Friday, 30 July 2021

Water rats

To the bridge over the Hogsmill to inspect the fish there yesterday, in the margins of a visit to Bachmann's of Thames Ditton for a spot of their apple strüdel. The fish were present, but there was also a couple busying themselves with preparations for the reintroduction of water voles (Arvicola amphibius) to the Hogsmill. Preparations in the form of setting special boxes in the stream - aka aquatic mammal detection rafts - which would record the foot prints of any mink which might pass through - mink having been seen in the general area and mink being rather keen on water voles for their lunch. If mink were found, the idea then was to trap them and release them somewhere vole-free. All part of the project celebrated at reference 1.

BH got credit for remembering that Kenneth Grahame's famous water rat - Ratty to his friends - was actually a water vole. There are a number of other animals which are properly called water rats and then there are the regular rats, black or brown, genus Rattus. Quite different again are the luvvies banded together in the Grand Order of Water Rats, to be found at reference 3.

PS 1: strüdel very good. taken with our afternoon tea, a change from the sort of cakes involving chocolate and/or cream which we more usually buy from Bachmann's.

PS 2: not altogether convinced of the merits of trying to turn the clock back for animals past their sell-by date, for one reason or another. Not keen on large carnivores at all and not sure about beavers. But water voles are inoffensive enough. Not like the rather larger copyus which got people in East Anglia in a lather when I was young. Not to mention their fishy friends, the zanders. From where I associate to a previous wonder about why it is that we don't farm elephants for their ivory - given that we farm plenty of cows for their meat.

Reference 1: https://www.citizenzoo.org/our-work/water-voles/. Rafts visible towards the end.

Reference 2: The Wind in the Willows - Kenneth Grahame - 1908.

Reference 3: http://www.gowr.net/.

Clarissa complete

This afternoon, I completed my first reading of Clarissa, it having taken a little under four months, a little under 120 days to consume the 1,500 pages of the Penguin edition. An average of twelve and half pages a day, significant at P>0.01.

Or to be more precise, mostly the Penguin edition, with a spell on the Kindle at the end of June, followed by reversion to Penguin on the Isle of Wight and then a rather longer spell with the Everyman edition for the rest of July. Just reverting to the Penguin on the last day, today, for the author's postscript, missing from the Everyman, which made up by having a rather longer version of Belford's conclusion preceding. Indeed, there were a number of differences between the two versions. Perhaps not surprising if we think of the of long streams of changes made in proof by the writers of other long books, such as Joyce and Proust. There is no definitive version.

Rather fuller notice will follow in due course, but suffice it to say for the present, that this is a very good book, still very readable despite its 250 or more years. Fully deserves its accolade as one of the treasures of English literature. The book might be long, the sentences might sometimes be a bit long, but the language is accessible and the plot grips - despite, by modern standards, there not seeming to be very much of it.

PS: I wonder how many women's rights people make use of it. They certainly could.

Reference 1: https://psmv4.blogspot.com/2021/04/clarissa.html. The Penguin edition.

Reference 2: https://psmv4.blogspot.com/2021/06/the-hunt-for-two-seas.html. The Kindle edition.

Reference 3: https://psmv4.blogspot.com/2021/07/clarissa.html. The Everyman edition.

Epsom library

This morning an email arrived from Epsom Library arrived telling me all about their new improved computer systems which they will be installing during August.

They will stop doing things like reminders by post and I get the impression that the library will not be a very friendly place for people who do not like computers - or supermarket-style checkout machinery.

They will be becoming part of something called the Libraries Consortium which already includes a lot of London Boroughs and appears to be run by computers operated by the Overdrive Corporation of Ohio. As far as I can make out the core business of this last is distribution of ebooks, not bricks and mortar books at all.

One wonders whether librarians these days have computer qualifications rather than old fashioned librarian qualifications, from the days when librarians might be expected to know all about books. A cursory investigation did not reveal much beyond the fact that a British School of Librarianship was founded in 1919 and subsequently subsumed by the Department of Information Studies of University College London. A rebranding which was echoed in the similar rebranding of the Treasury & Cabinet Office library in GOGGS during my time there, at about the time they sold off all their old books. While the once stuffy looking 'Journal of Documentation', once published by Aslib (founded as the Association of Special Libraries and Information Bureaux), has been gobbled up by Emerald Group Publishing. While CILIP - maybe the Chartered Institute for Library and Information Professionals - seems to have taken on the leadership role. See reference 6.

All that said, I do not use Epsom library very often, but the service is very good when I do. And I fully expect that, certainly as far as I am concerned, it will get better.

Reference 1: https://en.wikipedia.org/wiki/OverDrive,_Inc

Reference 2: https://www.overdrive.com/. The OverDrive HQ.

Reference 3: https://tlc.overdrive.com/. The Libraries Consortium.

Reference 4: https://www.ucl.ac.uk/information-studies.

Reference 5: https://www.emeraldgrouppublishing.com/. 'We’re a vibrant business full of energy and passion about making research count. Going beyond the bounds of a traditional publisher, we want to be a facilitator of impact, encouraging equitable, healthy and sustainable research and publishing for all'.

Reference 6: https://www.cilip.org.uk/.

Thursday, 29 July 2021

Platform library

A fine haul at the Raynes Park platform library today, in the margins of an expedition to be noticed in due course.

Clockwise from top right, we start with a reading copy of 'Anna Karenina', in a translation by the wife of the chap noticed at reference 1. My parents' copy was retired some time ago but I have been reminded by Clarissa of the merits of books with pages made of paper.

Next up, a novel by Pearl S. Buck, a name I remember because I inherited a book of hers called 'Good Earth' from my parents. I think I read it once, although I cannot now remember what it was about and I am fairly sure I have not owned if for a good few years now.

Refreshing my memory at reference 2, I learn that she had a complicated life, a fair bit of it in China and produced a large number of novels, with the 'Good Earth' being an early one, one which may have got her the Nobel Prize. Maybe I will now read this novel.

Next up, four romances from Elinor Glyn, a rather battered book from George Newnes of Southampton Street, near the Strand, possibly published in 1916. One of these M&B type romances, 'Three Weeks', I already own, a chance purchase from a table outside the lifeboat station at Bembridge, on the Isle of Wight, recently mentioned at reference 5. On the strength of which I bought a biography of the lady by one Joan Hardwick, it turning out that she was rather a strange bird. Good at working her way , not to say worming her way, into the lives of her potential subjects. Both these books still have a prominent place in the study in which I type, although neither has been opened for some years now. The fourth of the present romances is printed in two column format, perhaps lifted on the cheap from the type set up for a magazine, 1916 being well before the electronic era. Not something I have seen in a book before.

I had been meaning to notice Glyn for some time, but never got beyond a glancing mention at reference 3 and an entirely casual mention at reference 4. Maybe I am prompted to do better.

While last and not least we have a book of more or less salacious sketches of statues - high end seaside poster humour - the sort of thing which some middle aged men of my parents' generation used to titter over - by one George Molnar, not to be confused with the chap at reference 6. Probably not the chap at reference 7 either. But the book is well known to Bing and is available from places like eBay for a tenner or so. Published, as it happens, in 1954 by Phoenix House Ltd, of William IV street. The place that houses the wine house Terroirs, often mentioned in these pages.

Reference 8 looks more promising, but more digging is indicated.

PS 1: dead end. It seems that the statue Molnar was a Catholic who emigrated from Nagyvárad in Hungary to Australia in 1939. While the philosopher Molnar was the son of one Imre (Hungarian for Jim) Molnar who abandoned his middle class, Jewish family in Budapest for a new life with his secretary in Australia in 1939. The son he left behind somehow survived the war and made it to Australia in 1951, where he became the philosopher. I can only suppose that Molnar is a fairly common name among Hungarians.

PS 2: the following morning, still nibbling away. Nagyvárad appears to be the name of a tube station in Budapest, a little way out of the centre, say Clapham in London speak. The name of various streets in other places in Hungary. The former name of a city now called Oradea, in Romania, just over the border from (eastern) Hungary. In the past a very mixed city, part of the Austro-Hungarian empire, but which wound up in Romania after the second world war. A bit like the Breslau I notice from time to time, mosst recently at reference 11. Maybe it was all the chopping and changing which propelled the statue Molnar to Australia. Maybe all the street names are there to remind Hungarians of how it ought to be.

Reference 1: https://psmv3.blogspot.com/2018/01/midwife.html.

Reference 2: https://en.wikipedia.org/wiki/Pearl_S._Buck.

Reference 3: http://psmv3.blogspot.com/2016/08/guelph.html.

Reference 4: http://psmv4.blogspot.com/2020/03/the-case-of-literary-genre.html.

Reference 5: https://psmv4.blogspot.com/2021/07/up-lifeboat.html.

Reference 6: https://www.georgemolnar.com/.

Reference 7: https://en.wikipedia.org/wiki/George_Molnar_(philosopher).

Reference 8: https://www.original-political-cartoon.com/cartoon-gallery/artists/molnar-george-1910-1998/.

Reference 9: https://en.wikipedia.org/wiki/George_Molnar. A rather basic entry.

Reference 10: https://en.wikipedia.org/wiki/Oradea.

Reference 11: https://psmv4.blogspot.com/2021/06/breslau-drain-covers.html.

Showing off

Towards the end of the nineteenth century there was an epidemic of clock towers, and every self-respecting London borough had to have one. We even have one here in Epsom. Heritage now, but plenty of people were cross about it when it was going up. Vulgar monstrosity. Although there was the excuse that at that time there were plenty of otherwise decent people who could not afford their own watches.

Towards the end of the twentieth century it was the turn of the memorialists, and every self-respecting organisation had to put something up. Preferably some loud and ugly bit of sculpture, but at the very least a tablet fixed to some inoffensive wall.

While now, at the start of the twenty first century, the performance & conceptual artists seem to have got a good grip on the very important people who dish out (mostly) less important people's money on ridiculous art works. Hopefully they get their money's worth in the form of invitations to edgy parties in the metropolis. Perhaps it helps that our very own Dame Trace (of reference 2) has been made a Professor of Drawing - of all things - at the Royal Academy. Maybe the Prince Regent, who might have appreciated her stunts, was once their patron.

However that may be, in the present case it seems that people worried about the declining standing of Oxford Street in the world of retail thought that a visitor attraction was what was needed. And fell for the people at reference 1. Conceptual foreigners. Didn't the Oxford Street people know that we can build this sort of stuff at home? That is to say two million pounds worth of parched trees and grass perched on a sort of green mound, draped over a framework of scaffolding.

They have a smaller version at Wisley, looking equally parched last time we were there. Maybe the two million pounds should have been given to Wisley to help them bring their mound up to scratch?

PS: to be fair to MVDRV, some of the work showcased on their website below does look quite interesting.

Reference 1: https://mvrdv.nl/.

Reference 2: https://pumpkinstrokemarrow.blogspot.com/search?q=dame+trace.You get even more if you take the dame out of the trace.

Wednesday, 28 July 2021

Yarbridge two

The lunchtime outing to the Yarbridge Inn noticed at reference 1 having been deemed a success, we went back a couple of days later. But rather than taking a morning walk in the woods, we went down to Yaverland, not least to buy two of the excellent rock cakes to be found there to consumption at tea time.

Then down to the beach where it was hot but breezy, and we headed towards the red cliff, although we did not make it all the way on this occasion.

I thought about taking this brick home, but BH was not keen on being seeing walking around with such a thing so I left it. Also true that, while in one piece, the brick was a bit battered. Presumably not made on the island.

I learn from reference 2 that 'Phorpres' is not the name of some subsidiary of the London Brick Company, rather a brand name reflecting the fact that this particular sort of brick is pressed no less than four times in the course of its manufacture. Why one should want to do that I have yet to work out. While I wonder this morning whether to collect bricks or to collect drain covers would be best for the year to come. With a couple of drain covers to be found at reference 4. Plenty more where they came from.

As well as the brick, there were also a variety of cute small children, some of them quite possibly new to beaches, but very pleased with their new find.

And so home and onto to the Inn, where I settled for the same crab salad as I had had previously, while BH went for salmon for a change. We were both well pleased with our choices. Noting in passing, that while the bread rolls on the first occasion had been warmed up from the freezer, this time around I had a couple of chunks of brown tin loaf warmed in the microwave. Bread clearly not the subject of the same loving attention as the crabs and fish.

