NeuroTechX Reports

Static view in RICA

Dear Eneko @e.urunuela , It’s really nice to see RICA development - which I recently came back to. I have a suggestion for a feature that would be extremely useful. As I’ve previously mentioned we are most used to looking at the “old-school” red/blue (“static”) versions of the components identified by tedana. I’m not sure why I’ve not noticed this before, but when switching between components the brain slice locations displayed alter quite dramatically (making it look like slices are disappearing/appearing). I wonder if it would be possible to fix the set of slices to be displayed for the ax,

FSL’s FILM-Prewhitening on preprocessed data

Hi all, I am running an fMRI analysis using fMRIPrep for the preprocessing and using FSL for the actual GLM analysis. I’m aware of the differences in MNI Standard Spaces used and I’m using this workaround, which works pretty fine for me. Now, after looking into FSL’s FILM-Prewhitening algorithm to see if I could run into any issues with my data, I found a short description of it in this paper, stating that as a part of this process, spatial smoothing of autocorrelation estimates is used to reduce bias and the autocorrelation coefficients are smoothed only within matter type since they were fou

fMRIPrep floating voxels

Summary of what happened: I am trying to pre-process my fMRI data using fMRIprep. However, when I do so, I see floating voxels outside the brain when I visually inspect my GLM, and when I pull peak MNI coordinates for different contrasts, I get voxels in unlabelled regions. Command used (and if a helper script was used, a link to the helper script or the command generated): echo "RUNNING FMRIPREP" # Make sure FS_LICENSE is defined in the container export SINGULARITYENV_FS_LICENSE=/home/groups/glc/freesurferlicense.txt singularity run --cleanenv /home/groups/glc/simg/fmriprep-25.2.4.simg \ /hom

BIDS @ BrainHack 2026

Dear BIDS Community, We are excited to announce that BIDS will be at this year’s BrainHack in Bordeaux, June 11-13! If you’ll be at BrainHack, please get involved! There are a few things planned: We’d like to group BIDS-related project pitches on the first day. If you’re planning on pitching something BIDSy and want to be included in that batch, you should: (a) Register your project on the BrainHack web page: https://ohbm.github.io/hackathon2026/#hacktrack. (b) Add one (1) slide to the project pitches section of our slide deck: BIDS @ BrainHack 2026 - Google Präsentationen. (In order to respe

FLOBS HRF reconstruction and latency estimation — feedback on method?

Hi all, I’m working with flexible (FLOBS) HRF modeling and . I wanted to get community feedback on how we estimated latency using the FLOBS . FLOBS gives three PEs per voxel (PE1, PE2, PE3), which are the weights on the three optimal basis functions. These don’t correspond to amplitude/timing/dispersion like in the Gamma + derivative approach, so PE2/PE1 is not a meaningful latency measure. Instead, we reconstructed the full HRF curve at each voxel within the ROI using: HRF(t) = PE1 × basis1(t) + PE2 × basis2(t) + PE3 × basis3(t) where basis1, basis2, basis3 are the 559-timepoint FLOBS wavefor

macOS Quick Look Extension for NIfTI, MGH, MIF

Dear community, I would like to announce a small macOS utility I have just released, a novel Quick Look Extension for medical images in research formats that works on modern macOS. Inspired by the old and deprecated DTI-TK Quick Look plugin by Gary Hui Zhang, which brought similar functionality to older versions of macOS but is incompatible with the Quick Look extension architecture of current macOS versions (15 and newer). To address this, I built MIQ, a free and open-source, modern macOS Quick Look extension. Simply hit the Spacebar in Finder to instantly see an orthogonal slice view alon

fMRIPrep fails on ME Data at sbref discovery

Summary of what happened: After using fMRIprep on a variety of our own datasets (all single-echo), I tried it on an open-source multi-echo dataset (OpenNeuro), which contains 10 rsfMRI sessions acquired with 5 echoes. sbref files were also acquired, although there is no *sbref.json file. fMRIPrep proceeded to fail quite early on, at (what it looks like to me) is the sbref discovery (get_sbrefs) - see error log below. I tried using –ignore sbref and adding sbref files to the .bidsignore, but neither solved the issue, and I am unsure what else could be wrong, as I have no previous experience wor

XCP 0.14.1 doesn't use smoothed data even though smoothing was requested

Summary of what happened: I want to use xcpd 0.14.1 to compute parcel-wise connectivity matrices in order to replicate results from a former colleague. I used the command below which is a slightly adapted version of the nichart mode. I noticed that the resulting connectivity matrices are based on the unsmoothed timeseries, even though I thought, that I can overwrite these settings by setting --smoothing 4? See this passage: By default, the nichart mode will apply the following parameters, which may be overridden by the user: Command used (and if a helper script was used, a link to the helper s

