Bom dia ☀️https://inespereira.me/Recent content on Bom dia ☀️Hugo -- gohugo.ioen© 2026 Inês PereiraMon, 24 Aug 2026 20:58:34 +0200Evaluating computational assays of chronic fatigue using UK Biobank datahttps://inespereira.me/posts/ukb_fatigue_preprint/Mon, 24 Aug 2026 20:58:34 +0200https://inespereira.me/posts/ukb_fatigue_preprint/Tools for Code Reviewhttps://inespereira.me/posts/code_review_llms/Wed, 24 Jun 2026 17:10:12 +0200https://inespereira.me/posts/code_review_llms/<p>In my previous post, I shared a <a href="https://www.preprints.org/manuscript/202510.0133" target="_blank" >preprint</a> proposing a structured checklist to facilitate code review in mental health research. Our motivation to write this paper was straightforward: code review can improve the reliability of research results and fosters a culture of transparency and continuous learning. Yet, in practice it is often difficult to implement consistently. Getting started, if you&rsquo;ve never done it before, can be hard. That is why we shared our experience and checklists.</p>Structured Code Review in Translational Neuromodeling and Computational Psychiatryhttps://inespereira.me/posts/code_review_preprint/Thu, 02 Oct 2025 20:58:34 +0200https://inespereira.me/posts/code_review_preprint/Computational Psychiatry of Fatigue: Towards predicting individual symptoms from cognition and brain connectivityhttps://inespereira.me/posts/phd_thesis/Fri, 04 Jul 2025 20:58:34 +0200https://inespereira.me/posts/phd_thesis/She Sailshttps://inespereira.me/posts/she_sails/Mon, 30 Jun 2025 00:00:00 +0000https://inespereira.me/posts/she_sails/<p>🔔 Book announcement! 🔔</p> <p>After several years of ideating and much writing and rewriting, I have put out my very first book, called <em>She Sails</em> (links at the end of this post)!</p> <p>This project would not have been possible without the support and encouragement I received, in particular from my better half, David ❤️. He is the reason I got bitten by the sailing bug in the first place, and he has shown me what true partnership looks like.</p>Predicting future depressive episodes from resting-state fMRI with generative embeddinghttps://inespereira.me/posts/predicting_depression_paper/Thu, 01 Jun 2023 08:57:49 -0400https://inespereira.me/posts/predicting_depression_paper/Interoceptive and metacognitive facets of fatigue in multiple sclerosishttps://inespereira.me/posts/imefa_paper/Fri, 19 May 2023 08:57:49 -0400https://inespereira.me/posts/imefa_paper/Mechanismen von Fatigue bei Multipler Sklerose – Untersuchung mittels fMRI (FAMRI Studie)https://inespereira.me/posts/ms_perspektive_podcast/Mon, 02 Jan 2023 08:57:49 -0400https://inespereira.me/posts/ms_perspektive_podcast/Individual treatment expectations predict clinical outcome after lumbar injections against low back painhttps://inespereira.me/posts/trexi_paper/Sun, 01 Jan 2023 08:57:49 -0400https://inespereira.me/posts/trexi_paper/Welt-MS Tag - Radio Zürisee Interviewhttps://inespereira.me/posts/radio_zuerisee_interview/Sun, 01 Jan 2023 08:57:49 -0400https://inespereira.me/posts/radio_zuerisee_interview/Actigraphy - What is out there?https://inespereira.me/posts/actigraphy/Fri, 09 Dec 2022 11:30:04 +0300https://inespereira.me/posts/actigraphy/<div class="flex px-4 py-3 rounded-md bg-primary-100 dark:bg-primary-900" > <span class="text-primary-400 ltr:pr-3 rtl:pl-3 flex items-center" > <span class="relative block icon"> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M506.3 417l-213.3-364c-16.33-28-57.54-28-73.98 0l-213.2 364C-10.59 444.9 9.849 480 42.74 480h426.6C502.1 480 522.6 445 506.3 417zM232 168c0-13.25 10.75-24 24-24S280 154.8 280 168v128c0 13.25-10.75 24-23.1 24S232 309.3 232 296V168zM256 416c-17.36 0-31.44-14.08-31.44-31.44c0-17.36 14.07-31.44 31.44-31.44s31.44 14.08 31.44 31.44C287.4 401.9 273.4 416 256 416z"/></svg> </span> </span> <span class="dark:text-neutral-300" ><p><strong>2024 Update</strong>: The first two sections of this post still hold value. However, the market might have changed, new products might available or older products might not be sold anymore.