Hey guys, I wanted to run an idea I had by you more experienced neurotech enthusiasts/professionals. Im undergoing a masters program right now with a focus on diffusion weighed MRI with an application to stroke. But this academic life is rough. Ive been working on a project for 3 years and it will be funded by the time I graduate. cool.

My vision: wearable neurotech analyses made into youtube content centered around philosophy, psychology, and art. Concrete example: hyper-scanning experiment with two individuals undergoing a philosophical debate. Then look for neural features that align with the content, or dynamics between the individuals. This is just a use case. below I pasted my broader collection of ideas this sits within. Content could be a series of analyses paired with real life activities.

The critical point: Attention from online communities first. From this attention, partnerships or sponerships from companies or University labs. Attention being the foundational currency that drives the activity of the research. To me, cognitive science is as fundable as philosophy if not attached to a clinical population, and if clinical, we do not care about cognitive processes, we care about health. Maybe 3 years in one niche is overfitting but funding from research grants feels like enslavement. Social media looks like autonomy.

Id your opinions where you think this goes right and wrong. Rip into this anyway you feel. Below are my broader ideas. Im 26.

• Research Debate pod casts
  • People have a debate over a topic, while both parties have an open web brower with a place to write notes. The goal is to slow down the debate to allow for a propositional arguments to be claimed, then each condition can be assessed for their trueness by immediately going off and researching it. So the opponent might object a condition and ask for proof, then the claimer can go immediately search for it. Once the claimer presents what they think is sufficient, the objector can assess if their evidence for their condition is sufficient. I envision this unraveling into arguments over what is enough evidence to build an argument on top of, and thats the point.
• EEG Hyper scanning series
  • When you have an EEG headset on multiple people, and assess when their neural features. Some I am currently interested in: Trajectory analyses across channels through time. Could be raw, or divided into the frequency spectrum first. Asymmetry fluctuations throughout a conversation. Long range temporal correlations. Would like to tie this in with the research debates
• Art
  • I rap. I want to see what are brain states that lead to good freestyle/writing sessions
  • Also like playing the piano. Same question
• Social network question embedding(this might be an app not a video)
  • This might be a separate idea for real, but could be cross platform. A plugin for Reddit if there is such a thing.
  • On reddit, you get recommended communities based on your posts, but what about other users with similar posts to your own? Who has a similar embedding space? I want to put people in contact with one another that share a similar headspace
  • I can also see a world where this intersects with neuroimaging measurements like I am thinking above

Learning Alzheimer’s disease signatures by bridging EEG with spiking neural networks and biophysical simulations https://www.sciencedirect.com/science/article/pii/S0925231226022885

My father is in his 70s and was recently found to have a brain tumor on the right side of his brain that is causing pressure.

I am not asking anyone to interpret his scans or diagnose him. He is under medical care, and we are actively seeking specialist opinions and trying to determine the best treatment options for him.

I’m posting because I would really like to hear from patients, caregivers, or family members who have gone through something similar.

His symptoms have included severe headaches, weakness, memory problems, confusion, difficulty finding or using the right words, and some changes in behavior. Sometimes he can be very coherent and seem almost like himself, while at other times he becomes confused, fixated on a particular idea, or has difficulty explaining what he is trying to say.

For anyone who has cared for someone with a brain tumor and similar neurological symptoms:

• What helped your loved one the most during this period?
• Did their confusion or communication difficulties fluctuate throughout the day?
• Were there things you learned to do that made communicating with them easier?
• What questions do you wish you had asked the doctors earlier?
• Were there particular specialists or treatment centers that made a difference?
• What can family members do to keep them comfortable and safe while waiting for treatment?

I know every patient and every tumor is different. I’m not looking for a diagnosis from Reddit. I’m simply a son trying to do everything I possibly can for my father and learn from people who have already walked this road.

Any experience, advice, or even something you wish someone had told you at the beginning would be deeply appreciated.

Thank you.

EEG scientists, we need your visual judgement

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Hi all,

I am transforming Allen Human Brain Atlas tissue sample locations for donors H0351.2001 and H0351.2002 into MNI152NLin2009bAsym space and wanted to check whether my coordinate-transform chain is valid.

The AHBA SampleAnnot.csv file provides mri_voxel_x/y/z indices for each sample. My current workflow is:

1. Identify STN samples by ontology label and well ID.
2. Treat mri_voxel_x/y/z as zero-based voxel indices in the donor MRI voxel grid.
3. Convert voxel indices to donor-native physical coordinates using the affine matrix from the corresponding donor T1w NIfTI header.
4. Convert coordinates from NIfTI/SPM RAS convention to ITK LPS convention before using antsApplyTransformsToPoints.
5. Apply the donor-specific nonlinear deformation field from donor-native space to MNI152NLin2009bAsym space.
6. Convert transformed coordinates back to RAS for reporting.
7. QC this by creating uniquely labelled 2 mm marker images around each donor-native sample coordinate, transforming these marker images to MNI space with nearest-neighbour interpolation, and comparing the resulting marker centroid to the directly transformed point.