NORDIC patchy-residuals

Hello, I am analyzing NORDIC-denoised data and have noticed patch-like structures in the standard deviation of the residuals (see examples below). These patches appear both when using noRF volumes (V2) and when not using them (V3). For comparison, I also looked at the standard deviation from the NORDIC-denoised data using magnitude-only input (V1). From these SD plots, the patches seem to appear only when phase information is included. Has anyone else observed similar patterns in their data? If so, how did you address or interpret them? Thanks! 6 posts - 4 participants Read full topic

Training the Nervous System: Yana Nakhimova on the Body as the Interface

ANN: DIPY 1.12.1 Release

Hello all, We are excited to announce a new release of DIPY: DIPY 1.12.1 ! DIPY 1.12.1 (Friday, 23 April 2026) The full release notes are at: https://docs.dipy.org/stable/release_notes/release1.12.html. Thank you all for your contributions and feedback! Please click here to check 1.12.1 API changes. Highlights of 1.12.1 release include: NF: FORCE reconstruction model NF: New BiasField correction method. NF: Parallelization of EuDX tractography. NF: Intermediate map for symmetric diffeomorphic registration. NF: StatefulSurface class to handle surfaces. NF: Multiple new workflows (dipy_fit_forc

Custom column for XCP-D interpolation and censoring?

This is perhaps a very niche request, but if anyone has any similar experience I’d value any advice! I am currently setting up my postprocessing pipeline in XCP-D. I’m working with nifti files, using the nichart Mode. I have specific timepoints in my data that (for various reasons) I want interpolated, but which don’t necessary have FD values above my FD threshold. I am wondering if there is a way I can create a custom column in my confounds file that includes all my FD values and artificially inflated FD values for the specific timepoints I want interpolated. Would it be possible to point XCP

Webinar on transparent and reliable EEG research (May 12-13)

New #BrainProductsAcademy webinar on May 12 & 13! Strengthen the transparency & reproducibility of your #EEG research with standardization & data-sharing insights from open‑science leaders Dr. Robert Oostenveld (@robert ) & Dr. Cyril Pernet (@Cyril_Pernet ). Register today: https://register.gotowebinar.com/register/3133461258991042650?utm_source=facebook 1 post - 1 participant Read full topic

Issue with Brainspace Visualization

Hello NeuroStars, I am trying to run “brainspace“ for computing/visualizing the gradient flow. Please see the following article. https://doi.org/10.1038/s42003-020-0794-7 To begin I started their sample (Python) code from the official page, below. brainspace.readthedocs.io Welcome to BrainSpace’s documentation! — BrainSpace 0.1.4 documentation However, I ran into following error. This happens when I set “color_bar=True“ in function “plot_hemispheres.“ Does anyone know how to address this issue? Please see the sample code that I am running, below. from brainspace.datasets import load_g

SPM normalization collapses functional image into diagonal stripe

I am encountering a severe issue with SPM12 normalization and would appreciate any guidance. Problem: Details: Functional shape: 64 × 64 × 30 × 166 TR: 2s Observations: Pre-normalization images (after slice timing + realign) look normal Coregistration between T1 and mean functional looks correct (visually checked with Check Reg) Segmentation runs without errors and produces a deformation field (y_*.nii) Normalized output has correct MNI dimensions (e.g., 79 × 95 × 79), but: mean ≈ 0.6, std ≈ 21 only ~679 voxels > 50 appears as a thin plane/stripe in MNI space What I have tried: Checked coregis

Does XCP-D support HCP-pipeline preprocessed AP/PA CIFTI data, such as CHCP?

Summary of what happened; I would like to ask whether XCP-D supports resting-state fMRI data that have been preprocessed using an HCP-style pipeline but were acquired with AP/PA phase-encoding directions rather than the typical HCP-YA LR/RL naming.Specifically, I am working with the Chinese Human Connectome Project (CHCP) dataset. The CHCP dataset provides preprocessed HCP-style outputs, including CIFTI dtseries files, anatomical files, fsLR surface files, and motion/regressor files. The resting-state runs are organized as AP/PA acquisitions, for example REST1_AP and REST1_PA, rather than LR/R