</p>Conductance-based DCM: A reviewhttps://inespereira.me/posts/cb-dcm/Wed, 15 Dec 2021 08:57:49 -0400https://inespereira.me/posts/cb-dcm/Fatigue - Understanding its pathophysiologyhttps://inespereira.me/posts/fatigue-talk/Mon, 13 Sep 2021 08:57:49 -0400https://inespereira.me/posts/fatigue-talk/TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatryhttps://inespereira.me/posts/tapas_paper/Tue, 01 Jun 2021 08:57:49 -0400https://inespereira.me/posts/tapas_paper/Model interpretability in Healthcarehttps://inespereira.me/posts/dspt/Wed, 10 Mar 2021 08:57:49 -0400https://inespereira.me/posts/dspt/COVID & Tools for Online Eventshttps://inespereira.me/posts/online-events/Sun, 13 Sep 2020 00:00:00 +0000https://inespereira.me/posts/online-events/<div class="flex px-4 py-3 rounded-md bg-primary-100 dark:bg-primary-900" > <span class="text-primary-400 ltr:pr-3 rtl:pl-3 flex items-center" > <span class="relative block icon"> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M506.3 417l-213.3-364c-16.33-28-57.54-28-73.98 0l-213.2 364C-10.59 444.9 9.849 480 42.74 480h426.6C502.1 480 522.6 445 506.3 417zM232 168c0-13.25 10.75-24 24-24S280 154.8 280 168v128c0 13.25-10.75 24-23.1 24S232 309.3 232 296V168zM256 416c-17.36 0-31.44-14.08-31.44-31.44c0-17.36 14.07-31.44 31.44-31.44s31.44 14.08 31.44 31.44C287.4 401.9 273.4 416 256 416z"/></svg> </span> </span> <span class="dark:text-neutral-300" ><strong>2024 Update</strong>: By now, we all have a much better understanding of how to conduct online (or even hybrid!) events. I have however decided to leave this blog post as is, as an artefact of the 2020 zeitgeist.</span> </div> <blockquote class="twitter-tweet"><p lang="en" dir="ltr">When the corona crises started we decided to go online with our <a href="https://x.com/CompPsychiatry?ref_src=twsrc%5Etfw">@CompPsychiatry</a> course and make it free of charge. The result was a course that ended up being 4x bigger than usual (&gt;1000 participants) and more inclusive than ever. Thanks to everyone who helped pull this off!!! <a href="https://t.co/ybi8QrgI19">pic.twitter.com/ybi8QrgI19</a></p>Data Visualizationhttps://inespereira.me/posts/data-visualization/Fri, 07 Feb 2020 11:12:09 +0700https://inespereira.me/posts/data-visualization/<div class="lead text-neutral-500 dark:text-neutral-400 !mb-9 text-xl"> <p>Scientists are expected to be effective communicators, but that can be a little tricky without a few conscious tricks up your sleeve.</p> <p>Visualization, in particular, can be a very powerful means of conveying information, be it in your papers, posters, presentations, chapters, or blogposts.</p> </div> <p>🖍 <em>Nota bene</em>: In this post, I summarize a few recommendations from various sources that I, personally, found very useful. For a more in-depth take on the following and other points, do consult the series of Points of View columns published in <em>Nature Methods</em>. A collection of these can be found in the <a href="#references">resources section</a> below. Another great online read can be found <a href="https://www.knowablemagazine.org/article/mind/2019/science-data-visualization" target="_blank" >here</a> .</p>A beginner's guide to ETH's Eulerhttps://inespereira.me/posts/eth-euler/Wed, 03 Jul 2019 15:21:13 +0200https://inespereira.me/posts/eth-euler/<div class="flex px-4 py-3 rounded-md bg-primary-100 dark:bg-primary-900" > <span class="text-primary-400 ltr:pr-3 rtl:pl-3 flex items-center" > <span class="relative block icon"> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M506.3 417l-213.3-364c-16.33-28-57.54-28-73.98 0l-213.2 364C-10.59 444.9 9.849 480 42.74 480h426.6C502.1 480 522.6 445 506.3 417zM232 168c0-13.25 10.75-24 24-24S280 154.8 280 168v128c0 13.25-10.75 24-23.1 24S232 309.3 232 296V168zM256 416c-17.36 0-31.44-14.08-31.44-31.44c0-17.36 14.07-31.44 31.44-31.44s31.44 14.08 31.44 31.44C287.4 401.9 273.4 416 256 416z"/></svg> </span> </span> <span class="dark:text-neutral-300" ><strong>2024 Update</strong>: Euler is now using Slurm instead of LSF. While this blog post can this be still useful, the LSF commands need to be translated into Slurm commands. See <a href="https://scicomp.ethz.ch/wiki/LSF_to_Slurm_quick_reference" target="_blank" >this quick reference</a> .