I have already noticed the fake flowers. This time we had rather contrived wallpaper and a sturdy iron door, which might have been an old oven but was actually a small safe, installed at a time when this part of the building served as the town post office. Which may be connected with the fact that the place is not marked 'PH' by Ordnance Survey. Although checking back this morning, none of the houses in the town are so marked. Perhaps they only do that in real villages.

A lot of houses, in this era of celebrity chefs and television cooking programmes, find it necessary to load up one's meal with elaborate trails of brown goo of one sort or another, sweet, savoury or sour. A trap they avoided here by having the brown goo spotted onto the plates in the form of glaze, fired into the plate. Much better.

I varied my meal to the extent of taking a pink sorbet for dessert rather than chocolate brownie, while BH took ice cream. We wondered inconclusively about the recipe for sorbet, which did not look that much different from ice cream. Checking this morning, I find the difference is the omission of any form of milk: just raspberries (say), sugar, water and a dash of lemon - much the same as jam. Perhaps the looking so like ice cream is the result of whisking it up after it has been more or less frozen.

For the second half of our meal we had a young and pretty waitress, content to work on the island without aspirations to break out onto the big island. But she did say that she had found all the lockdowns rather trying. Talkative in the way of waitresses in New York State, where they seem to think that they have to talk a tip out of you, although I don't think that was the idea here at all. She was just being friendly. There being a passing allusion to such waitresses at reference 5.

Another excellent meal. We will be back next year.

PS: but not so excellent that we did not take tea and rock cakes a few hours later.

Reference 1: http://psmv4.blogspot.com/2021/07/yarbridge-one.html.

Reference 2: http://www.solwaypast.co.uk/index.php/14-brick.

Reference 3: http://www.solwaypast.co.uk/. A chap who clearly knows his bricks; a chap after mine own heart.

Reference 4: https://psmv4.blogspot.com/2021/07/no34-continued-with-drains.html.

Reference 5: https://psmv2.blogspot.com/2014/11/watertown-bars.html.

Teach myself all about fMRI

Contents

  • Introduction
  • My story
  • The machinery
  • The signal
  • The data
  • The process
  • Other matters one
  • Other matters two
  • Conclusions

Introduction

The paper at reference 1 appears to be homing in on an area well inside the brain, the anterior insular cortex, as being key to consciousness, this last being something in which I have taken an interest. Turn this area off and while plenty of stuff might be going on in the brain, it won’t make it upstream to consciousness. But some way into the paper, which is built on a sophisticated analysis of fMRI images, I decided that I did not know enough about fMRI – functional magnetic resonance imaging – technology which has been around for around twenty years now – to understand what was being suggested. So I embarked on a spot of Bing-enabled teach yourself.

For once, I did not find the Wikipedia article (reference 2) particularly helpful: it wasn’t pitched at the right place for me. But then I got to references 3 (9 pages) and 4 (27 pages), both a little long in the tooth now, but open access and both helpful. And being long in the tooth was hopefully not a problem for me; hopefully the basics that I wanted to get a grip on are not changing that fast. After all, the underlying physics is not changing. So the short story followed of reference 4 followed by the long story of reference 5. But first, what is it all for?

Figure 1

While fMRI with the ‘functional’ might be mostly about brains, MRI more generally can be used to image any part of a body, human or otherwise, as in the figure above, an image of a knee and the anterior cruciate ligament (ACL), apt to be unpleasantly damaged by high performance athletes.

While the functional bit might be taken here as being about taking pictures of a brain at work, rather than as a static structure – and fMRI can do just that: it can show us what bits of the brain are involved in what sort of brain work. And it can do that with a live person in a reasonably non-intrusive way. At least it doesn’t (usually) involve drinking beakers of odd tasting fluids, sticking anything in or opening the head up – although I did come across some concerns about transient side effects of the very large electrical and magnetic fields involved.

Figure 2

The image above shows regions of the brain activated during a sentence completion task from the library of science photos at reference 18, turned up for me by Bing. Very much the sort of thing that crops up all the time in computational neuroscience.

Figure 3

While this third image is a rather more heavily processed set of images, the sort of thing that cropped up towards the end of reference 16. But is actually one of the supplementary figures at reference 1, my starting point.

My story

MRI and fMRI is a big scientific and medical success story. It is used all over and it is either the subject or the vehicle of what must be a huge number of scientific papers. I dare say both the machines and the work they are put to are coming on by leaps and bounds. But as I read somewhere in the course of all this, in trying to write explanatory material, it is hard to strike the right balance between being elementary and being far too deep for the non-specialist. It is a complicated jigsaw as well as being a moving target and it is hard to make it into popular science. References 3 and 4 notwithstanding, I did not find a story which really satisfied me, which was pitched at the right level for me.

With the result that the whole business has soaked up a good deal of time as I brushed up on my sketchy knowledge of all the science, statistics and mathematics which has gone into MRI and fMRI. As I attempted to work my way through a digestible portion of the huge amount of tutorial material available on the Internet, for some of which you are invited to pay. See, for example, reference 8. For which you are not invited to pay.

At the end of all this, mainly to test my own understanding, I have attempted my own summary, which now follows. A summary of what seems important to me, another short story. Not very sure what the target audience might be, but I do associate to FIL, who on reading a pamphlet I had given him about organising for mental health, an industry of which he was very much part at the time, remarked that it was a fine summary for those who already knew. And I dare say that traditional civil service minutes of my day about things that were complicated, by way of cunning compression of a lot of tricky detail into a very small number of words, sometimes fell into something of the same trap. But nonetheless, something to aim for.

Figure 4

Lifted from reference 3.

Figure 5

Lifted from reference 4.

Maybe the first point to make is that both brains and fMRI data contain a great deal of noise, illustrated first by a simple graphic from reference 3, second by a more complicated graphic from reference 4. With the latter showing how much noise is left after fitting the model (black line) to the signal (grey line). In which circumstances, one clearly needs to have a care not to erect elaborate castles in the air, to erect castles on feeble foundations. Serious statistical input is essential – with reference 4 being something by way of a job creation scheme for statisticians.