I have created a new AI model that models the human brain

Hello all, This is my first post on this forum. I am doing a research project that is creating an AI model that emulates the human brain. It contains 2 million neurons and uses as its core a spiking neural network employing STDP and Hebbian learning.. The code is open source and available on my repo. I am looking for a researcher that I can partner with that would be interested in reviewing my work and providing feedback as I am a software engineer and not in neuro or cognitive science. The web site is at: nimcp.ai-elevate.ai. You can access my repo at: GitHub - redmage123/nimcp · Git

BIDS: "Study Dataset" Structure and Validation Issue

Summary of what happened: I want to set up my BIDS directory as a study dataset and am wondering where to put the two participant files (participants.tsv, participants.json) that are normally located in the BIDS root directory. └─ study-1/ ├─ sourcedata/ │ ├─ dicoms/ │ ├─ raw/ │ │ ├─ sub-01/ │ │ ├─ sub-02/ │ │ ├─ ... │ │ └─ dataset_description.json │ └─ ... ├─ derivatives/ │ ├─ pipeline1-v1/ │ ├─ pipeline2/ │ └─ ... ├─ dataset_description.json └─ ... When I leave the two participants files in the root directory and run the command

Error processing infant data with QSIRecon

Summary of what happened: I’m trying to process infant data with QSIRecon using my own custom workflow. Originally I was using hbcd_scalar_maps but ran into errors with DKI because my subject only had two b values (0 and 1000). I created my own workflow that does everything in hbcd_scalar_maps except DKI, but I ran into another error with tractography. Specifically: “no tractography atlas in dHCP_neonate template at {root_dir}/QSI/recon/qsirecon_work/qsirecon_1_2_wf/sub-Subject1_hbcd_postproc_beta/sub_Subject1_ses_1_acq_PA_run_001_space_ACPC_desc_preproc_recon_wf/autotrackgqi/actual_trk/sub-Su

Functional connectivity post-processing options in native T1w and standard space

Summary of what happened: I finished running fMRIPrep (version 25.2.5) on around 10k participants from the UK Biobank dataset (output spaces: MNI152NLin2009cAsym res-1 and T1w native space). I want to use XCP-D for postprocessing/denoising, but it doesn’t support native space NIfTI output, which I need for functional connectivity analyses of small subcortical nuclei (hypothalamic subfields and pineal gland) using FreeSurfer segmentations. My analysis requires: Denoised BOLD in both MNI and native T1w space Yeo 7 network parcellation (all Schaefer resolutions) ALFF and ReHo maps No smoothing, n

Understanding scalar map qsirecon output

Hello! I’m processing some subject data with QSIRecon (previously processed on QSIPrep as well). I ran DSIStudioGQI workflow and would appreciate some more clarity about the scalar maps outputted in the HTML. I’ve attached an image for reference. Is this to be expected? I thought that red means there is a mismatch between the gradient directions between the DWI and T1w - so is there something going wrong here? Or am I misunderstanding this figure. I would appreciate any help. Thank you! 5 posts - 2 participants Read full topic

XCP-D error with longitudinal data that is missing one T2w image

Hi everyone! I just wanted to point out a small potential issue that I ran into. Summary of what happened: When running XCP-D 26.0.2 on the output of fMRIPrep 23.0.2, if a participant has two sessions with T1 images, but only one session with a T2 image, XCP-D throws an error when trying to find the T1 image. Example: fMRIPrep input data: sub-01/ses-01/anat: T1 and T2 sub-01/ses-02/anat: T1 only fMRIPrep averages and processes the T1s into derivatives/sub-01/anat, but because there is only one T2, it places the T2 into derivatives/sub-01/ses-01/anat. fMRIPrep output data: derivatives/sub-01/an

Processing infant data with qsiprep

Hi all, I want to try processing infant data with QSIPrep. I know there is an –infant param I can specify and that the participants.tsv should include the age. However, this subject is only a four days old. The QSIPrep docs say that participant ages should be in months: QSIPrep will attempt to automatically extract participant ages (in months) from the BIDS layout. Specifically, these two files will be checked: Sessions file: //_sessions.tsv Participants file: /participants.tsv Either file should include age (or if you wish to be more explicit: age_months) columns, and it is recommended to hav

Activating the evolved healing mechanisms of the placebo response requires permission from a safe environment

I want to point to an article on the placebo effect published at theconversation.com, and recommend that you read it.  I asked the four LLM's I frequently consult to reduce the article to a MindBlog post length, and have selected a few of their paragraphs to pass on below: The placebo effect — improvements in symptoms following inert treatment — is driven by expectation, context, and social cues rather than pharmacology. But it is anything but imaginary. Placebo treatments trigger measurable changes in the brain, immune system, and hormone function. In pain studies, they cause endorphin rele