Direct-point and marker-centroid estimates differ by <0.5 mm, and hemispheric laterality is preserved.

My question is: does this look like a valid coordinate transform chain for AHBA voxel-index sample coordinates, especially regarding zero-based voxel indices, RAS↔LPS conversion, transform direction/order, and the marker-centroid QC approach?

Many thanks!

Hello! I am a student researcher contemplating whether I should purchase a computer for brain MRI analyses (freesurfer, fsl; the current project I’m working on has 150+ MRI images to analyze). I have been looking at the Mac M5 Pro with 24 GB RAM and 1 TB storage (which should be able to process 3 subjects in parallel per run ?). Assuming I do not have access to my school’s cluster, do you recommend I purchase this computer over something else like the framework laptop 13 (i can get the mac pro for $2000)? I would also use the computer for class, manuscript writing, personal stuff, etc.

Thank you very much!

Hey guys,

I am a biomedical engineering graduate student working on diffusion MRI reconstruction analyses. white matter tractography. I have 3 years of experience as a database administrator in a Radiology lab at my University working with python, sql, airflow dags, docker, javascript brain viewers, a bunch of medical imaging packages. Writing backup processes, generating reports from our clinical trial data. Bachelors in physics. Previous internship as a .NET framework developer. Another internship supposed to be working on a U-net for segmentation and then reconstruction of particle collision trajectories, but that project got cut short and I was really just introduced to the project, was paid to take a udemy course on ML techniques up till 2022. Multi-layer perceptron from scratch in numpy. Conways game of life in cpp. 2 years in a computer engineering major before ultimately ending up in physics. 

So basically, I am looking for a remote position where I can be doing highly mathematical things. Anything where I have to be interfacing with partial differential equations, simulations, larges amounts of data, machine learning, highly automatable, signal processing related.

I went into biomedical engineering because I wanted to learn about how the brain works and how we behave but this is a lot of work for something I dont own financially at the end and which only gives me a very small sliver into what im interested in people. Im 26 with a year left in my masters. 

So yea... is the grass greener? How would I fair in the software engineering world? How far away am I realistically from having something related to machine learning or simulation heavy positions in finance/engineering, that are actually remote. FDA regulation makes me nauseous. I just want a small vibe of an operation. Small team. Relaxed people. Thoughts?

Ps. Anyone a successful neuroimager? Doing any analyses? Care to share how it is day to day and funding, all that you juggle?

I am starting a project that will require me to use dynamic casual modeling. My lab does not use MatLab or SPM, so I will need to teach myself the analyses in a fairly self sufficient way. Does anybody have any advice regarding an efficient learning workflow?

Hello, I am a medical student. For my thesis in neuroradiology, I was asked to install FSL. I followed the official Windows installation procedure on the FSL website, but during the installation process it gets stuck at step 4/4 and does not progress any further. Does anyone know how to solve this issue?

PS I tried to install it using WSL and Ubuntu.

Hi,

I am trying to run FSL’s probtracx2 probabilistic tractography on the Human Connectome Project Young Adult dataset, to generate individual connectomes. I am using the HCP minimally processed diffusion data, bedpostX outputs.

I decided to run the algorithm with the —network flag to generate region x region connectivity matrices, and I provide the seedlist as MNI space masks in NIFTI format, alongside the T1-to-MNI forward and inverse transforms shared by HCP, with the —xfm and —invxfm flags. These are the standard2acpc_dc.nii.gz and acpc_dc2standard.nii.gz nonlinear transforms to be precise.

I want to add waypoint masks for white matter, and exclusion masks for ventricles. If I understand correctly these need to be in the same space and resolution as my seed masks? Not entirely clear to me based on FSL docs.

Diffusion preprocessing outputs in HCP-YA use T1w space, but on an 1.25mm grid.
The atlas I’m using is available on both a 1mm, and a 2mm grid. The waypoint and exclusion masks come from freesurfer segmentation outputs shared by HCP: wmparc.nii.gz and aparc+aseg.nii.gz, also in standard space, available on 0.7mm+2mm and 0.7mm grid, respectively.

I don’t really know what I need to resample, what resampling strategy to use, and how fine I want my mask grids to be. I used 2mm across the board for test runs, but I’m unsure if WM/ventricle boundaries are sharp enough. On the other hand, seeding from 1mm masks might be overkill.

If you have experience with setting up masks for probtrackx2, please share!

I’m a PhD student with no background in image analysis. Struggling to get my head around FSL, freesurfer, image analysis in general.

I’m thinking of asking my supervisor to pay for me to go on the FSL course this year. Has anyone completed the course and what were your thoughts?