3 ms·

I brought this up in a grand-cousin thread, but to what degree does numerical analysis matter here? I mentioned [0], which is a must-read paper for folks doing

I brought this up in a grand-cousin thread, but to what degree does numerical analysis matter here? I mentioned [0], which is a must-read paper for folks doing numerical work, and the author brings up two examples (sections 9 and 11) where averaging over an ensemble of pipelines could not just fail to converge on the right answer, but actually mask systemic biases in the ecosystem. If your effect of interest disappears with slight changes to your pipeline (perturbation), then maybe the effect is weak or chaotic or unstable, but also maybe there is a systemic bias in your pipeline! [0] https://people.eecs.berkeley.edu/~wkahan/Mindless.pdf https://people.eecs.berkeley.edu/~wkahan/Mindless.pdf

fluidcruft 6y ago
IMHO there are far bigger differences in how the different pipelines approach very basic things such as how to identify which parts of one person's brain corresponds to which part of a different person's brain and what sorts of corrections should be applied for the distortions. There's a lot of stuff done that "looks good" or based on analogy (for example by assuming the brain is essentially a block of jello or a fluid) or because a particular structure is needed for a type of desired analysis (i.e. the need for an invertible displacement field) that don't necessarily have any biologic basis. There's also the issue that some people just don't have "extra" or "missing" cortical folds depending on your perspective. Additionally a real problem in general is we can't really see enough of the microstructure of the brain with enough detail to see basic things that are seem to relate to processing capabilities like the cortical layer structure without histology.
jonnycomputer 6y ago
Agree with fluidcraft here. I don't want to discount the importance of numerical analysis, but the different preprocessing and analysis packages that I am personally aware of make substantively different decisions about how to proceed. For example, a psycho-physiological analysis, a connectivity analysis that tries to show how connectivity with a seed region changes in response to task condition, done in SPM will deconvolve the BOLD signal in the seed region to get at a purported neural signal, while in FSL, the condition regressor is convolved with haemodynamic response function. Both are "correct" in that in an ideal world you should get similar results doing either thing, but in the real world you very well may not. Similarly, different packages may make different assumptions about smoothness of brain regions in calculating whether the size of a cluster is significantly above zero. And even when you use the same software package, there are various things you might do differently, parameters you might set differently; even the order of certain operations maybe switched around. A classic example of that has to do with slice timing correction. Since fMRI slices are acquired at different times, a typical thing to do would be to interpolate the slices so that you can treat them as if they were acquired all at the same time. However, motion correction between volumes, in which subject motion is partially corrected by jiggling around each image until they maximally overlap each other, can be done before or after slice timing correction; but the consequences of that is that motion artifacts can propagate through volumes in different ways depending on the order you do it in; but neither order is definitely better, because it matters how much motion is a problem in the scans, and how long it takes to acquire a volume (e.g. tr 2 seconds), and so on.

fluidcruft 6y ago

IMHO there are far bigger differences in how the different pipelines approach very basic things such as how to identify which parts of one person's brain corresponds to which part of a different person's brain and what sorts of corrections should be applied for the distortions. There's a lot of stuff done that "looks good" or based on analogy (for example by assuming the brain is essentially a block of jello or a fluid) or because a particular structure is needed for a type of desired analysis (i.e. the need for an invertible displacement field) that don't necessarily have any biologic basis. There's also the issue that some people just don't have "extra" or "missing" cortical folds depending on your perspective. Additionally a real problem in general is we can't really see enough of the microstructure of the brain with enough detail to see basic things that are seem to relate to processing capabilities like the cortical layer structure without histology.

jonnycomputer 6y ago

Agree with fluidcraft here. I don't want to discount the importance of numerical analysis, but the different preprocessing and analysis packages that I am personally aware of make substantively different decisions about how to proceed. For example, a psycho-physiological analysis, a connectivity analysis that tries to show how connectivity with a seed region changes in response to task condition, done in SPM will deconvolve the BOLD signal in the seed region to get at a purported neural signal, while in FSL, the condition regressor is convolved with haemodynamic response function. Both are "correct" in that in an ideal world you should get similar results doing either thing, but in the real world you very well may not. Similarly, different packages may make different assumptions about smoothness of brain regions in calculating whether the size of a cluster is significantly above zero. And even when you use the same software package, there are various things you might do differently, parameters you might set differently; even the order of certain operations maybe switched around. A classic example of that has to do with slice timing correction. Since fMRI slices are acquired at different times, a typical thing to do would be to interpolate the slices so that you can treat them as if they were acquired all at the same time. However, motion correction between volumes, in which subject motion is partially corrected by jiggling around each image until they maximally overlap each other, can be done before or after slice timing correction; but the consequences of that is that motion artifacts can propagate through volumes in different ways depending on the order you do it in; but neither order is definitely better, because it matters how much motion is a problem in the scans, and how long it takes to acquire a volume (e.g. tr 2 seconds), and so on.