</span> </div> <p>🖍 <em>Nota bene</em>: You will need to be an ETH member to use Euler. However, this post might still be useful if you happen to be working on another cluster which uses the <a href="https://en.wikipedia.org/wiki/Platform_LSF" target="_blank" >LSF</a> batch system. Also relevant: I am currently mainly using MATLAB to run my simulations, so you&rsquo;ll find some MATLAB specific advice. For Python specifics, check out <a href="https://scicomp.ethz.ch/wiki/Python" target="_blank" >this page</a> .</p>Freeview from FreeSurferhttps://inespereira.me/posts/freeview/Sun, 31 Mar 2019 11:17:49 +0200https://inespereira.me/posts/freeview/<p><a href="https://surfer.nmr.mgh.harvard.edu/" target="_blank" >FreeSurfer</a> is an open source software package for the analysis and visualization of structural and functional neuroimaging data. It is developed by the <a href="https://martinos.org/lab/lcn" target="_blank" >Laboratory for Computational Neuroimaging</a> at the <a href="https://martinos.org/" target="_blank" >Athinoula A. Martinos Center for Biomedical Imaging</a> . It&rsquo;s a really useful tool that allows for automated processes as well as manual interventions, mainly through it&rsquo;s GUI, Freeview.</p> <p>I started using FreeSurfer and Freeview last year and, albeit the documentation being quite thorough, I had a harder time navigating the website than I expected.</p>The Art of Foot Ticklinghttps://inespereira.me/posts/the-art-of-foot-tickling/Tue, 03 Apr 2018 20:12:34 +0200https://inespereira.me/posts/the-art-of-foot-tickling/<p>One can sometimes feel very puzzled when watching a physician perform the neurological examination. I mean, what information is there to extract from a retracting big toe, from feet constantly a bit more apart from each other than they should be or even from an absent tendon reflex? How were these signs observed in the first place and how did we come to know how to interpret them?</p> <p>Let us focus, for example, on reflexes. A reflex is an involuntary movement in response to a stimulus. Reflexes in general represent a key part of the neurological examination because of their more objective nature and lesser dependency on patient cooperation. Actually, reflexes and their characteristics are crucial: in conjunction with other signs and symptoms and knowledge of the anatomy of the nervous system, the observer can localize the neurological lesion(s) with a surprising degree of precision&hellip; before even resorting to CT or MRI imaging!</p><link>https://inespereira.me/posts/predicting-csd/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://inespereira.me/posts/predicting-csd/</guid><description><!-- +++ title = "Predicting CSD" subtitle = "" # Math mode needs to be cool markup = "mmark" # Add a summary to display on homepage (optional). summary = "" date = 2019-08-03T19:31:11+02:00 draft = true # Authors. Comma separated list, e.g. `["Bob Smith", "David Jones"]`. authors = [] # Is this a featured post? (true/false) featured = false # Tags and categories # For example, use `tags = []` for no tags, or the form `tags = ["A Tag", "Another Tag"]` for one or more tags. tags = [] categories = [] # Projects (optional). # Associate this post with one or more of your projects. # Simply enter your project's folder or file name without extension. # E.g. `projects = ["deep-learning"]` references # `content/project/deep-learning/index.md`. # Otherwise, set `projects = []`. # projects = ["internal-project"] # Featured image # To use, add an image named `featured.jpg/png` to your page's folder. [image] # Caption (optional) caption = "" # Focal point (optional) # Options: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight focal_point = "" +++ ## What are CSD?? The cross power spectral density (or cross spectral density) $S_{xy}(\omega)$ between two signals $x(t)$ and $y(t)$ can be defined as the Fourier transform of these series' cross-correlation function $R\_{xy}(\\tau)$: $$S_{xy}(\omega)=\int_{-\infty}^{\infty}R_{xy}(\tau)e^{-j \omega\tau}d\tau = \int_{-\infty}^{\infty} \left[ \int_{-\infty}^{\infty} x(t)^* \cdot y(t+\tau) dt \right] e^{-j \omega t} d\tau$$ When $x(t)=y(t)$, we talk of power spectral densities. ## What's a Volterra series? A Volterra series is similar to a Taylor series. They differ in that the Taylor series can model non-linear systems with no memory, whereas the Volterra series can capture this memory effect. A continuous time-invariant system with $x(t)$ as input and $y(t)$ as output can be expanded in Volterra series as: $$y(t) = h_{0}+\sum_{n=1}^{N}{\int_{a}^{b}\cdots\int_{a}^{b} {h_{n}(\tau_{1},.\,.\,,\tau_{n})\prod^{n}_{j=1}{x(t - \tau_{j}) d\tau_{j}}}}$$ Looks complicated, but you understand what is going on if you start the expansion yourself: $$y(t) = h_{0}+{\int_{a}^{b}{h_{1}(\tau_{1})\cdot{x(t - \tau_{1}) d\tau_{1}}}} + {\int_{a}^{b} \int_{a}^{b} {h_{2}(\tau_{1}, \tau_{2})\cdot{x(t - \tau_{1})\cdot x(t - \tau_{2}) d\tau_{1}d\tau_{2}}}} ...$$ The function $$h_{n}(\tau_{1},.\,.\,,\tau_{n})$$ is called the $n$-th order Volterra kernel, It can be regarded as a higher-order impulse response of the system. Issues: - By looking at the Volterra series, you don't know the order of your system - Individual Volterra operators (H, different from kernels h!) are not independent --></description></item><item><title>About mehttps://inespereira.me/about/Mon, 01 Jan 0001 00:00:00 +0000https://inespereira.me/about/<p>Physician, computational neuroscientist, offshore sailor, and newly-minted mother. I&rsquo;m a curious, avid learner (and major nerd) who is happiest when exploring.</p> <h2 class="relative group">Exploration portfolio 🏂 <div id="exploration-portfolio-" class="anchor"></div> <span class="absolute top-0 w-6 transition-opacity opacity-0 ltr:-left-6 rtl:-right-6 not-prose group-hover:opacity-100"> <a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700 !no-underline" href="#exploration-portfolio-" aria-label="Anchor">#</a> </span> </h2> <div id="carousel-2bc053111729a74bce2ff033e7cdfe90" class="relative" data-twe-carousel-init data-twe-ride="carousel"> <div class="absolute right-0 bottom-0 left-0 z-[2] mx-[15%] mb-10 flex list-none justify-center p-0" data-twe-carousel-indicators> <button type="button" data-twe-target="#carousel-2bc053111729a74bce2ff033e7cdfe90" data-twe-slide-to="0" data-twe-carousel-active aria-current="true" class="mx-[3px] box-content h-[3px] w-[30px] flex-initial cursor-pointer border-0 border-y-[10px] border-solid 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motion-reduce:transition-none" type="button" data-twe-target="#carousel-2bc053111729a74bce2ff033e7cdfe90" data-twe-slide="next"> <span class="inline-block h-8 w-8"> <svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="4.5" stroke="currentColor" class="h-6 w-6"> <path stroke-linecap="round" stroke-linejoin="round" d="M8.25 4.5l7.5 7.5-7.5 7.5" /> </svg> </span> <span class="!absolute !-m-px !h-px !w-px !overflow-hidden !whitespace-nowrap !border-0 !p-0 ![clip:rect(0,0,0,0)]" >Nextsads</span > </button> </div> <h2 class="relative group">🎓 Work background <div id="-work-background" class="anchor"></div> <span class="absolute top-0 w-6 transition-opacity opacity-0 ltr:-left-6 rtl:-right-6 not-prose group-hover:opacity-100"> <a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700 !no-underline" href="#-work-background" aria-label="Anchor">#</a> </span> </h2> <ul> <li>Doctoral studies @<a href="https://www.tnu.ethz.ch/" target="_blank" >Translational Neuromodeling Unit</a> , UZH &amp; ETH Zurich, Switzerland 🇨🇭 (2020-2025)</li> <li>Master&rsquo;s degree in <a href="https://www.nsc.uzh.ch/en.html" target="_blank" >Neural Systems and Computation</a> @UZH &amp; ETH Zurich, Switzerland (2018-2019)</li> <li>Neurology resident @<a href="https://www.median-kliniken.de/de/klinik-berlin-kladow/" target="_blank" >MEDIAN Klinik Berlin