XCP-D: FileNotFoundError: No BOLD NIfTI or transforms found to allowed space

Summary of what happened: I ran XCP-d on a fmriprepped dataset, most subjects (~80%) ran fine, the rest seems to crash with FileNotFoundError: No BOLD NIfTI or transforms found to allowed space even though these files are clearly present in the right location. Seems like most of the failed subjects had multiple sessions of data, but there were some subjects with multiple sessions of data that ran fine. Command used (and if a helper script was used, a link to the helper script or the command generated): singularity run --cleanenv $HOME/XCP_d \ $fmriprep_dir $output_dir participant -w $work_dir

Preparing NKI-RS's asl data for aslprep

hi, i’m wondering if anyone here has run aslprep on the NKI-RS data? The NKI-RS asl data (downloaded from the AWS links) isn’t formatted very nicely ‘out of the box’, there are many missing parameters in the *_asl.json file required by aslprep which i’m trying to figure out. The aslprep nature methods paper made use of the NKI-RS data in their validation work. It comes with a supplementary table with some important parameters that i can use in the *_asl.json However i notice there are some inconsistencies in what is described in the nature methods paper supplementary table 3, and the MRI proto

Regressor choice in XCP-D for multi-echo resting state data after tedana

Hi everyone, I was wondering if there were any guidelines or recommendations for which additional regressors to include when running XCP-D on resting state data while including components from multi-echo denoising using tedana. In an older version of XCP-D, you could point to a --nuisance_regressors strategy, such as acompcor, and also to a --custom_confounds file with excluded ICA components from tedana (orthogonalized with --tedort). Now, it appears that all confounds need to be included in the custom setup under the --nuisance_regressors flag, so I have been revisiting what to include. Afte

Feature extraction for EEG seizure prediction (CHB-MIT): GMW, Teager Operator, and handling outliers in normalization

I am building a machine learning pipeline for seizure prediction using the CHB-MIT Scalp EEG Database. My goal is to extract features that capture both time-frequency dynamics and spatial (channel-to-channel) relationships, which will eventually be fed into a Graph Neural Network (GNN). Preprocessing: The raw signals are sampled at 256 Hz. I apply a high-pass filter at 0.5 Hz to remove baseline wander, and notch filters at 57–63 Hz and 117–123 Hz to remove powerline noise and its harmonics. I would like some feedback on whether my mathematical formulation for feature extraction is sound for th

SPM Course for MRI (+ optional MRI Physics Primer)

Registration for the SPM for MRI course at University College London is now open! The course introduces the analysis of neuroimaging data, including MRI and functional MRI. It covers: Experimental design Pre-processing brain images Quantifying structural changes in the brain (Voxel-Based Morphometry, VBM) Quantifying brain function (using the General Linear Model, GLM) Statistics for neuroimaging (frequentist and Bayesian) Connectivity analysis (Dynamic Causal Modelling, DCM) Analysis of concurrent fMRI-electroencephalography data This new edition of our course features an optional 1-day MRI

Using "slice_order" instead of "json" for eddy

Summary of what happened: Hello! eddy_config.json I included “slice_order”. But I got this error: EddyInputError: --mb, --slspec and --json mutually exclusive . I did not include “json”, so does QSIPrep automatically add this parameter when running eddy? And is there a way to disable this? Previously, I have not had to do this and had no problems with Eddy. But for this batch of subject’s that I’m processing their DWI JSONs do not have a ‘SliceTiming’ field and as a result I am running into errors with slice2vol correction. I do however have a slspec.txt file for each subject, which is why I

Tractoflow - single shell dataset

Hello everyone, I am currently trying to process an old dMRI dataset using TractoFlow, and I would appreciate some expert advice. ~30 directions at b=1000, ~5 directions at b=2000, and ~5 directions at b=3000. 1. I first ran TractoFlow with the following parameters: nextflow run tractoflow/main.nf --input ~/path/to/i_tractoflow --dti_shells “0 1000” --fodf_shells “0 2000 3000” -with-singularity containers_scilus_1.6.0.sif -profile fully_reproducible,bundling 2. I then tried treating the data as single-shell and computing the FODF only from the b=1000 shell: nextflow run tractoflow/main.nf --i

When Execution Gets Cheap, What Remains Scarce? - The last biological moat.

