Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Thursday, July 9, 2015

Functional MRI of trained dogs

One of the delightful aspects of running an imaging facility is the sheer variety of projects coming through the door. Late last year my boss told me he'd been discussing with a group from Emory University about doing fMRI on trained dogs at our center. I'll confess to receiving the suggestion unenthusiastically, if only because I envisioned a mass of bureaucracy followed by a head-on logistical collision between the dog group and the dozens of human users. Activity at our center oscillates between hectic and frenetic, depending on the day. But, as it turned out I needn't have worried. The bureaucracy was handled admirably by the Emory folks while the logistical issues simply failed to materialize because of the professionalism of the dog fMRI team. It's been an enjoyable experience. And there are dogs. Many boisterous, happy, playful yet exceedingly well-trained dogs. Like these:

Monday, May 18, 2015

Checklist for fMRI acquisition methods reporting in the literature: version 1.3

The latest version of the fMRI acquisition checklist is now available at The Winnower via this link. It can also be located/cited using DOI: 10.15200/winn.143191.17127 .

Updates/changes from v1.2:
  • The “Pre-scan normalization” parameter has been renamed “Signal intensity correction/normalization” to broaden its scope.
  • Reviewed and revised explanatory notes.
  • New parameters: RO partial Fourier scheme, Number of echoes, Saturation bands, Gradient non-linearity correction, Z-shim gradient correction, On-resonance adjustment.

The current list should work now for most simultaneous multislice (SMS) EPI, multi-echo EPI (or spiral) and 7 T experiments, but additional emphasis will be placed on these advanced methods in the next round. Please let me know of parameters you'd like included. The next planned update will include as far as possible the vendor-specific nomenclature for each parameter. I anticipate a late 2015 release date. There are no plans yet to do a machine-readable version of the checklist, as originally discussed, but that is only because nobody has been asking for it. Please get in touch if this is something you're interested in.

Thursday, May 14, 2015

Uploading to The Winnower from Blogger: A real time tutorial

So I have a memory like a sieve except that it's profoundly less useful in the kitchen. And because I know from painful experience that anything I don't document never happened, I am going to help myself and you by creating in real time a tutorial to upload blog posts from Blogger to The Winnower, should you be so inclined. Why do it? DOI is one reason.

Those of you who were smart enough to begin your blog's existence on Wordpress can use a fancy plugin for your API. Those of us who now have too much inertia on Blogger to relocate must do a little more work and use some intermediate steps, but it really isn't that hard. What's more, the intermediate steps offer an opportunity for proofreading and fine-tuning that you might like to do anyway. Let's do it!

Thursday, April 16, 2015

Another way to find posts: The Winnower

Open access online science publisher The Winnower has made a huge leap in scientific publishing and now offers bloggers a way to assign a digital object identifier (DOI) to any post uploaded to their site. Once there, the post can be reviewed, etc. just like any other online paper. They will also be archiving soon via CLOCKSS. (See Note 1.) With a DOI plus archiving it means that a post (and any reviews) should be traceable in perpetuity. Very good developments!

I had the privilege of helping Josh, The Winnower's industrious founder and administrator, create a new publication category for Neuroimaging and then used my post on physiologic confounds as the first test case. The post now has its own DOI (DOI: 10.15200/winn.142919.97862 ) should you prefer that to a URL. I submitted via a Word document because I've found that Blogger will occasionally hide irrelevant HTML code that needs to be edited out by hand. This can be a problem if you're in the habit, as I am, of copy-pasting text (e.g. quotes from papers) into a blog post. There is a new facility that will submit directly from a blog but in my first test (using Blogger) there were some major formatting issues. Josh informs me that he will be adding a facility for the Blogger API eventually, but using Word as an intermediate step gives me a chance to clean up links to references and that sort of thing. I have plans to submit many other posts to The Winnower so please let me know either in the comments below, in a review on the The Winnower version of the post or via Twitter whether you encounter problems, have suggestions for improvements, etc. Also, do please consider submitting your own blog posts to The Winnower. Let's build the Neuroimaging category!

