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?
ON THE RIGHT TRACK? LET ME SAY A FEW THINGS. I AM NOT AN EXPERT IS THE AREA OF SEXUAL FUNCTIONING. I AM IN THE CLINICAL FIELD, AND I TRY TO APPLY BRAIN NETWORK DATA WITH CLINICAL DATA. SO, I WILL ATTACH ONE MORE PAPER. ALTHOUGH IT IS ABOUT ADHD, IT IS REALLY ABOUT THE IDENTIFICATION AND FUNCTIONS OF LARGE SCALE BRAIN SYSTEMS. THE PAPER IS APPLICABLE TO ANY DISORDER/SYMPTOM; THE CHALLENGE IS TO VIEW THE PREVIOUSLY ATTACHED PAPER, ALONG WITH YOUR IDEAS, WITHIN THE CONTEXT OF THESE LARGE SCALE BRAIN SYSTEMS. DRS. WANG, BUCKNER, AND IUE HAVE TOGETHER RECENTLY PUBLISHED ADDITIONAL PAPERS ABOUT HOW THESE BRAIN NETWORKS ARE PREFERENTIALLY CONNECTED WITHIN THE LEFT AND RIGHT HEMISPHERES OF THE CORTEX AND WITHIN THE CONTRALATERAL HEMISPHERES OF THE CEREBELLUM. TAKEN TOGETHER, COMBININHG THIS INFORMATION, SHOULD PUT YOU WELL ON YOUR WAY TO FINDING LIKELY ANSWERS TO YOUR QUESTIONS. THE OTHER AUTHORS ARE MEMBERS OF RESEARCH GATE. - LKFollowing
- Irina G Makarenko added an answer:Problems with long storage of brain material in 4% paraformaldehydeAfter 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?
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 DiIFollowing
- 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?Following
- 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.
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.Following
- 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?
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
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.Following
- 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.
Thanks for providing a copy of the article!
- 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.
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.Following
- 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?Following
- 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).
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!Following
- 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...
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.Following
- 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?
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.Following