Tell me your thoughts on a "Mental Health" Second Brain

I have files and resources strewn across Finder, Craft, Dropbox, Paperpile etc and I’m trying to make sense of all this mess.

Right now I’m using Craft as my “Second Brain.” I’m a narrative therapist but I also lead a team of practitioners and provide clinical supervision, leadership, mentoring etc. I’m at a loss of how to organize or structure my second brain because of the variety of contexts (e.g. my job has many hats from practice to leadership), breadth of topics (could be information on a diagnosis like major depression or a type of modality etc), file types, audiences etc.

For example, I have my own notes on workshops/conferences, books, podcasts, videos etc; a variety of resources some of which are handouts for clients, some are for professionals; files which could be docs, pdfs, slides, videos; a vast research library of journal articles; web clippings and highlights etc.

It’s enough data to be overwhelming and every time I come across something I spend so much time thinking “where should this go?” Lately, I’ve tried to use Craft to link it all together and I’m stuck on organization.

How would you organize something like this? What are your thoughts on where I should put all this stuff? I tend to overcomplicate many things, so I’m hoping to find the simplest solution that would still enable me to find everything - so I can reference it, send resources to folks who might find them useful, use in my own practice, and take notes on new things I come across.

How would you go about this?

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If it were me, I would:

Pick a single app for your index and new notes that you create.

Make sure the app is something you can export or get your data from.

Organize your files in the Finder. You need to have a folder hierarchy. You seem to be thinking of items in terms of audience; might start with


You could have sub-folders; perhaps based on kind of therapy or diagnosis.

Consider using Finder tags.

Make sure you clearly name files with descriptive titles.

Build an index/table of contents in your notes app. Refer to files with names/locations, or links.

Feel free to expand on the TOC Index; it will constantly be a work in progress. You can move bits of it as it grows to create separate sub-notes.


how about using Notebooks . The app natively works with iCloud (so there is no need to export any data). You can use nested folder structure to suit your needs. It also supports Markdown notes and many other formats

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I agree with @Medievalist here - pick a single app. It removes a lot of the friction.

There is a huge amount of writing online on Personal Knowledge Management (PKM) which is essentially what you’re doing, but I’m guessing you don’t have time to go down that particular rabbit hole - it’s addictive reading about this stuff, but at the end of the day time spent reading about that could’ve been spent on your actual field of interest and you have to find a balance :upside_down_face: Speaking as someone who hasn’t found that balance and loves reading about PKM, here’s what I did:

I use DevonThink Pro (DT), which is great for my use case and yours. For you, it’s got the following benefits:

  • Files are stored locally on your Mac, so you do not need to worry about protected data sitting on a third party cloud service somewhere

  • DT’s search function is out of this world and you will be able to find all sorts of gems in your files

  • DT can handle any file type, so you can store PDFs, emails, notes you’ve made, etc. It has in-app OCR for any files that need to be turned into searchable text

  • Groups and tags are your friend, and DT can also create smart groups (essentially imaginary groups based on criteria you set - great for temporary projects, etc.)

“Groups” is DT’s language for folders. For me, I have a rigid folder/group structure that separates all my files by topic. I vaguely use Johnny Decimal for my folder-naming conventions. This is top level sorting by topic because this is how I like to navigate. So for example I’m an ecologist, so my folder structure looks a bit like this (this is imaginary but based on what my actual structure looks like):

10. Conservation
   10.01. Marine
      10.01.01. Saltmarsh Kelp Sediments
      10.01.02. Deep sea
   10.02. Woodland
      10.02.01. Trees
      10.02.02. Woodland soil carbon

I have a rule that I don’t go more than 4 folders deep, and if a file fits in more than one folder it only goes as deep as I can file it. So for example if I had a paper that discussed both salt marsh and deep sea sediments, I would file it in 10.01. Marine because it cannot go any more precise.

In addition to a rigid folder structure, DT has tags. I don’t use my tags to manage topics, since I already have my file structure for that. I use tags to manage the type of file, and I have 5 bonus tags that record the action pending for a file. This is really useful though I know lots of people would be horrified at this from a knowledge management perspective. Here’s the actual list of file types I track:

(DT allows tag colours to be set, so e.g. my 5 action tags are yellow and denoted by an emoji.)

All of this combined basically means I can do things like find all my notes on talks about saltmarshes, etc.

Nowadays I pretty much file everything into my database. It has made my life so much easier. BUT. DT does have a big learning curve. It is well-worth it in my opinion, and some of the things you need to think about will have to be done for all apps and are not app-specific.

Step 1 is figuring out whether you’re a folders or tags person, and identifying how you like to navigate (do you run a search to find the file you’re after or do you prefer to navigate to a file yourself?)

Step 2 is mapping out the structure (or indeed having no structure at all - if you prefer to find files by search you don’t need folders necessarily, just pick an app with a powerful search function and let it do all the work!).

Step 3 is identifying the file types you work with. Is everything you handle in PDF, for example, or do you have a mix of different file types that need an app that handles it all? Do you have a lot of emails that ideally would also be in your library? (I’m guessing you have no weird file type that is unique to your sector, but if you do you need to think about that too. E.g. for me I have GIS files. Do I want those in the same library, and if not, where should they be stored to be easily found?)

Step 4 is figuring out what you intend to do with these files. Do you just need to be able to find things quickly? Are you planning to do research from these files? Do you want to be able to easily add notes or is it more like a library you extract data from and move elsewhere for “processing”?

Then come back here and tell us what you want to do, and we’ll recommend the app :joy:


Hello @jaketheo . For what it’s worth, and before you sink hours into reorganising everything into a single ‘solve my problems’ app, try and figure out where your pressure points really are. There’s no reason, in fact, to move everything into a single place if your system works, if only in part. But I’d guess from posting this that you are experiencing friction and overwhelm.

For the longest time, I have stored my research in DEVONthink. I’d recommend it without hesitation - THE BEST APP for organising disparate material and file types into databases, ‘groups’ (folders); tags if you are so inclined, and allows you easy ways of creating Smart groups that cut across whatever organisational structure you have put in place. @Pupsino 's use case above is nice. It’s also totally different from the way I organise mine. DT is infinitely adaptable, and will suit your needs without doubt.

Yet, despite this, I still store all my teaching materials in Finder (and this Christmas hols have planned some migration into DT). I have a Simplenote account shared for short life stuff notes with my partner. I run Obsidian for my personal note taking. My bibliographical references (metadata only, not PDFs) are stored in Zotero. To-dos are in ToDoist. And so on. It’s all ticking along nicely, and helped with linking between these applications, that all do their own job well.

I suppose the idea is that you make sure that the underlying system is sound, and that’s something you could sketch out by hand before putting all your eggs into a single-app basket. You could identify material by role; the extent to which you need to share with others; the extent to which you need to habitually search complex collections; and whatever else is on your list of requirements.

I guess what I am saying is that no app will sort you out unless the underlying system is planned, well understood, and adhered to! But these things are fun (for some people … perhaps hellish for others!). I diagrammed mine at some point, using Keynote. But a napkin will do just fine.

BTW – I am an academic in the Humanities working on literature, and my better half is a psychotherapist / counsellor. So your job description of ‘narrative therapist’ is intriguing!


+1 for Devonthink!
It is, from my point of view, the best solution currently available for Apple-User on the market.
I, for example have created a database I called “Collector”, and just “threw” everything into that database I had previously strayed across my system.
I then startet to give everything a structure within a different database, where I move objects from the first database into, if I have some sparetime, or if I have to work with this objects anyway.
The strong search function allows to use the objects still within the Collector-Database already, so you could take your time to get order into this, without the problem of not be able to use the documents in the meantime.
There are also a couple of other apps, that play nicely together with Devonthing, for Example I use LiquidText often during the last weeks, to annotate and extract from my Documents stored within Devonthing.


You mentioned your team. Is this “second brain” for you alone? Or do you anticipate ever sharing any part of this with your team members?

Are you subject to HIPAA regulations? If so, it appears you will not be able to sync your data via iCloud or store anything on Apple’s servers (iCloud, Apple Mail, etc).

Do you anticipate needing to access this information on an iPhone or iPad?

“If you are a covered entity, business associate or representative of a covered entity or business associate (as those terms are defined at 45 C.F.R § 160.103), You agree that you will not use any component, function or other facility of iCloud to create, receive, maintain or transmit any “protected health information” (as such term is defined at 45 C.F.R § 160.103) or use iCloud in any manner that would make Apple (or any Apple Subsidiary) your or any third party’s business associate”

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I agree with the recommendations regarding DEVONthink with one caveat, DT is, in my estimation, clunky on the iPad and iPhone. Obviously this is not an issue if you do your work exclusively on a Mac but keep in mind if you want a seamless experience across devices, DT may prove to be less than satisfactory.


I wonder if you can recommend any app in the same class as DEVONthink (collects large numbers of any and all document types and stores its data locally) that isn’t clunky on iPad and iPhone? I know I can’t. :slightly_smiling_face:

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I don’t know of one either, which is why I use Finder/Obsidian for my research documents and a note application for my other notes because I’m constantly switching between devices for my work.

I only mentioned the clunkiness of DT to ensure that @jaketheo was aware of DT’s mobile app limitations before making a large purchase if he frequenlty uses mobile devices for his work. I think DT is great on the Mac, but sadly lacking on mobile devices. :slightly_smiling_face:


echoing others above me but pick a single app.

You need something that can handle a variety of inputs, keep files locally and grow as your needs grow and for privacy reasons. That will basically eliminate all iCloud based systems.

I also agree that most external files should be a shallow folder structure. ideally no more than 1 level of folders or maybe 2.

DEVONThink may be suitable but if you choose it be aware of the potential for disasterous data loss and do regular backups, testing file integrity and more at least weekly. Personally I got burned so badly that I won’t use DT anymore.

I use Obsidian and have adapted most everything to it. new improvements in how Obsidian can support opening files in external apps, and using external links have made it even more useful for me. There are drawbacks, I don’t use it to store bibliographic references to scientific papers, I use Zotero for that but I can still get all my notes and highlights into Obsidian where they are more useful for me.

I am not a tagger by nature. I like well defined folders but I also find myself looking for things in my system in multiple ways. This is where Obsidian shines. I can put links to the item of interest in any place that I am likely to need oto refer to it or all the places I look. I’ve been doing that by first linking into the place I think I will look for things. As I use my ever-growing PKM system when I know I have something in there and it’s not the first place I look, when I do find it I go back to that first place and add another link to it. Over time my web of knowledge improves and I can usually get to everything with one quick lookup and never have to resort to search. I HATE search with a passion. It is cumbersome and results are always filled with false positives for me no matter how I use it and no matter what app I am using so I’ve basically given up on it.

Tags for me are a problem because unless I am really careful about my taxonomy they proliferate and are hard to manage. The few tags I do use are in a strict hierarchical system with a tightly controlled vocabulary so they retain usefulness.

Edit to correct some typos


This is a great idea!


Without knowing more about how you work, my first impression is that choice of app is not your immediate issue. Instead of asking “Where should this go?”, I’d recommend asking “What do I intend to do with this information?”

Maybe you already do that and you’re just not mentioning that part of your process here. But I wouldn’t know where to put anything without knowing the answer to that question first.

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And also, what will I be looking for - why will I need - this information.


Great ideas! I’ve never built a map of content/index before but I’ve started to read more about this. Looks like it can be helpful to catalog and cross link everything.

Thanks for your thoughts on PKM! I’m almost finished with Tiago’s BASB book, which has some great ideas. Most of my files are PDF, but I have a mix of file types and would prefer an app to handle them all. Nothing unique – mainly pdfs, Word docs, spreadsheets, slides etc. I don’t usually store emails, just copy the contents of important ones into a note.

I need to be able to find things quickly. Ideally I’d like OCR but I’m struggling post-Evernote. I “consult” these files and often share them with colleagues. For example, say I’m working with a client who struggles with assertiveness, or mentoring a colleague who is working with a client. I will often do a “lit review” of my own resources and research and find resources that might be helpful. I also like to take notes on various topics, link things together, and highlight and distill content I find on the web.

Great advice! I’ve been guilty in the past of tinkering, changing apps, introducing new workflows etc to see what helps, but this can have downsides. The pressure points for me are probably a combination of 1) no clear structure so I don’t know where to file, 2) getting things into the app 3) being able to search or find things easily and 4) ability to share with others easily.

Ah, amazing! Narrative therapy is just another counselling modality like CBT. I provide supervision for a lot of other counsellors and psychotherapists and I’m always appreciating the breadth of knowledge and skills. I’m always learning!

In terms of the notes and distillation of notes, it’s usually just for me. But I share things frequently – for example, I’ll share resources/pdfs with folks who are looking for something on a particular topic.

Not subject to HIPAA and the types of content I put here isn’t confidential or client-related. It’s mainly resources on topics, my own notes or reflections, or notes from workshops, books, podcasts etc.

Yes, it needs to be iOS, Mac and PC and ideally web. This usually rules things like DT out. I can’t install anything on my work laptop, so I’ve been using Craft web (and Evernote web previously) so that I can quickly access and add at work.

Yes, your question is a great one. I think the pressure point here is that I’m overwhelmed by the amount of files and information I have. In terms of what I intend to do (which is perhaps different to what I currently do) is to build a library of resources and research that I can consult, make notes on these resources, and have things on hand to share with colleagues and folks I mentor. Some of the items get shared with clients if it’s a handout they would find useful (e.g. mindfulness exercise).

I really appreciate all of your thoughts and wisdom here folks! All of you have already given me so many things to think about and I will do my best to really consider a system and workflow that works for me … I will try to stop fiddling! :smiley:


The only one that comes to mind is Keep It but this probably isn’t the same class as DEVONthink. DT-lite perhaps.

You could use Devonthink Server-Edition for that.

I agree 100%. And what’s even more frustrating about devonthink on mobile is it’s sooooo close for so many things. They add a text editor, but it doesn’t support basic functions (like list or bullet in rich text), markdown doesn’t support wiki links.

There are no smart groups on mobile. Nested tags don’t work. Search is spotty if not completely downloaded files.

I wish it sucked more, since currently it sucks just enough to see that it is so close to be the one go to app.

Yes, and don’t forget, for some inexplicable reason, you can’t make the editor full screen on the iPad. That completely baffles me.

Background sync is my wish. I’m aware of their explanations of the limitations, but I think more is possible with the same APIs.