The machinery

Figure 6

Scanners are room-filling pieces of machinery on which you might make a capital spend of the order of £500,000. Then there are the running costs.

Scanners use a lot of energy, perhaps 25KWH for a head scan, with consumption peaking at 75KW. Over time, supercooling the magnets accounts for getting on for half the total, I think additional to the figures just given. Reference 6 suggests that energy planning is not taken as seriously as it might be.

Machinery which one might think was potentially dangerous to the subject given the huge magnetic fields being generated, but the people concerned appear to have satisfied themselves that exposing a brain to these sorts of fields is safe, be they resonating ever so fast. Machinery which one might think was potentially dangerous in a more general, H&S sort of way, given the huge magnetic fields being generated, given the use of liquid helium to cool the magnets and the amount of electricity needed. Do they ever catch fire?

There are five main components. The biggest, outer ring is the magnets generating the huge static field, measured in something called Teslas (for a Serbian-American engineer), perhaps as many as 10 of them, running through the middle of the white doughnut in what is called the z direction. Then something called the shims which smooth out that generated field. Then a middle ring for the three sets of coils – one set for each of the usual x, y and z directions – generating the rather smaller gradient fields – fields which change very fast during a scan – gradients which provide the spatial information needed to build an image. Then an inner ring for the coils transmitting and receiving radio frequency (RF) bursts of energy, otherwise the transceiver. And, fifth and last, the computers and software needed to drive all this.

The resonance in question is the oscillation of the magnetic fields generated by disturbing the spin state of polarised protons and neutrons in the nuclei of atoms of living tissue, for these purposes nearly always the protons in the hydrogen atoms in the head of the subject. You also get a lot of them in water. The frequency of these oscillations is a function of the element – hydrogen in this case – and the size of the external magnetic field; perhaps 50 or 100MHz in VHF radio-speak. It might also be thought of the frequency of rotation, of the spin of the nuclei in question. While the N for nuclear got dropped from NMRI as it put people off.

So, in short, you put a pulse of RF energy from the transceiver into the sample, disturbing the spins away from their equilibrium values. These disturbed spins then relax back to the low energy equilibrium state, giving out RF energy, putting energy back into the transceiver, as they go. 

This relaxation might take place in tens of milliseconds, or hundreds, depending how you look at it. And the speed of relaxation depends, inter alia, on the tissue in question. Part of this is the amount of oxygen in the blood, a popular proxy for neural activity, from which we get BOLD for blood oxygen level dependent, an acronym which crops up everywhere. A popular proxy despite the fact that the blood oxygen response is rather blurred in both space and time, making resolution below millimetres and seconds difficult.

Figure 7

Discussion is often framed in terms of T1 relaxation, T2 relaxation and T2* relaxation. The snap above, taken from reference 3b, gives some idea of the (millisecond) values of the first two of these for a range of field strengths then available. With the headline being that T1 relaxation is a lot slower than T2 relaxation, which makes it possible to focus on one rather than the other.

It is the big static field which polarises these protons in the first place; the RF pulses which excite those protons from that equilibrium polarisation; and, the gradient fields which translate position inside the scanner to the frequency of the decay resonance of the excited protons. Note that the frequency of the decaying signal is a function of the field at the time the signal is sampled, not the field at the time that the protons were excited in the first place. With the former field changing very rapidly during that decay.

It is all these very fast changes to the gradient fields which make the (considerable amount of) audible noise which subjects of both fMRI and MRI complain of, particularly when heads are involved.

The signal

The object of all this machinery is a interesting map of signal across the brain. And to be interesting, there has to be contrast, there have to be systematic and significant differences in the signal between one place in the brain and another. The grey scale of the Figure 1 we started with.

Figure 8

The above being a block diagram version of the more usual pulse sequence diagram reproduced below, from Wikipedia. As it happens, for a spin echo type of pulse sequence.

Glossing, we need a big enough sample of the signal in frequency space, often called K-space, in order to be able to map, by means of an inverse Fourier transform, that sample into the regular space we can look at in the ordinary way.

Figure 9

These pulse sequence diagrams are widely used and there are a number of different varieties, but the plan is always much the same: the time course of various activities, five of them in the diagram above. Activities on the vertical y axis and time on the horizontal x axis. The top line is the exciting RF pulses, with the shape of these pulses being that of the sinc function, that is to say sine(x)/x. The middle three lines are the activities of the three gradient magnets: z for through the middle of the doughnut, x and y for the orthogonal plane. In the simple case a value of z corresponds to a slice of the recumbent brain, selected by resonant frequency by the z gradient. The bottom line is the sampling of the RF signal from the decaying resonance.

PE is the phase encoding applied to the y-axis, FE is the frequency encoding applied to the x-axis. Have yet to work out what SS stands for, but the second one is the spin inverting pulse which generates the spin echo, for which see below.

Scanners often come with a portfolio of pulse sequences from their manufacturers. A popular one from Siemens is called FLASH – flash for ‘fast imaging using low angle shot’.

Remembering that the object is to produce an image of the brain every so many seconds (functional) or minutes (structural), an image expressed as a value for every voxel. With the two sorts of image using different contrasts and yielding different resolutions.

This value is sometimes called intensity, otherwise local spin density, and if figures 4 and 5 are anything to go by, is of the order of 10,000.

The data

It is convenient to present the end point at this point, that is to say the images that emerges from the scanning process – which process will be covered in the section following.

Figure 10

So we have an experiment to explore something or other brainy, with the main business being fMRI scans of the brains of a number of subjects, usually while they are doing some set, time delimited, repetitive task; often arranged in blocks. Perhaps 25 or so subjects, perhaps a lot more. Noting that a huge amount of fMRI data is freely available online these days, so sometimes you don’t even have to bother with your own experiment.

A complete scan of a head is called a volume and might take a few seconds to complete. In course of any one experiment any one subject might be scanned 100 times or more over a period of a quarter of an hour or so, the idea being to see what changes as the subject’s activities change – mostly mental rather than physical activities as the subject is inside the scanner for the duration – which some find claustrophobic and there is a panic button. These functional volumes about brain activity will be supplemented by a rather more detailed structural scan of brain anatomy. This takes rather longer. So maybe more than 2,000 volumes in all, for the whole experiment.