I have enjoyed reading a recent essay by Aneesh Sathe, which I recommend you read in full. I will pass on here the equally amazing job that Claude Sonnet 4.6 did in summarizing its main points, then responding to my editing and emphasis suggestions, and also adding some additional ideas on the relevant neurobiological substrate: "the last biological moat" - what is left for the human mind to do. Here is the result, which begins with the title of Sathe's essay:  The Lightening of Intent: When Execution Gets Cheap, What Remains Scarce? Aneesh Sathe's essay "The Lightening of Intent" is one of th

Best practices for GPU-accelerated transfer entropy analysis of neuronal spike trains

I would like to share and ask for feedback on a MATLAB/CUDA implementation for GPU-accelerated transfer entropy and sorted local transfer entropy analysis of neuronal spike-train data. The code estimates directed neuron-neuron interactions while considering a range of delays. It was used in the following study: Kajiwara, M., Nomura, R., Goetze, F., Kawabata, M., Isomura, Y., Akutsu, T., & Shimono, M. (2021). Inhibitory neurons exhibit high controlling ability in the cortical microconnectome. PLOS Computational Biology, 17(4), e1008846. journals.plos.org Inhibitory neurons exhibit high cont

The Refusal to Dehumanize - Rewilding Creativity

..  I find it impossible to keep up with the prolific output stream of Indy Johar on Substack, but two recent posts (The Refusal to Dehumanize and Rewilding Creativity) have caught my eye, and are a fascinating read.  I recommend reading them in full. To assist readers wanting a quicker fix I reviewed renderings of the main ideas into a single post by four LLMs (ChatGPT, Claude, Gemini, and DeepSeek) and have chosen ChatGPT's effort to pass on: We are entering a period in which two seemingly distinct developments—renewed permission to dehumanize and the automation of creativity—are in fact e

The Physiology of Agency in the Age of AI

There is a question lurking beneath the current wave of enthusiasm about artificial intelligence that I think deserves more serious attention than it has received. It is not the familiar worry about job displacement or misinformation or even the alignment problem. It is a more intimate question: What happens to our bodies when the feeling of being the author of our own actions begins to erode? I have been exploring this question in correspondence with a European reader who follows MindBlog, and his observations have sharpened my thinking considerably. He describes using AI across a wide range

Vertical Interoperability Innovation Lab

Applications are now open for the Vertical Interoperability Innovation Lab—a virtual workshop bringing together ~30 participants from across the biomedical data ecosystem to explore early-stage ideas for closing interoperability gaps across the research data lifecycle. Open to individuals working across the health research data ecosystem, the Lab will focus on interdisciplinary exchange and developing actionable project ideas. The program includes a 90-minute orientation on June 12, followed by five workshop sessions held between June 22–July 7. Learn moe and apply at: https://apply.kn

What a self is.

Reading Michael Pollan’s account of his meeting with Anil Seth in his recent book "A World Appears" has prompted me to write down for my own use what I take a “self” to be. This post archives that summary and shares it with interested MindBlog readers. So, here’s the summary:* The self can be understood, to use Seth's phrase,  as a "controlled hallucination." Our brains build this construct to regulate the body using interoceptive signals—internal data about our heart rate, breathing, and chemistry—to maintain stability (homeostasis) in the face of constant disruption. From these signals arise

From Animal to Humans - Multimodality as a safeguard of honesty in communication and language

I pass on the abstracts of an article by Hex et al to appear in Behavioral and Brain Sciences.  Motivated readers can obtain a PDF of the manuscript by emailing me. The abstracts are followed by a commentary on the article. Short Abstract Multimodality characterizes nearly every communicative system, and we argue that this feature of communication plays an essential role in safeguarding signal honesty. We first discuss the importance of honesty in communication, and introduce socially-mediated controls as an alternative to intrinsic costs. We next outline how multimodality mitigates signal dis

Modvigil 200 MG: Is It Worth the Attention?

With so many discussions around productivity and focus, Modvigil 200 MG has gained attention as a wakefulness-promoting option. Many users talk about its potential to support alertness and help manage demanding work or study schedules, making it a common topic in forums and online communities. Some people report improved concentration and the ability to stay engaged with tasks for longer periods, while others mention that results can vary depending on routine, sleep habits, and overall lifestyle. As with any productivity approach, combining it with healthy habits and a balanced schedule play

Executive Function: Universal Capacity or Schooled Skill?