I was around for and involved in the nascent Web of the early '90s (see Note 2) and I distinctly remember NCSA's Mosaic, the Planet Earth Home Page virtual library, UC Irvine's online bookshop, and the Cambridge coffee pot. But the development of open, online publishing supported by social media like blogs and Twitter, as well as post-publication peer review (PubPeer and PubMed Commons), feels like a true revolution for science. I may be wrong but it feels like we will look back at the current period as a major change in the way we interact. It only took us two decades. Now, however, The Winnower is contributing disproportionately to our future. Thank you.



1.  I already archive my important blog posts at The Internet Archive's Wayback Machine. In addition to providing an invaluable service, the Wayback Machine is also a wonderful way to get nostalgic and kill a few hours :-/

2.  I had an online poster at NMR Poster95, the first e-poster meeting of folks doing NMR and MRI. The front page of the poster got archived but the clickable poster itself is now defunct, I'm afraid. The wonderful Internet Archive does have other pages from my website at the time, however. They began archiving in 1996, and the earliest copy of my old website dates from January, 1997. Thank you, Internet Archive! There is also a summary of the first two NMR e-poster conferences in this paper from 1997.

Friday, January 2, 2015

Potential of ultralow field T1 and high field T1ρ in evaluating brain trauma

Crazy Scientist sent me a link to a paper, "Neuroimaging after mild traumatic brain injury: Review and meta-analysis," (doi:10.1016/j.nicl.2013.12.009) and it prompted me to do something with a brief review I wrote this time last year as a way to plan some research activities on MRI of mild traumatic brain injury (mTBI). By a remarkable coincidence the review paper was made available online four whole days before I completed my own review. I've yet to read the published review so I can't yet tell if I wasted my time. In any event, the document I wrote was for internal consumption (for my collaborators, and to clarify my own thoughts) and was never designed to become a public document. But since our research direction changed mid-year I figured I might as well stick my review out there in case anyone can make use of it.

The title of my document is the same as the title of this post. You will find the contents pasted below, or if you prefer you can download a PDF from this Dropbox link. I have quickly re-read it to check for major bloopers, and I've added a couple of update notes highlighted in yellow. There may well be some direct copy-paste of parts of a few of the papers I reviewed, especially those with heavy neuroradiology content where I am generally a long way out of my depth and would prefer to accept charges of plagiarism than get the medical terminology wrong!

For the record, we are still interested in mTBI but the logistics of studying acute brain injury in a non-hospital setting, using a home-made machine (the ULFMRI) sitting in a second basement lab in a physics department, made it all too hard to pursue right now. We have shifted instead to studying chronic conditions where we have a fighting chance of getting a few people scanned in our unorthodox facilities.

Tuesday, December 16, 2014

Updated checklist for fMRI acquisition methods reporting in the literature

This post updates the checklist that was presented back in January, 2013. The updated checklist is denoted Version 1.2. The main update is to include reporting for simultaneous multi-slice (SMS) (a.k.a. multi-band, MB) EPI.

Explanatory notes for parameter names appear in the lower portion of the post. Note that the present checklist was devised by considering typical fMRI experiments conducted on 1.5 T and 3 T scanners but the list should work reasonably well for 7 T sequences, too.

Please keep the comments and feedback coming. This is an ongoing, iterative process.

Release notes for Version 1.2

All changes from Version 1.1 have been highlighted in yellow, both on the list PDF and on the explanatory notes (below).

1. The "Spatial Encoding" parameter categories have been renamed "In-Plane Spatial Encoding" to better differentiate in-plane acceleration (e.g. GRAPPA) from slice dimension acceleration (SMS/MB).

2. When using slice dimension acceleration (i.e. SMS/MB), certain parameters that are listed as Supplemental for other EPI variants should be considered Essential. Specifically, it is suggested to report:
Matrix coil mode
Coil combination method

All the In-Plane Spatial Encoding parameters in the Supplemental category should be considered because there is a tendency to use SMS/MB to attain high spatial resolution, requiring long readout echo trains that can have higher distortion than found in typical EPI scans.