Each volume is organised as a number of slices, rather in the way that a lump of bacon used to be fed through a bacon slicer. Each slice is organised as a two dimensional array of voxels, which might be as small as a cubic millimetre.

Remembering that while the discussion here is rather space orientated, we can also think in terms of a time series for each voxel, and we might be as interested in variation in time as in variation in space, in particular in the correlation between the two.

In order to compare one scan with another and one subject with another, scans are mapped onto a reference head, examples of which are to be found at reference 5. A mapping which is disturbed to the extent that one subject’s brain is different from another subject’s. Further disturbance might result from mapping the three dimensions of the reference head onto the two dimensional plane, for ease of visualisation. The sort of thing noticed at reference 16.

Remembering in all this that a voxel contains a lot of neurons, tens of thousands at least and usually a lot more. Mechanical neurons in these sorts of numbers can do a great deal of work, and it reasonable to suppose that real ones can too. We might have a lot of voxels, but they are giving us the macro view, not the micro view.

The registered images from a session with a subject, perhaps an array of real values, that is to say numbers like 26.09 and 484.63, for 100,000 voxels in space by 100 points in time, are quite a good break point. Images which can readily be converted to grey scale images on a computer screen. To the extent that those images work, that they tell us something interesting (and true) about the workings of the brain, we may not interest ourselves in all the science and all the work which generated those images. 

The process

Figure 11

Lifted from reference 4.

As noted above, the end product of an fMRI scanning session is usually a large matrix of real valued numbers, perhaps 100 times by 100,000 voxels worth of them, so a lot of data – quite intractable without modern computing machinery. Data analysis is working out whether there is something interesting to say about that data. Has the experiment identified regions (localising brain activity in the figure above) or networks (connectivity in the figure above) in the brain of particular interest?

But quite a lot has to be done to get to that point, starting with capturing the data from the scanner. Getting all that right was a challenge in itself, certainly in the early days. More mature technology now.

Next comes building the image, that is to say one value (of something) for each voxel.

Figure 12

Lifted from reference 4.

Perhaps the place to start is the fact that the resonant frequency, the frequency of the radiation produced by these disturbed nuclei, is proportional to the strength of the ambient magnetic field. In brief, by putting suitable gradients on that magnetic field we can extract information about position from information about frequency collected by the RF transceiver and then convert than information about position into images. One such gradient, the z gradient, runs through the hole in the middle of the doughnut.

Slightly less briefly, the brain is usually nose up in the hole in the middle of the scanner. An often vertical slice across that brain (from ear to ear, as it were) is selected by adjusting the frequency of the exciting RF pulse from the RF transceiver, which has to be near the resonant frequency of the target nuclei to work. The decay of that excitation results in a signal which can be picked up by the RF coils. That signal is a function, inter alia, of the x gradient and the y gradient, otherwise the two dimensional k-space. The signal is then sampled for a sequence of k-space values which span that space. An inverse Fourier transform is applied to yield a sequence of values which span the slice, a value for every voxel, in other words an image of that slice. The scanner then moves onto the next slice and eventually you have a three dimensional image of the brain, including here the interior. All this being another rather glib gloss on a rather complicated story. But it is worth adding that there is a trade off between the number of sample points, that is to say the resolution of the image, and the time taken to produce the image.

Pre-processing

Next comes the pre-processing phase, which can be divided into four components. First, given that each slice is taken a different time, the data is adjusted so that all the slices making up a volume can be given the same time. The volume can then be regarded as an instantaneous snapshot. Second, corrections need to be made for head movement. Perhaps corrections for breathing. After which each low resolution functional scan is mapped onto the high resolution structural scan. And the high resolution structural scan is mapped onto whatever reference brain is being used, the brown box in the box model above. This means, some loss from the mapping process apart, all the functional scans are now coded to the same frame of reference and may be compared. Third, a bit of spatial smoothing is applied, in line with the intuition that activation of one voxel is likely to be influenced by the activation of neighbouring voxels.

Data analysis

We now have a set of functional images, which might be considered as a three dimensional matrix of voxel values: subject (maybe ~25) by time (maybe ~100) by voxel (maybe ~100,000), and which we wish to analyse. Maybe the form in which fMRI data is usually made available to others.

The workhorse of data analysis seems to be general linear modelling (GLM). Glossing, the user provides a ‘prior’ in the form of the time course, perhaps several hundred times, of various experimental variables or conditions, perhaps half a dozen or so of them, say a matrix of N times by M variables, and the model provides a best fit ‘posterior’ in the form of data values, one for each of K voxels, that is to say an image, plus an error for each of those K voxels. Perhaps, by way of an example, an image of regions of the brain which have been deactivated by thinking about fish and chips. With the experiment being, for each subject, a twenty minute random sequence of 20 seconds blocks of thinking about fish and chips, squeezing a small rubber ball in the right hand and rest.

Note that in this example we have lost time. All we get out at the bottom is an image. With Figure 2 being a slice from such an image. But a manufactured image, at some considerable distance from the image from a tissue slide taken through an optical microscope with a Box Brownie.

Data analysis includes the tricky business of deciding when an interesting looking image is significant. That one is not looking at some chance result or some artefact of the complex systems which have been deployed to produce it.

Other matters one

Various topics turned up along the way, most of which a proper statistician (that is to say, not me) might be expected to know about.

Echoes

Figure 13

The caption to the original of the snap a above reads: ‘A single RF pulse generates a free induction decay (FID), but two successive RF pulses produce a spin echo (SE).  The time between the middle of the first RF pulse and the peak of the spin echo is called the echo time (TE)’.

One might use the term ‘echo’ a little loosely to cover the whole of the RF output response (yellow in the example above) to the RF input pulse (blue). But there is also a rather special meaning, derived from the spin echo discovered by Erwin Hahn, more than seventy years ago. I rather struggled with what this was, but eventually I turned up reference 7 which put me on the right track.

Gradient echoes and spin echoes are important in technical treatments of fMRI. They crop up in the methods sections of papers depending on or about fMRI.

Balloon models

One of the alternatives to GLM is one of the balloon models, in which blood flow in cerebral blood vessels is modelled, rather than just summarised in a linear model. Balloon comes from the tendency of some blood vessels to swell and shrink back, rather in the way of an elastic balloon, in the course of the heart’s pumping cycle.