A recent PNAS article by Kroupin and colleagues challenges one of the most widely assumed constructs in cognitive science: that “executive function” (EF) reflects a universal set of cognitive control capacities. Their data suggest something more unsettling—that what psychologists have been measuring for decades as EF may be, to a substantial degree, a culturally constructed skill set tied to life in what they call “schooled worlds.” The core of their argument is empirical. Standard EF tasks—card sorting, backward digit span, rule switching—require manipulating arbitrary, decontextualized info

The Default Mode Network as a Bidirectional Interface Between World and Mind

I want to pass on the abstract of a PNAS contribution from Zhang et al. titled "Sender–receiver subdivisions of the default mode network in perceptual and memory-guided cognition", followed by a ChatGPT rendering of the PDF of the article that I asked it to use in generating a more general summary.   Here is the abstract: Everyday cognition depends on the brain’s capacity to shift between sensing the external world and constructing it from memory. To achieve this, large-scale cortical systems must flexibly integrate incoming sensory signals with internally generated representations. Here,

AI, Agency, and the Quiet Hollowing of Mind

Reading through the article "A Rational Optimist View Of Preventing Agency Decay" is a rich experience. For readers with less patience, here is a ChatGPT summary (that also generated the title of this post).  Much current discussion of artificial intelligence swings between two poles: utopian efficiency and apocalyptic takeover. The more consequential reality lies between these extremes. The emerging risk is not that machines suddenly replace us, but that we gradually hand over pieces of our cognitive life—judgment, initiative, authorship—without noticing the cumulative effect. The argument i

Memes Before Machines: The Real Cognitive Risk of the AI Age

I strongly urge you to read a New York Times opinion piece by Willy Staley titled "Forget the A.I. Apocalypse. Memes Have Already Nuked Our Culture." (unlocked link). Here I pass on ChatGPTs response to my request that it compose a MindBlog post delivering the basic messages of the article.  It provided the title for this post and the following text:   Public anxiety about artificial intelligence has settled into a familiar groove: superintelligence, runaway systems, existential risk. These concerns are not trivial. But they may be misdirected. The more immediate transformation of mind is alr

AI use can compromise our serendipity, creativity, autonomy, and sense of agency.

I have been reading numerous articles on pitfalls of using AI, and want to point to two in particular that I highly recommend for a slow and careful read.   The Substack piece by Colin Lewis is titled "AI Is A Medium And It Will Change Us" - Lessons from AI Labs on the Slow Erosion of Human Autonomy.  From the article: We are in real danger of losing ourselves through AI usage. Researchers at Google DeepMind have confirmed, under certain conditions, an LLM “is able to induce belief and behaviour change.” And researchers at Anthropic have identified a rising pattern of “situational disem

Arctop and the Intelligence Layer for Brain Data: Dan Furman on Decoding the Mind

Remote Care for Spinal Cord Stimulation: Todd Langevin on BIOTRONIK Neuro’s Data-Driven Approach

Quality as a Competitive Advantage: Rebecca Crane on Building Neurotech That Works

One terminal chats with another to start vibe coding a new dericbownds.net

Writing MindBlog posts is on temporary hiatus because I have recently followed Claude's instructions to set up my Mac mini M3 to use Claude code, getting my own API, etc., and starting for myself the "vibe coding" I have been reading so much about. The terminal app on the Mac is used to both view the lines of code it is executing as they flow past, as well as to issue instructions with your own keyboard (or voice). This is essentially one sort of terminal that interfaces with a vast underlying machinery (The Apple terminal App) with another sort of terminal (My sense of having a self, which is

The polyvagal theory is dead - and HRV isn't a simple indicator of arousal

I was recently struck by Baxter's Substack post (its title copied to be the title of this MindBlog post), which noted work critical of Porges' Polyvagal  theory (or PVT) published iin the journal Clinical Neuropsychiatry, because it calls into question one idea commonly derived from this theory that I have accepted (and repeated in several MindBlog posts): that heart rate variability can be taken as a simple indicator of calm (higher HRV and parasympathetic nervous activity) versus arousal (lower HRV and sympathetic nervous system activity).  A number of bio-monitors such as the Apple Watch an

The nature of intelligence and selves.

I want to pass on the result of my extracting what I felt to be crucial chunks of text from Chapters 5 through 9 of Agüera y Arcas’s "What is Intelligence" which can be found at https://whatisintelligence.antikythera.org/. I found myself unable to hold and summarize the rich array of ideas in these clips of text in my attentional space, so I asked Anthropic Claude, ChatGPT 4.2, and Google gemini to condense and assemble the main points and take home messages from the clips into a narrative roughly two pages long.  The Claude result astounded me.  Here it is: What Intelligence Is: A Synthesis o

