 |
 |
They indicate the number of voxels needed for a cluster to be significant in the current map. They are determined based on the clusters you have in the data. If you had smaller clusters, then they could also be significant, but there is no exhaustive search to determine the exact threshold. For example, if your smallest cluster is 500 voxels and the corrected p-value is 0.0001. Then likely a cluster that is smaller would also be significant, but there is no smaller cluster to be significant, so SPM reports 500 as the cluster extent required. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Fri, Jun 20, 2014 at 4:14 PM, Victoria Klimaj <[log in to unmask]> wrote: > Donald, > > Do the numbers corresponding to cFWE and cFDR indicate voxel threshold, or > cubic millimeter threshold? Mine are showing up as FWEc=629 and FDRc=103, > which is much larger than I would expect a voxel threshold to be for my > scans. > > Thanks! > -Victoria > > > On Fri, Jun 20, 2014 at 1:26 PM, MCLAREN, Donald <[log in to unmask] > > wrote: > >> You can use SPM to determine the cFWE or cFDR extent thresholds. They are >> at the bottom of the results window. >> >> You can also use 3dClustSim in AFNI to do a monte carlo simulation to >> determine the extent criteria. >> >> Best Regards, Donald McLaren >> ================= >> D.G. McLaren, Ph.D. >> Research Fellow, Department of Neurology, Massachusetts General Hospital >> and >> Harvard Medical School >> Postdoctoral Research Fellow, GRECC, Bedford VA >> Website: http://www.martinos.org/~mclaren >> Office: (773) 406-2464 >> ===================== >> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >> intended only for the use of the individual or entity named above. If the >> reader of the e-mail is not the intended recipient or the employee or >> agent >> responsible for delivering it to the intended recipient, you are hereby >> notified that you are in possession of confidential and privileged >> information. Any unauthorized use, disclosure, copying or the taking of >> any >> action in reliance on the contents of this information is strictly >> prohibited and may be unlawful. If you have received this e-mail >> unintentionally, please immediately notify the sender via telephone at >> (773) >> 406-2464 or email. >> >> >> On Fri, Jun 20, 2014 at 2:17 PM, Victoria Klimaj < >> [log in to unmask]> wrote: >> >>> Donald, >>> >>> Thank you for the explanation! That is very helpful. >>> >>> However, if we don't end up exploring TFCE in FSL, what cluster >>> threshold would you advise for SPM given a voxel size of 3mm and smoothing >>> kernel of 8mm? >>> >>> -Victoria >>> >>> >>> >>> On Fri, Jun 20, 2014 at 8:05 AM, MCLAREN, Donald < >>> [log in to unmask]> wrote: >>> >>>> Please see inline responses below. >>>> >>>> >>>> On Wed, Jun 18, 2014 at 6:46 PM, Victoria Klimaj < >>>> [log in to unmask]> wrote: >>>> >>>>> Hi SPM experts, >>>>> >>>>> A quick question on thresholding: >>>>> >>>>> For my data, I'm not using cluster-level thresholding because it >>>>> doesn't seem to change the corrected T in SPM. If this is the case >>>>> (unless I'm doing it wrong), there doesn't seem to be any justification >>>>> for using cluster level thresholding and ignoring even a single significant >>>>> voxel. >>>>> >>>> >>>> The voxel T-statistics and corrected voxel T-statistics are not >>>> influenced by clustering. You want to use cluster thresholding because you >>>> can make inferences on the clusters and people don't believe that single >>>> voxels are active because you likely started with larger voxels and have >>>> smoothed your data. >>>> >>>> >>>>> >>>>> Why don't people use a hierarchical approach, simultaneously implementing >>>>> different corrections for different sized clusters? >>>>> >>>> >>>> I'd take a look at TFCE in FSL, its close to what you are suggesting. >>>> >>>> >>>>> Using something like this, a single voxel would have the most >>>>> stringent requirements, and each additional voxel would lower the >>>>> required T (as determined by Monte Carlo simulation or some such >>>>> thing?). I'm not a statistics expert, but it seems like this would be >>>>> a very effective default procedure. Is there any way of utilizing this kind >>>>> of thresholding in SPM? >>>>> >>>> >>>> In one of my earlier papers, we used several voxel height and extent >>>> thresholds and selected voxels that were included in any of them. Look for >>>> papers by Burton and McLaren. A few people raised questions about whether >>>> using multiple thresholds increased the false positive rate beyond 5% >>>> because of the multiple corrections. I don't have a good answer for that >>>> question. In the extreme case, where you have 1 voxel with a height >>>> requirement, then 2 voxels with a different height requirement, etc. This >>>> is an interesting concept that I've thought about myself; however, it would >>>> be time consuming to run all possible permutations. The idea behind TFCE is >>>> to account for the height an extent criteria at the same time and only do >>>> the thresholding once. I believe TFCE requires non-parametric testing >>>> though, so it has to be implemented through randomise. I think someone may >>>> have implemented in SPM as well, but I'm not entirely sure. >>>> >>>> >>>>> >>>>> >>>>> Thanks so much for any help! >>>>> -Victoria >>>>> >>>> >>>> >>> >> >