Not linear and admirably general, but with plenty of problems of its own.

Markov random fields and Gaussian random fields

One of the ways to look large arrays of (say) two dimensional statistics is to generalise the idea of a Markov chain – where the probability of the nth member of the chain taking any particular value depends only on the value of the (n-1)th member – to two dimensions. Whereby the probability distribution of the value of a cell in a two dimensional array depends only on the values taken by neighbouring cells.

Much work has been done on this, drawing on prior work in statistical physics and agricultural plot trials. Including something called the Hammersley-Clifford  theorem.

Gibbs sampling

It has been shown, that under various assumptions, that if you know the probability of a vector x given a vector y and the probability of that same vector y given the vector x, that it is possible to extract the probability of x. Or, put another way, if you know the conditionals you can get the marginals. Gibbs sampling is an iterative procedure for getting those marginals, by way of a suitably large number of sample points from that marginal distribution.

Random number generators

It seems that one of the workhorses of statistical computing is the random number generator, something that will generate random numbers uniformly distributed between zero and one; the sulphuric acid, as it were, of said statistical computing. I once made quite a lot of use of the ‘Rnd’ function supplied by Microsoft’s Excel and was never able to detect any irregularities. But how can you be sure? Especially if you are using the function on an industrial scale, generating millions of random numbers?

Figure 14

By way of an elementary experiment I gave Excel another go. Which looked well enough.

Figure 15

But not so well when one changes the scale, the one immediately above being that selected by default, by Microsoft. Which serves to remind one that care with presentation is essential.

Figure 16

Despite appearances, things are getting better. Ten times the number of numbers, but the range of the bin counts has stayed at not much more than 1,000.

Other matters two

It seems that reference 9a, a poster for a paper about doing fMRI on a dead salmon, did much to highlight the poor quality of the statistical work going into a lot of real fMRI papers at that time, around ten years ago. The paper itself, reference 9b is not open access so not yet looked at, but it does seem that things have got a lot better since.

Scare stories about sloppy statistics more generally pop up from time to time, not all fuelled by the explosion of work on fMRI. For example references 10-13. While I worry about the amount of statistical knowledge needed to do brain or psychology flavoured research. Worries which surfaced at references 14 and 15.

The good news is the amount of information about almost anything that can be dug up from the Internet. With the fMRI learning resources from Canada at reference 8 being a good example.

Conclusions

It seems that all self respecting teams working with fMRI need to include a statistician with appropriate expertise and experience. Or at the very least have access to one such. And, more tricky, even the lowly reader of reports from these teams needs such knowledge or access.

In which connection, I imagine the increasing availability of well-packaged computer software is something of a mixed blessing. Such software might hide a lot of unpleasant statistics away, out of sight – but out of sight is out of mind – which last might well be the source of much error.

Nevertheless, I now feel I now know enough about fMRI to go back again to my starting point at reference 1.

Figure 17

PS: my copy of the book at reference 3b, started life in the library of St. Thomas’ Hospital, apparently part of Kings College, and was then sold to me in aid of the Rainbow Centre in southwest Sri Lanka. The snap above being taken after a storm there in November, 2017.

References

Reference 1: Anterior insula regulates brain network transitions that gate conscious access - Zirui Huang, Vijay Tarnal, Phillip E. Vlisides, Ellen L. Janke, Amy M. McKinney, Paul Picton, George A. Mashour, Anthony G. Hudetz – 2021.

Reference 2a: https://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging

Reference 2b: https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance

Reference 3a: Overview of fMRI analysis – S M Smith – 2004. 9 pages. Smith is Professor of Biomedical Engineering at the Wellcome Centre for Integrative Neuroimaging at Oxford. 

Reference 3b: ‘Functional MRI: an introduction to methods – Jezzard P, Matthews P, Smith S, editors – 2001’ – which appears to be something of a standard text. It includes prior publication of reference 3a.

Reference 4: The Statistical Analysis of fMRI Data - Martin A. Lindquist – 2008. 26 pages. Lindquist is a professor at the Bloomberg School of Public Health, at John Hopkins, at Baltimore, Maryland.

Reference 5: http://nist.mni.mcgill.ca/?s=Stereotaxic+Registration+Model

Reference 6: The Energy Consumption of Radiology: Energy - and Cost-saving Opportunities for CT and MRI Operation – Tobias Heye, Roland Knoer,  Thomas Wehrle,  Daniel Mangold, Alessandro Cerminara, Michael Loser, Martin Plumeyer, Markus Degen, Rahel Lüthy, Dominique Brodbeck, Elmar Merkle – 2020.

Reference 7: Atomic memory: atomic systems that have decayed from some ordered states can be induced to recover their initial order. The degree to which order is restored allows investigation of interactions difficult to observe – Richard G. Brewer, Erwin L. Hahn – 1984. 

Reference 8a: http://www.fmri4newbies.com/. Part 1. A learning resource from Western University, London, Ontario, for which see reference 13.

Reference 8b: http://www.newbi4fmri.com/. Part 2.

Reference 8c: https://www.uwo.ca/. Western University.

Reference 9a: Neural correlates of interspecies perspective taking in the post-mortem Atlantic salmon: An argument for multiple comparison correction (open access poster) – Bennett, Baird, Miller, Wolford – 2009.

Reference 9b: Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: an argument for multiple comparisons correction (paywalled paper) – C M Bennett, M B Miller, G L Wolford – 2009. 

Reference 10: The Salmon of Doubt: Six Months of Methodological Controversy within Social Neuroscience - Daniel S. Margulies – 2011.

Reference 11: P  > .05: The incorrect interpretation of “not significant” results is a significant problem – Richard J. Smith – 2020. Paywalled.

Reference 12: Why Most Published Research Findings Are False – John P. A. Ioannidis – 2005.

Reference 13: http://psmv2.blogspot.com/2016/01/voodoo-time.html. One of my own contributions. Mostly about fMRI as it happens. 

Reference 14: https://psmv4.blogspot.com/2019/06/hard-for-me-to-know.html

Reference 15: https://psmv4.blogspot.com/2019/06/more-hard-for-me-to-know.html.   

Reference 16: https://psmv4.blogspot.com/2018/11/places-in-brains.html

Reference 17: https://www.sciencephoto.com/. The source of Figure 2.

Reference 18: http://mriquestions.com/spin-echo1.html. The source of Figure 13.

Reference 19: https://1drv.ms/b/s!AvPvDT7vzzpQhuMXVdkxwlJ75OI30w?e=Tb4Cll. A publicity brochure for what I assume is a modern scanner from Seimens. Not much liquid helium at all. Also an experiment with OneDrive sharing.

Microscopes

I had been intrigued in the course of my visit to the optician, noticed at reference 1, by there being two or three regular microscopes in among all the fancy equipment. Used, according to the optician for looking at lenses, rather than at preparation of eye.

Then today, having been summoned to pay a visit to the eye people at St. Helier hospital, I got to examine a bit of the fancy equipment at greater length, very similar if not identical to the one in the optician. And it turned out to be another sort of microscope, probably something called the 700GL slit lamp microscope from Takagi. Not available from Amazon, but eBay offer microscopes from India, which look much the same, costing between £1,000 and £2,000. Rather less than I had been expecting.

The doctor also made use of something which seemed rather like the oil immersion objective which came with my father's microscope. With the difference that instead of being screwed into the objective tube and then would down into oily contact with the slide's glass slip cover, after anointing it with oil, he sort of stuck the thing onto the eye in some way.

Lots of bright lights, but no present cause for alarm.

PS 1: it seems that it is not worth wiring the thing into a computer so that snaps of the backs of eyes can be saved for the record, for posterity. 

PS 2: 16:30: after having been warned about it for several days, we have finished the first tropical cloudburst and are now well into the second. Maybe fifteen minutes altogether so far.

Reference 1: http://psmv4.blogspot.com/2021/07/trolley-424.html.


Reference 3: https://www.leightons.co.uk/. The optician, formerly Lingwood Strong.

Tuesday, 27 July 2021

Yarbridge one

The Yarbridge Inn has been there all the time we have been coming to Brading, but for one reason or another we never paid it a visit. We did try on one occasion, without booking, to find it full, but that was as near as we got. Whereas this year we paid it two lunchtime visits, separated by just one day. This being notice of the first visit.

Format of the day, morning up in woods behind Brading, lunch at the Inn, afternoon snoozed away with a book, quite possibly Clarissa.

So up Doctor's Lane, once a minor road, now a farm track, running along one side of a field of maize, not that you could see it at that point, there being substantial banks and hedges to both sides. Turned south onto a path running down the next side of the field, ending up in the woods, on the edge of Nunwell Down. Patches of field where the maize was not doing very well at all. The 'M' on the map, perhaps for maize, marking the corner of the field. Nunwell House used to be the seat of the Oglanders, the founder of which line was a companion of the Conqueror. Having sat there for hundreds of years, they sold out to the rather less illustrious, but still county and/or army family who have it now.

Quite a lot of the stuff on the right, which I guessed to be field maple, Acer campestre. Checking this evening, Wikipedia offers a wide variety of leaves, including the one on the left, which looks near enough. So I think it was a good guess. Not a tree I remember coming across in Surrey, although I dare say it is there.

Quite a lot of hollows and holes, some large, probably mostly places where chalk was dug out to build the cheaper houses and walls in the town below - a town which might be village sized now, but is also an ancient town, once fairly important. One of the hollows contains a memorial to Camilla Peterson, a Danish student, murdered there in 2013.

Having seen a couple of pyramid orchids in the woods, the unmown portions of the recreational field above the Mall seemed to be full of them. Noticed in the very same place, in rather smaller numbers, just about two years ago. See reference 4.

Heard one buzzard in the woods. Saw another over the town, being buzzed by a seagull. Perhaps the seagull had a nest in the vicinity.

Back to the house for a wash and brush up, then back out to the Yarbridge Inn. Noticing on the way this handsome red brick house. Looking to date from the time when you might use chalk and low grade limestone down below, but you had brick where it showed.

At the Inn, we elected for inside. It was not crowded and outside had the potential to be either or both of sunny or windy. Then we both went for the crab salad, which turned out to be really excellent. And not just because of the Chablis from a real vineyard that came with it - for which see reference 5. This wine looks to be their everyday brand, with some much fancier looking wines a bit further down the list. At the end of which we find a very fancy look marc, described as 'hors d'âge', which judging from Linguee (my favourite online dictionary for French) here means very old. Sadly I have never got on with the stuff, despite Maigret being rather fond of it. Simenon too, I dare say.

Extra bread, fresh from the freezer, via the microwave, not so clever. But it served.

A strong line in fake flowers above where we were sitting. But it seems a bit mean to clock them up in the fake series, considering what a good meal we had. So included with less fanfare here.

Note also the contraption in front of the bottle, which we used once or twice to summon the waiter, or perhaps the waitress. The first time we have gadget enhanced dining since the rather different gadget noticed a couple of years ago at Polesden Lacey. Also at reference 6. Not seen since.

Rather smoother presentation of their chocolate brownie than back at the Blenheim, although it was much the same sort of thing inside.  Served with Jameson here as, while they had a very large Bells bottle on the bar for collecting for charity, they didn't actually sell the stuff. Or Teachers, the other big brand of my youth, a time when I barely touched the stuff. Bitter man in those days. The good news was that they charge pub prices for the whisky, unlike plenty of restaurants in London.

Talking of which, we learned at some point in the day that Brading ran to ten public houses at one time. Two and a half now.

Brading being a real village, not all chocolate box. But back in West Street we met a man we had met in 2019, a man who kept a considerable number of Shih Tzu dogs, to be heard on this occasion, but not seen. But we did learn that the doctor's surgery in the Mall was no more, so in the event of my needing a warfarin test on holiday in the future, something that has happened at least a couple of times in the past, we will have the inconvenience of having to go to Ryde or Sandown. And not so clever if you are old, live in Brading and have got used to having the surgery more or less on the spot, as we have here in Epsom.

PS: the Inn is near the bottom right hand corner of the junction of the red and brown roads, just below where it says 'Yarbridge', bottom right on the map above. But it does not say 'PH'. From which we deduce that, while it is quite possibly an old building, it has not always been a public house. Perhaps it had been degraded to some other use when the men from Ordnance Survey came by with their chains.

