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.


UPDATES:

(Since this post release on 8th Dec, 2014.)
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.
______________________



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.

Friday, November 14, 2014

A failed quench circuit?


UPDATE: 20th Nov, 2014, courtesy of Greg Brown on Twitter

It is being reported that the quench button was disabled by GE Healthcare engineers to the point that it was only usable by authorized personnel, presumably thus requiring a specific piece of kit that neither the hospital staff nor the first GE engineers to arrive on-site either possessed or perhaps even knew about. This story is set to run and run....

___________________

No doubt you've seen this news doing the rounds:

Two stuck to MRI machine for 4 hours

There was, of course, a huge procedural failure that allowed a large, magnetic oxygen cylinder into the MRI facility in the first place. No doubt the investigation will find ample blame to spread around. But the solution to the problem is rather simple: education/training coupled with standard operating procedures to nix the threat. As procedures go it's not especially difficult. (By comparison, over 34,000 people manage to get themselves killed on US roads every single year. Clearly, we can't drive for shit. Our procedures are severely wanting in this department.) And if you're ever in doubt as to whether an item can be brought safely into the MRI suite there is always - always! - someone you can go to for an expert opinion. In my facility no equipment is allowed through the door without that expert opinion being cast.

So let's shift to the part of this fiasco that really got my attention: the claim that the magnet quench circuit malfunctioned. From the second article, above:
"At a press conference on Wednesday, a day after this newspaper broke the story, senior officials of Tata Memorial-run Advance Centre or Treatment Research and Education in Cancer (ACTREC) in Khargar said that because a switch to disable the machine's magnetic field malfunctioned, it took engineers four hours to disengage the two employees - a ward boy and a technician -- stuck to the machine, when it should not have taken more than 30 seconds."

Thursday, October 30, 2014

Concomitant physiological changes as potential confounds for BOLD-based fMRI: a (draft) checklist

**Please let me know of errors or omissions!**

This post is a work-in-progress. It will be updated based on feedback. I will remove (draft) from the title when I consider this version to be complete.


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. As it says at the top, I'll consider this a draft post pending feedback. Subsequent posts will be designated with a version number.

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.

Wednesday, October 1, 2014

i-fMRI: My initial thoughts on the BRAIN Initiative proposals


So we finally have some grant awards on which to judge the BRAIN Initiative. What was previously a rather vague outline of some distant, utopian future can now be scrutinized for novelty, practicality, capability, etc. Let's begin!

The compete list of awards across six different sections is here. The Next Generation Human Imaging section has selected nine diverse projects to lead us into the future. Here are my thoughts (see Note 1) based mostly on the abstracts of these successful proposals.

Friday, August 15, 2014

QA for fMRI, Part 3: Facility QA - what to measure, when, and why


As I mentioned in the introductory post to this series, Facility QA is likely what most people think of whenever QA is mentioned in an fMRI context. In short, it's the tests that you expect your facility technical staff to be doing to ensure that the scanner is working properly. Other tests may verify performance - I'll cover some examples in future posts on Study QA - but the idea with Facility QA is to catch and then diagnose any problems.

We can't just focus on stress tests, however. We will often need more than MRI-derived measures if we want to diagnose problems efficiently. We may need information that might be seem tangential to the actual QA testing, but these ancillary measures provide context for interpreting the test data. A simple example? The weather outside your facility. Why should you care? We'll get to that.


An outline of the process

Let's outline the steps in a comprehensive Facility QA routine and then we can get into the details:

  • Select an RF coil to use for the measurements. 
  • Select an appropriate phantom.
  • Decide what to measure from the phantom.
  • Determine what other data to record at the time of the QA testing.
  • Establish a baseline.
  • Make periodic QA measurements.
  • Look for deviations from the baseline, and decide what sort of deviations warrant investigation.
  • Establish procedures for whenever deviations from "normal" occur.
  • Review the QA procedure's performance whenever events (failures, environment changes, upgrades) occur, and at least annually.

In this post I'll deal with the first six items on the list - setting up and measuring - and I'll cover analysis of the test results in subsequent posts.

Tuesday, July 29, 2014

Free online fMRI education!


UCLA has their excellent summer Neuroimaging Training Program (NITP) going on as I type. Most talks are streamed live, or you can watch the videos at your leisure. Slides may also be available. Check out the schedule here.

I am grateful to Lauren Atlas for tweeting about the NIH's summer fMRI course. It's put together by Peter Bandettini's FMRI Core Facility (FMRIF). It started in early June and runs to early September, 3-4 lectures a week. The schedule is here. Videos and slides are available a few days after each talk.

Know of others? Feel free to share by commenting!