The In-plane reconstructed matrix parameter should be reported whenever partial Fourier sampling is used, as it often is for SMS/MB EPI.

All the RF & Contrast parameters in the Supplemental category should be reported because the shape, duration and amplitude of the excitation RF pulse are all integral components of the acceleration method.

The Shim routine should be reported if a non-standard shim is performed before SMS/MB EPI.

3. Pre-scan normalization has been added to the Supplemental section of RF & Contrast parameters. Large array coils produce strong receive field heterogeneity and the use of pre-scan normalization may improve the performance of post hoc motion correction.

Monday, December 8, 2014

Concomitant physiologic changes as potential confounds for BOLD-based fMRI: a checklist

Many thanks for all the feedback on the draft version of this post.

Main updates since the draft:
  • Added DRIFTER to the list of de-noising methods
  • Added a reference for sex differences in hematocrit and the effects on BOLD
  • Added several medication classes, including statins, sedatives & anti-depressants
  • Added a few dietary supplements, under Food

Please do continue to let me know about errors and omissions, especially new papers that get published. I'll gladly do future updates to this post.


(Since this post release on 8th Dec, 2014.)
27th Feb 2015: Added a new reference, hematocrit effects on resting-state fMRI.
17th Dec 2014: Update for cortisol, highlighted in yellow.
18th Dec 2014: Update for methylphenidate, atomoxetine & amphetamine, highlighted in orange.
19th Dec 2014: Update for oxytocin, highlighted in blue.
13th Jan 2015: Update for effects of the scanner itself, highlighted in green.

A recent conversation on Twitter led to the suggestion that someone compile a list of physiological effects of concern for BOLD. That is, a list of potentially confounding physiological changes that could arise sympathetically in an fMRI experiment, such as altered heart rate due to the stress of a task, or that could exist as a systematic difference between groups. What follows is the result of a PubMed literature search (mostly just the abstracts) where I have tried to identify either recent review articles or original research that can be used as starting points for learning more about candidate effects. Hopefully you can then determine whether a particular factor might be of concern for your experiment.

This is definitely not a comprehensive list of all literature pertaining to all potential physiological confounds in fMRI, and I apologize if your very important contribution didn't make it into the post. Also, please note that I am not a physiologist so if I go seriously off piste in interpreting the literature, please forgive me and then correct my course. I would like to hear from you (comments below, or via Twitter) if I have omitted critical references or effects from the list, or if I have misinterpreted something. As far as possible I've tried to restrict the review to work in humans unless there was nothing appropriate, in which case I've included some animal studies if I think they are directly relevant. I'll try to keep this post up-to-date as new studies come out and as people let me know about papers I've missed.

A final caution before we begin. It occurs to me that some people will take this list as (further) proof that all fMRI experiments are hopelessly flawed and will use it as ammunition. At the other extreme there will be people who see this list as baseless scare-mongering. How you use the list is entirely up to you, but my intent is to provide cautious fMRI scientists with a mechanism to (re)consider potential physiologic confounds in their experiments, and perhaps stimulate the collection of parallel data that might add power to those experiments.

Getting into BOLD physiology

There are some good recent articles that introduce the physiological artifacts of prime concern. Tom Liu has reviewed neurovascular factors in resting-state functional MRI and shows how detectable BOLD signals arise from physiological changes in the first place. Kevin Murphy et al. then review some of the most common confounds in resting-state fMRI and cover a few ways these spurious signal changes can be characterized and even removed from data. Finally, Dan Handwerker et al. consider some of the factors causing hemodynamic variations within and, in particular, between subjects.

Once you start really looking into this stuff it can be hard not to get despondent. Think of the large number of potential manipulations as opportunities, not obstacles! Perhaps let The Magnetic Fields get you in the mood with their song, "I don't like your (vascular) tone." Then read on. It's a long list.