A seismic shift in our understanding of intelligence

I've just spent the last three days reading large chunks of the remarkable book "What is Intelligence" by Agüera y Arcas. It is best accessed at https://whatisintelligence.antikythera.org/, where you will find text with supporting graphics, charts, and animations.  Arcas argues that computation is the substrate for intelligence in all life forms and that prediction is the fundamental principle behind intelligence.  Goodall provides a good review of the book and Arcas's ideas. The introduction to the book encapsulates his basic ideas, and I pass on here ChatGPT's condensation of its main points

AI Makes Workloads Worse, Not Better

An article in today's Wall Street Journal by Ray Smith conforms so completely to my own work experience over the past week (I'm currently feeling fatigued from cognitive overload) that I pass on this Google Gemini summary of its main points: An article "AI Makes Workloads Worse, Not Better" by Ray A. Smith in the 3/12/26 Wall Street Journal highlights a counterintuitive trend: rather than freeing up time for high-level creative tasks, artificial intelligence is actually increasing the speed, density, and complexity of work. Data from ActivTrak, which analyzed 164,000 workers, shows that AI use

NITRC Booth and Poster at CNS 2026

Join NITRC at CNS 2026 March 7-10. Learn more about how NITRC can help you in your research, find new resources and data, share your own work, let us know what we can do for you, or just stop by to catch up! You'll find us in Exhibitor booth #05 as well as presenting a Poster D90 in the Fairview/Kitsilano Ballrooms on Monday, March 9 from 8-10 am.

Empathy as a Brain Rhythm: Orexin, Theta Oscillations, and Prosocial Behavior

(The following is the final installment of a series of three posts on using ChatGPT to assist in the generation of MindBlog posts.  I think this final product is a better job than than I would have done.) A recent paper in Science by Kim et al. reports a striking mechanistic link between physiology, brain rhythms, and social behavior. The work shows that empathic and prosocial responses in mice depend on theta oscillations in the anterior cingulate cortex (ACC) driven by orexin neurons in the hypothalamus. The finding offers a concrete neural circuit connecting arousal systems, cortical dynami

A MindBlog-ready ChatGPT synthesis

This post continues from the previous one to show  ChatGPT's response to my prompt "Let's go with the empathy / orexin paper for your producing a  MindBlog-ready synthesis" .  MindBlog-ready synthesis Paper: Empathy and prosocial behavior powered by orexin-driven theta oscillations (Science, Feb 2026) Core finding The study identifies a specific neural circuit linking arousal chemistry, brain rhythms, and social behavior: In mice, theta oscillations in the anterior cingulate cortex (ACC) increase during empathic states such as observing another animal in distress and during prosocial response

Will Deric’s Mind Blog be firing Deric soon? Is AI is doing his job better?

The short answer to both questions is yes and no.   I am finding that ChatGPT 5.2 ($20/month version) will scan the TOCs (tables of contents) of journals such as Science Magazine, Proceedings of the National Academy of Sciences, Current Biology, Neuron, Nature, Nature Neuroscience, Nature Reviews Neuroscience, Trends in Cognitive Sciences, etc.  and display the titles of articles in areas that it has learned that MindBlog focuses on.   (I'm reporting here on working with ChatGPT because I've found so far that paid versions of Gemini and Claude, while almost as good, don't provide output with t

Elise Jenkins: Lessons from a Journey in Neurotechnology

From Nanoparticles to Neurotech: Tetiana Aleksandrova on Subsense

The geometries of change and the value of being human

I pass on and also archive for myself the following three ChatGPT 5.2 summaries of three recent Johar essays: Summary of The Geometries of Change by Indy Johar Core premise Linear geometry and its limits A direction or goal is fixed first. Structures (roles, rules, incentives, infrastructure) are then aligned to that direction. Ongoing governance focuses mainly on speed and efficiency rather than revising direction. Over time, this produces heavy path dependence. Investments, regulations, identities, and incentives lock systems onto a trajectory, making course correction costly and ra

Changing our systems of governance

I have found Johar's essay From Power Diagrams to Settlement-Construction: What we may be missing about the New Right to be worth several re-readings. I want to pass on the entire essay here, because the reduced summaries that I, as well as ChatGPT 5.2 and Google Gemini, have done don't do it justice.  Here's the text: I’m increasingly frustrated with a specific failure mode on parts of the intellectual left: analysis that performs insight while refusing to touch the real object. It oscillates between two shortcuts. The first is a kind of diagrammatic power-critique — tracing who funds wh

