The Story Behind the Atlantic Salmon
The Atlantic Salmon fMRI poster has garnered a fair amount of attention since its presentation at the Human Brain Mapping conference last June in San Francisco. So far the reaction from other researchers has been almost unanimously positive. A sizable number of people stopped by the poster while it was displayed and Rainer Goebel (of BrainVoyager fame) was kind enough to give the fish a shout-out during the closing ceremonies (see photo).
All in all I am quite pleased that the Salmon seems to be generating a fresh discussion of multiple comparisons correction in neuroimaging.But, how did it all begin? I mean, really, why would anybody want to scan a fish? This was one of the top five questions I was asked during the HBM poster session. It it a story that deserves to be told, and a weblog post is perhaps the ideal medium to tell it. So, for all readers who are curious, I have written up the story of the Salmon.
The story begins during my first year in graduate school at Dartmouth College. I was working with Abigail Baird on fMRI studies investigating the maturation of decision-making and we were developing a large number of new MRI protocols to use with adolescents and adults. Not wanting to waste valuable magnet time imaging and reimaging a MRI phantom, we instead challenged ourselves to scan the most curious objects we could find at the local grocery store.
For our first attempt we scanned a pumpkin. One result of this endeavor can be seen here. This is a pretty standard fruit to scan, as just about every imaging center around the country obtains a T1-weighted image of them in late October. Still, it was exciting to us. During the next pilot testing session Abby brought in a Cornish game hen to be scanned. This really upped the ante, as we had now put a dead bird into the head coil. When pondering our next step the comment was made: “we should scan a whole fish”.
I picked up the salmon from our local supermarket early on an early Saturday morning in spring of 2005. The clerk behind the counter was a little shocked to be selling a full-length Atlantic salmon at 6:30 AM, especially when I told her what was about it happen to it. About an hour later we were in the imaging center with the fish wrapped in plastic and securely placed within the head coil. We proceeded to test our entire protocol with the salmon in the magnet. In total, we did an anatomical localizer scan, four functional runs, a T1-weighted anatomical scan, and a diffusion tensor imaging (DTI) scan.
After transferring the data off of the scanner we first took a look at the high resolution anatomical image. It was simply incredible. Slice the fish along the sagittal plane and you could see the fish split right down the middle. Slice the fish coronally and you could see what looked like salmon steaks on the viewer. By far it was our crowning achievement in terms of ridiculous objects to scan. Then, our curiosity satisfied, I socked the salmon data away for the next three years.
In early 2008 I was working with my co-adviser George Wolford on a presentation he was giving regarding the multiple comparisons problem in fMRI. We were discussing false positives in MRI phantom data and I brought up the idea of processing the salmon fMRI data to look for some ‘active’ voxels. I ran the fish data through my SPM processing pipelines and couldn’t believe what I saw. Sure, there were some false positives. Just about any volume with 65,000 voxels is going to have some false positives with uncorrected statistics. Rather, it was where the false positives occurred that really floored me. A cluster of three significant voxels were arranged together right along the midline of the salmon’s brain. If they would have been anywhere else the salmon would have been just a curious anecdote, but now we had a story.
George presented the salmon data at our local fMRI methods group, but nothing much happened for a while after that. George was convinced that we could/should publish the data and that it was an excellent example of the multiple comparisons problem. I was less convinced, remarking about how silly that would be and how terrible it would be for a young postdoc to become known as ‘the fish guy’. For the next year we went back and forth about the issue, until one day in January, 2009. George was out in Los Angeles and came up to UCSB to visit. Over lunch he said that it was time to ‘get the fish out’. I relented, and agreed to start writing the paper.
About a week later the HBM conference poster deadline came around and we decided to submit the salmon as an abstract. We genuinely wanted it to be a part of the conference, but we really doubted that it would be approved. How right we were. Through some sources close to the matter I have learned that the salmon poster was indeed rejected by every reviewer who saw the abstract. Just about everyone thought it was a joke – some rogue student who was playing a prank on the OHBM. It was only when the rejected abstract went before the OHBM Program Committee that it was given approval to stay as part of the conference. I hear that even that vote was contentious.
While the abstract reviewers were busy rejecting the salmon poster my co-authors and I were diligently writing a full-on salmon manuscript. The overall outline of the paper had been in our heads for some time and the writing went rather quickly. By April we had a polished manuscript ready for review and we sent it off to a major neuroimaging journal. Within a week we heard back that it was being rejected on an editorial basis. We heard that there were several major discussions within the journal staff regarding whether to even review the piece. In the end they decided to pass the responsibility, and the trouble, on to another journal.
That brings us to today. The ‘Post-Mortem Atlantic Salmon’ was a strong success at the OHBM conference. It is also under review at a second major neuroimaging journal. The more I think about the affair the more I believe that the fish has the chance to impact the field of neuroimaging in a very positive way. Predefined significance thresholds with a specified cluster extent are a weak control to the problem of false positives in imaging data. Statisticians and methods researchers have argued about the need for multiple comparisons correction for some time. In just one figure the salmon data illustrates exactly why we need stronger controls for the false positive problem in fMRI. I hope it finds a good home in an open-minded journal.
You can find a copy of the ‘Post-Mortem Atlantic Salmon’ poster at this link: