I realized today that 10%+ of my thoughts (1200 of a total of 10000) are "corrupted" ie. 2 thoughts contain the same mixed-up attachment an notes information.

It seems that this behaviour must have existed at least since April.

I tried (in vain):
- deleting the brain_db subfolder and reopening the brain in order to let TB recreate the DB > no change
- overhaul the database which (according to the description) should solve my issue.

The bad news : nothing has worked.

The semi-good news : the overhaul the database fonctionality was able to identify my "mixed up thoughts" and created a list of them with in a newly created folder "cleanedFolder" which has 254 html files (reason : I have no clue...) and a file called "ThoughtGroups" that contains a list of my problem thoughts with displays :
- a number (ranging from 5651 to 6512)
- the name of the thought

So forinstance I have the following entries in ThoughtGroups which means that the attachments and URLs of these thoughts are mixed up:
- 5659 Book Icon
- 5659 Turing Test

First: can someone (brain support) please let me know if I am doing something wrong in regards to the brain overhaul ?

Secondly, theoritically I could clean things up manually but :
- with 1260 thoughts that is a hell of a lot of work !!
- cleaning up is not straightforward. Let me explain...

Thought A :
- has link to windows folder A (correct)
- has a link to another windows folder B (should not tbe there - as it belongs to thought B)
- has url-A (correct)
- has url-B (which belongs to thought B and should not be there).

Thought B has exactly the same mixed up behaviour.
>> when I delete the incorrect folder B-link and url-B from thought-A, all is OK.

>> Subsequently when I then delete the incorrect folder A-link and url-A from thought B > everything disappears (links and urls) from Thought B!!

Can someone please advice ?

Many thanks in advance.

PS Windows 7 TB 32 bits J-1.7.0

I have the same problem. I am not sure when it happened but I suspect it was during the initial webbrain upload. Two different thoughts will share the same notes. Call them Thought A (original) and Thought B (unrelated). When I deleted the note for Thought B, the note for  Thought A disappeared as well.

The only work around I could come up with was to create a new thought (Thought A new), copy notes and links to it. Then when I delete (forget) Thought B, Thought A is forgotten as well. Very strange. 

I have only found a few dozen thoughts with this problem but it is a real pain to try to fix the database this way.

Like sjeeke, I would appreciate any suggestions you have.

This sounds like a problem that existed a year or two ago involving a particular beta release that left an insiduous corruption in brainzips. If you email I beleive they have a solution to the issue that should work. In any case, I would email them directly and do keep frequent backups.

Good luck for a quick resolution.

TB8022 32bit
Java 32bit Version 8 Update 141


Firefox, Office 2013 Pro Plus 32bit
64bit Win10Pro
64bit Primary Laptop, 8GB RAM, Intel Core i7
64bit Secondary Laptop, 64GB RAM, Intel Xeon E3
Brain user since 1997
I was affected by this as well a while ago. When I contacted support they were able to fix some of the thoughts with issues, and provide a list of thoughts which were they weren't able to recover notes. 

I believed this resolved the issue for a while, but kept noticing new corrupt thoughts as I moved on, and it started to show up in weird issues keeping my databases synchronized via WebBrain. Specifically, new thoughts would lose or switch notes, thought icons or hyperlinks.

I tried copying and pasting thoughts into new brains and at least in my case the corruption followed into the new database. 

Eventually it got to the point that I didn't trust my database. I created a new brain and started again from scratch. copied and pasted information from my original brain, but NEVER the thoughts. Only text and the images and attachments themselves. This cleared up any syncing issues and other weirdness that had been cropping up.

I hope you don't have the same level of corruption I was dealing with, although 10% sounded about right. I would contact support and provide them a brainzip of your database.
I'm sorry that I don't bear better news.
macOS 10.14.6
TheBrain 11.0.119
Hi Zenrain,
are you still using webbrain?
Yes. With my new database it's been working fine, except every now and then it drops or replaces pinned thoughts for some reason.
macOS 10.14.6
TheBrain 11.0.119
I read somewhere that dropping pins could be happening when changing a theme ...

@ZenRain: Are you not using any functionality in TheBrain after your restart. For instance virtual folder links?

I had the same 'experience' happen to me as Sjeeke and you have and I also started again with a fresh Brain. My old brain had only 2408 thoughts and in the brain I restarted I came to 300 thought but I lack a bit of trust at the moment.

The fact that you restarted and have not experienced any problems anymore resparked my use of thebrain and I am starting over yet again (as I did copy thoughts over from my old 'corrupted' brain). 

I have one other question about CPU use. I noticed in my old brain that even when I was not using it, it constantly was using  about 20 to 30% CPU. Did you notice that also in your corrupted brain or not?


The pins don't get dropped, they are replaced with completely different thoughts. It's weird. I unpin them, re-pin the existing thoughts and sync and it's fine again. I think it's a syncing issue between OS X and Windows, but I haven't been able to find a pattern. It only happens once a month or so and I'm afraid I've gotten complacent and just fix it rather than sending support sync logs.

I stopped using virtual folders a long time ago. I don't like the way it behaves on OS X, it treats package files as folders, so it shows applications as folders.

Most other functionality I use, and has worked fine for the time I've been using it (*Whew*). Prior to starting over one way thoughts were showing up all the time (I posted it here under issues quite a few times). That's also cleared up with the new DB.

My old brain was 7,000 + thoughts. My new brain is starting to get close to 1,800 after about 3-4 months. I did have a couple of false restarts where I copied thought over, but after a while of using them the corruption reared it's head again until I gave up and started fresh without copying thoughts.

The trust thing is difficult. I pretty much lost it when I first noticed the corruption and couldn't restore to fix it. You may have seen my "so long and thanks for all the fish" forum post and subsequent deletion and recreation of my username (that's why it shows it was created in April 2011). I battled with the issues stemming from the corruption in my original database for about 10 months. However, I couldn't find better PIM software (for my workflow) that's actively maintained and developed, and although I haven't met the folks at TheBrain, the interactions I've had with them have always been positive. They care about their product and their customers. That carries a lot of weight for me. 
Some other tools I use have gained more weight since the corruption. I use Pinboard for bookmarking and send everything there before adding it to TB. I also started to use Evernote. The hardest thing I'm facing now is if TheBrain doesn't get into the mobile market with a product soon, and make it easier to add files and thoughts from outside sources I'm going to be faced with dropping it for personal use. I think like everyone here I'm trying to be patient for a mobile release, but my mobile use is getting more and more frequent and my current workflows are getting cemented in. 

So that's my long answer to how I dealt with the trust thing. It probably doesn't help you any, except the best thing to do is evaluate if there is something else you can move to that will fit your need that's backed by a company you trust to help you to the best of their ability should an issue arise. If there is, switch. If not, take a deep breath and start again.

Oh, and I will never again use a beta release for my primary brain. If I do work in a brain I copied for the beta release (because who am I kidding, I'm not that patient), I won't copy any thoughts from the beta brain to the old brain either. I don't recall doing this ever, but it's a good distinction.

I haven't noticed the CPU spiking. I think I may have noticed it when using the corrupt brain, but not since. 

Sorry about the long reply. Hope it helps.

macOS 10.14.6
TheBrain 11.0.119
ZenRain, thanks for your very eleborate answer. 
The trust thing is indeed a pesky thing that won't be easy to solve. I already stopped using beta's and even regular updates I install only after a few weeks to see if some strange behaviour pops up. 

I have been using Smereka TreeProjects as my main PIM for the last year with TheBrain on the side as kind of an archive. TreeProjects is a wunderfull piece of software with absolute perfect stability and light CPU/memory footprint. It has a very nice way to use the clipboard to add data .

The one thing I miss in TreeProjects and almost all other PIM software is the Plex, how easy it is adding relationships and the quick search... so I was itching to start to use TheBrain again. 

For me the mobile thing is not so much an issue. I use Dropbox to store documents, photo's, links, ect... and add them to TheBrain/TreeProjects when I am behind my laptop again. 


Click image for larger version - Name: brein_statistieken.png, Views: 220, Size: 32.41 KB

An update: indeed it seems that one of the older beta releases is the culprit. I am working with support if anything can be done to facilitate understanding what can be done. In any case manuel intervention will be needed.

Lessons learnt:

-          Like zenrain: never test a beta release on precious data (that one has spent hundreds of hours in building)

-          TB is the only tool of its kind that meets my needs so no need to look for an alternative (I have tried almost all of them).

-          The fact of having to clean up my brain has a good element to it: it forces me to revisit many thoughts and clean them up / re-link / delete / etc, or build a copy from scratch (like zenrain) – but I have not made my mind up yet as what is the best way to go. So, although not an ideal situation it has a positive side...


The fact of having to clean up my brain has a good element to it: it forces me to revisit many thoughts and clean them up / re-link / delete / etc, or build a copy from scratch (like zenrain) – but I have not made my mind up yet as what is the best way to go. So, although not an ideal situation it has a positive side... 

Agreed, it is nice to start from scratch and take everything you learned from your previous database.
macOS 10.14.6
TheBrain 11.0.119
I have been looking at a solution and here is how I go about "restoring" my "mingled" thoughs....

The brain overhaul has been able to identify the thoughts that are causing me problems.

Of the list of 1200+ problem thoughts that my brain contains, I copy  about 10 pairs (the overhaul function identifies the names of the 2 thoughts that are mixed up) over into another clean brain.

In this second brain I do the clean up (move URLs and file attachments to the correct thought).

After clean-up I copy the cleaned-up thoughts back to my original brain.

This is a time consuming process but I have calculated that if I spend about 15 minutes a day I should be able have all corrupted thoughts treated before end of year (and perhaps even sooner).

The only issue that is not resolved by this process is that when I have cleaned up 2 thoughts that are intermingled, the notes in one of the thoughts needs to be reconstructed (the mingling up of thoughts caused the notes of one thought to be displayed in the notes of the second thought (and has thus overwritten the original notes of the second thought)).

I will add another posting when I am done :-)

You may want to think about just copying the attachments, notes and hyperlinks and place them in a new thought you created on your clean brain (if you already are doing this, sorry, I couldn't tell from your post).
This ensures any corruption isn't copied over in the thought xml data. I don't know if this is actually occurs, but it definitely stopped general wierdness for me that I attribute to copied thoughts in my database.
macOS 10.14.6
TheBrain 11.0.119
Thanks for the tip.
I have tagged all my corrupted and cleaned-up thoughts so I can track if any weirdness reoccures (after clean-up) in which case I will be going for a major "start from scratch". At this moment the least time consuming is the approach I have taken but I am very aware that there might be some surprises along the road so I am setting things up to not be taken off guard.
Expect the best, plan for the worst. Sound like a good plan to me.
macOS 10.14.6
TheBrain 11.0.119

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