Reference 1: https://www.theyarbridgeinn.co.uk/.

Reference 2: https://www.nunwellhouse.co.uk/.

Reference 3: https://psmv3.blogspot.com/2017/07/fragonard-fail-aka-yaverland-five.html. A previous visit to Nunwell Down. Slightly depressing how much more we managed to pack into a day, just four years ago.

Reference 4: https://psmv4.blogspot.com/2019/07/epsom-to-firestone-copse-to-brading.html.

Reference 5: https://domaine-testut.fr/.

Reference 6: https://psmv4.blogspot.com/2018/12/osberts-day.html.

Monday, 26 July 2021

Dates for our diaries

Having occasion to find notice of voodoo - there turned out to be two of them - I also turned up the Very Reverend Pastor Chris. A pastor on the Bible Belt model, but actually Nigerian.

It is good to be able report that a good, godly week is coming up - at the very least to a computer near you, if not an arena near you.

Reference 1: https://pastorchrisonline.org/upcomingevents.php.

Reference 2: http://psmv3.blogspot.com/2018/06/hot-air.html. The first coming.

More ants

More flying ants today, a little over a week since the last lot, noticed at reference 1. Two nests on the go, both more or less under the washing line, with this one being the larger disc at around nine inches across. 

At least two sorts of ant involved: large black ones with big wings and smaller brown ones. While the ants in the smaller nest seemed smaller.

The telephone didn't cope very well with all the movement, so presumably the ants were too fast for the shutter. Which I dare say I could speed up if I were to poke around - but I don't suppose I shall.

All done about five minutes later.

Reference 1: https://psmv4.blogspot.com/2021/07/flying-ant-day.html.

Trolley 424

Trolley 424 had been dumped at the entrance to the passage between the chipper (behind the trolley) and Leightons the opticians, just by some High Street bus stops, and was captured in the margins of a visit to that same Leightons. Visited because they prompted me - and, as it happened, visited to have the interior of my eyes scanned, during which scan one could see arrays of bright red, mostly horizontal lines, possibly something to do with a raster scanning process. Which was entirely appropriate as I am presently spending quality time on the mechanics of scanning the interiors of heads, otherwise fMRI.

A month since I captured the last trolley, so I no longer care to hazard a guess as to when I will hit the half millennium, once pencilled in for the autumn of last year. With this trolley being a rather weather beaten, but entirely serviceable trolley from Waitrose. It looked as if it had been out all night, so I thought it OK to return it to their stack.

PS: interested to read this morning that the once mighty Boeing is still in trouble. First the long grounding of their 737 Max, now back in the air, then last year's massive drop in the passenger carrying businesses of their customer airlines and now what look like serious production problems with their 787 Dreamliner, with deliveries flatlining on the graphic in today's FT. Will they manage to keep out of junk bond land? Are aeroplanes getting too complicated for their own good?

Reference 1: https://psmv4.blogspot.com/2021/06/trolley-423.html.

The mainly yellow corner

The mainly yellow corner looking a bit bedraggled after yesterday's rain. Of the ten potted on, the three up by the ponds, more or less in the shade, never really got going and succumbed to slugs and worms. Not sure where this last came from, with my having thought that the compost came sterile. The remaining seven are rather a mixed bag, so I clearly need a bit more practise and a bit more volume if I am to produce 5 prize winning blooms for the Stamford Green Summer Show. I think judges at such shows can get just a touch pedantic about the blooms submitted being identical, or failing that at least smoothly graded.

But they have come on since they were last snapped in the middle of June, at reference 1, during which period they had a holiday in the shade, while we were in the Isle of Wight.

The two sage plants from left might date from last Christmas, when we made sage and onion stuffing (unstuffed) to go with the festive fowl. With little pots of rooted sage being sold by Sainsbury's and Waitrose at that time of year - with the catch seeming to be that however it was that these plants were propagated and brought on for sale, they take a very long time to recover from being mowed and potted on.

Reference 1: https://psmv4.blogspot.com/2021/06/sunflowers.html.

Sunday, 25 July 2021

Shanklin

Just under a fortnight ago, in the absence of the Island Line, by bus to Shanklin, a place at which we have spent quality time over the years: town, honey pot thatch, chine and beach.

Another No.34 on the road between Lake and Shanklin. A good augury.

First stop, the new-to-us bookshop where I ran down a proper, reading copy of Clarissa, already noticed at reference 1.

Second stop, the nearby café, where we took at look at the dubious news sheet snapped at the top of this post. The sort of rubbish I thought only existed in darker corners of the Internet. The sort of rubbish which the vulnerable feed on. Nothing at reference 2 that I can see owning up to who is responsible. While the names in the snap above have all been redacted.

On the up side, for the first time for a while, the tea came in a teapot, together with a tea strainer and a purpose built bit of crockery to put the strainer in after use.

Somehow, we managed to miss the junk shops we remembered from our last visit, and wound up at the top of the chine, which we proceeded to descend. Plenty of water in their waterfall on this occasion. A decent, if not particular large specimen of carex penula.

Plenty of this stuff on the damp, shady rock faces. Probably some thing a bit primitive which does spores rather than flowers.

Took a sausage sandwich in the café half way down, where we were entertained by a lady blackbird, which seemed to have the knack of not appearing to pay any attention at all, but knew very well when a crumb (or better) appeared.

Down to the bottom, wandered along the esplanade for a bit, then up the cliff and back to the bus station. Cherries and sliced white from Morrisons, this last for the manufacture of fried egg sandwiches, not the same on brown. Although, as it turned out, a bit let down by having to use oil in a non-stick frying pan. Not the same as lard in a real frying pan at all.

Home to a spot of corned beef hash, taken with green cabbage and a spot of white. What seemed like the first bit of regular cooking for a while. Rounded out with the cherries from Morrisons, which were fine, despite being shaken up a bit on the bus home.

I must have a little too much hash, as a little while later I was trounced at Scrabble.

Reference 1: https://psmv4.blogspot.com/2021/07/clarissa.html.

Reference 2: https://thelightpaper.co.uk/.