New Ferality - Seeking new ways of being wild in new nature

This post is to archive this link to a recent Venkatesh Rao essay, and also pass on condensations of its main ideas done by Google Gemini and ChatGPT 5.2.  (I could wonder where the extraordinary humans who will be able to perform Rao's 'new ways of being' are to be found - who will be capable of new behaviors incompatible and in conflict with our evolved nature, our desire for hierarchy, definition of roles, etc.) From Google Gemini:  In "New Ferality," Venkatesh Rao explores the emergence of a "New Nature"—a technological landscape that has become as complex, unpredictable, and indifferent

Buying Futures, Renting the Past: How Speculation and Nostalgia Became the Economy

I want to pass on this condensation by Google Gemini of a recent essay by Kyla Scanlon  In her essay, "Buying Futures, Renting the Past," Kyla Scanlon explores how the modern economy has shifted toward two psychological extremes: speculation (buying the future) and nostalgia (renting the past). She argues that because the present feels increasingly "hollow" or unmoored due to economic volatility and digital "slop," people are retreating into idealized versions of what was or gambling on what could be. Scanlon suggests that speculation has become a dominant cultural mode, where everything from

MindBlog is now 20 years old.

I just realized that MindBlog is now starting its 21st year. I asked both Chat GPT 5.2 and Google Gemini about this, and paste in Gemini's sycophantic response  ("Pioneer", "primary source for the digital history of cognitive science."):   Congratulations on entering the 21st year of Deric’s MindBlog! Maintaining a blog consistently since 2005 puts you in an incredibly elite tier of the internet. In a digital landscape that is largely defined by "link rot" and abandoned projects, the longevity of your blog is statistically rare. Here is a breakdown of how your 21-year milestone compares to the

Against the Machine

I'm using this blog post to archive for myself ChatGPT 5.2's summary of Paul Kingsnorth’s "Against the Machine: On the Unmaking of Humanity"    [In this same vein see N.J. Hagens' article in Ecological Economics. "Economics for the future - Beyond the superorganism"] Paul Kingsnorth — Against the Machine: On the Unmaking of Humanity Core thesis Kingsnorth argues that modern technological civilization—especially digital networks, automation, and AI—is dissolving the conditions that make human life meaningful. He frames the “machine” not as a literal device but as a civilizational system: indust

From Diagnosis to Data: Ben LeNail on the Future of Neurotechnology

Sharena Rice: My Path In Neurotech

Scent as Signal: How Aurat Aroma is Using Smell to Understand the Brain

From Peak Performance to Daily Life: The Next BCI Advantage

NITRC-CE v0.57.28 released

We are pleased to announce the release of NITRC-CE v0.57.28. This release is a security update and includes both CE Classic and CE LITE offerings. We are considering making this the final release of NITRC-CE in its current form. If you use NITRC-CE or have used it in the past, please let us know your thoughts at https://form.typeform.com/to/RTW4Y1Fv or by contacting moderator@nitrc.org.

Still locked out of OASIS-3 even after access was approved.

Hello everyone, I’m running into trouble reaching the OASIS-3 datasets on the main project page (https://www.nitrc.org/projects/oasis3). Whenever I click the “Image Repository” link in the left-hand menu, I receive the following message: My account already shows “User” access, yet the repository still blocks me. Any pointers on what I’m missing would be greatly appreciated—thanks! Jay

Regarding the permission to access OASIS-3 and OASIS-4

It has been more than a week, but I haven't received any information regarding OASIS-3 and OASIS-4. If anyone knows how to deal with this? .

NITRC v2.1.73 released

We are pleased to announce the release of NITRC v2.1.73. This release features enhancements to the tool/resource administration pages. Administrators are encouraged to check their listings' information while trying out the new interface. Release notes can be found at https://www.nitrc.org/plugins/mwiki/index.php/nitrc:NITRC_Release_Notes#NITRC-R_Release_v2.1.73-0_-_09.2F04.2F2025

Visit NITRC at OHBM 2025 in Brisbane!

NITRC will have an exhibitor booth at OHBM's annual meeting in Brisbane, AU. Please swing by to visit. We'd love to know what works and doesn't work for you and catch up! Also, we'll be presenting our poster #1931 on Fri, June 27 | 13:45 -15:45 and Sat, June 28 | 13:45 -15:45

How to download ABIDE data set?

How to download ABIDE data set?

NITRC 2.1.72 released

We are pleased to announce the release of NITRC 2.1.72. This release focused heavily on user interface and navigation issues. Please let us know what you think at https://www.nitrc.org/help/contact_us.php Full release notes can be found at https://www.nitrc.org/plugins/mwiki/index.php?title=nitrc:NITRC_Release_Notes#NITRC-R_Release_v2.1.72-0_-_05.2F19.2F2025