Hi Carl,
The option -logp makes the p-values be stored in log scale, so the threshold would be, for alpha = 0.05, -log10(0.05) = 1.301. You can use that when overlaying the images.
You didn't ask but the -C usually goes with a positive, somewhat high value (say, +3.1).
All the best,
Anderson
On 12/14/22, 2:58 PM, "FSL - FMRIB's Software Library on behalf of Carl" <[log in to unmask] <mailto:[log in to unmask]> on behalf of [log in to unmask] <mailto:[log in to unmask]>> wrote:
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Dear PALM experts,
We are running the FreeSurfer PALM adaptation fsPalm with the following PALM-parameters to get TFCE data:
-i thickness.mgh
-m mask.mgh
-d design.mat
-t design.con
-logp
-n 1000
-C -Inf
-o fsp
-T
-tfce2d
-savemetrics
-s fsaverage/surf/rh.white
(passed to fsPALM with fspalm --glmdir /path/toglmdir --cft 0 --name rh.thickness --cwp 0.05 --onetail --iters 1000 --2spaces --pargs='-T -tfce2d -savemetrics' )
We get two clustere_tstat mgz-files, three dpv_tstat mgz-files, and three tfce_tstat mgz-files as output, in addition to logfiles and config-files. For the dpv and tfce-files, one in each is a tstat_fwep, one in each is a tstat and one is a tstat_uncp. However, we are struggling in interpreting the values we get. I've interpreted the PALM-user guide as the tcfe_fwep being fwe-corrected p-values and just overlaying this file on a FreeSurfer fsaverage hemisphere gives us a lot of areas showing up. We're however not sure if this is the correct way of looking at the data. In addition to just overlaying the tfce_fwep file, should we also follow this example when viewing the overlay (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwa-jisc.exe%3FA2%3DFSL%3B6c300ad4.0708&data=05%7C01%7Canderson.winkler%40UTRGV.EDU%7C414bad7eb20c4ec696b608dade15ed17%7C990436a687df491c91249afa91f88827%7C0%7C0%7C638066483112824294%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=apkCl9JQEKyN98JpgUfcOYZwOQQ5PjPgTstfQ8hw8qo%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwa-jisc.exe%3FA2%3DFSL%3B6c300ad4.0708&amp;data=05%7C01%7Canderson.winkler%40UTRGV.EDU%7C414bad7eb20c4ec696b608dade15ed17%7C990436a687df491c91249afa91f88827%7C0%7C0%7C638066483112824294%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=apkCl9JQEKyN98JpgUfcOYZwOQQ5PjPgTstfQ8hw8qo%3D&amp;reserved=0>), e.g set the min value to 0.949 and max to 1? Any assistance in interpretation would be most welcome!
Kind regards,
Carl
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