Kladow</a> , Berlin, Germany 🇩🇪 (2016-2018)</li> <li>Medical degree @<a href="https://www.nms.unl.pt/en-us/faculty/about-us/nova-medical-school" target="_blank" >NOVA Medical School</a> , Lisbon, Portugal 🇵🇹 (2010-2016)</li> </ul> <h2 class="relative group">⛵ Sailing <div id="-sailing" class="anchor"></div> <span class="absolute top-0 w-6 transition-opacity opacity-0 ltr:-left-6 rtl:-right-6 not-prose group-hover:opacity-100"> <a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700 !no-underline" href="#-sailing" aria-label="Anchor">#</a> </span> </h2> <p>I&rsquo;m an experienced sailor with internationally recognized <a href="https://www.rya.org.uk/" target="_blank" >Royal Yachting Association</a> certifications (see below), adept in handling both monohulls and multihulls. I have 15,000 nm sailing experience under my belt, including offshore and ocean sailing:</p>Readinghttps://inespereira.me/books/Mon, 01 Jan 0001 00:00:00 +0000https://inespereira.me/books/<p>Besides papers, I love reading books. Here is a selection of books I love.</p> <div id="gallery-c182ecca1ad171eba770fa80cf0a3f69" class="gallery"> <img src="https://inespereira.me/books/img/ryan-north.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/imposter-handbook.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/hpmor.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/romeo-and-or-juliet.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/schnitt.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/atomic-habits.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/bad-science.jpg" class="grid-w33" /> <img src="https://inespereira.me/books/img/bad-pharma.jpg" class="grid-w33" /> </div>Toolshttps://inespereira.me/tools/Mon, 01 Jan 0001 00:00:00 +0000https://inespereira.me/tools/<div class="lead text-neutral-500 dark:text-neutral-400 !mb-9 text-xl"> Things I&rsquo;ve built and tools that make my work (and life) a little better ❤️. </div> <h2 class="relative group">🔬 Things made by me <div id="-things-made-by-me" class="anchor"></div> <span class="absolute top-0 w-6 transition-opacity opacity-0 ltr:-left-6 rtl:-right-6 not-prose group-hover:opacity-100"> <a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700 !no-underline" href="#-things-made-by-me" aria-label="Anchor">#</a> </span> </h2> <ul> <li>📇 Work <ul> <li>Code Review for Mental Health Research: A <a href="https://chatgpt.com/g/g-6a3be6f2b3208191ba92efdbb7cc6e09-code-review-for-mental-health-research" target="_blank" >custom GPT</a> that performs structured code review using the framework from <a href="https://www.preprints.org/manuscript/202510.0133" target="_blank" >Pereira, Galioulline et al., &ldquo;Structured Code Review in Mental Health Research&rdquo; (2025)</a> .</li> </ul> </li> <li>🎭 Leisure <ul> <li><a href="https://glittermap.io/" target="_blank" >Glittermap</a> , a map + directory of burlesque &amp; cabaret events across Europe, listing festivals, shows, and (the big one for performers) open calls.</li> </ul> </li> </ul> <h2 class="relative group">🛠️ Amazing things made by others <div id="-amazing-things-made-by-others" class="anchor"></div> <span class="absolute top-0 w-6 transition-opacity opacity-0 ltr:-left-6 rtl:-right-6 not-prose group-hover:opacity-100"> <a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700 !no-underline" href="#-amazing-things-made-by-others" aria-label="Anchor">#</a> </span> </h2> <h3 class="relative group">Research <div id="research" class="anchor"></div> <span class="absolute top-0 w-6 transition-opacity opacity-0 ltr:-left-6 rtl:-right-6 not-prose group-hover:opacity-100"> <a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700 !no-underline" href="#research" aria-label="Anchor">#</a> </span> </h3> <ul> <li> <p><a href="https://www.biorender.com/" target="_blank" >BioRender</a> : my go-to tool for making publication-quality scientific figures and illustrations&hellip; since 2018. Templates are great for getting started, and the icon library covers most of what you&rsquo;d need for neuroscience and biomedical work.</p>