FWE-corrected p values in peak_nii

[Monica Leslie]

Hi Aaron and Donald,

I have just finished using GLM Flex Fast 4 and running peak_nii to identify significant clusters in my data. After perusing JISCMail and this group, I have seen several discussions which refer to both corrected and uncorrected p values in the output from peak_nii; however, I don't seem to be getting any p values in my output at all. 

Peak_nii has been helpful in identifying clusters in my data at the p < .001 uncorrected level and yields T statistics for peaks, but I'm not sure how to generate or find FWE-corrected p values.

I have been using the peak_nii script from the following webpage (https://www.nitrc.org/projects/peak_nii), but I would be very grateful if you could point me in the direction of an updated script or an additional option I should use to generate FWE-corrected p values.

Many thanks,

Monica

[Monica Leslie]

Hi All,

After a little more trouble-shooting it seems that whether I use peak_nii directly from the command line calling for [voxels voxelstats clusterstats sigthresh regions map parameters UID] or use FIVE to get Peak Info I get the following error message:

Error using peak_nii

Too many output arguments.

Has anyone else come across this before or know what might be causing the issue? For the moment, it seems that this is preventing me from being able to view FWE-corrected p values for my data.

Many thanks,

Monica

[MCLAREN, Donald]

Hi Monica,

I'll try to do some testing this week to identify the issue and the patch.

Best Regards, 

Donald McLaren, PhD

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[Monica Leslie]

Hi Donald,

That would be amazing. Thank you very much.

Monica

On Tuesday, 10 September 2019 02:19:17 UTC+1, Donald McLaren wrote:

Hi Monica,

I'll try to do some testing this week to identify the issue and the patch.

Best Regards, 

Donald McLaren, PhD

On Wed, Sep 4, 2019 at 9:42 AM Monica Leslie <monica...@gmail.com> wrote:

Hi Aaron and Donald,

I have just finished using GLM Flex Fast 4 and running peak_nii to identify significant clusters in my data. After perusing JISCMail and this group, I have seen several discussions which refer to both corrected and uncorrected p values in the output from peak_nii; however, I don't seem to be getting any p values in my output at all. 

Peak_nii has been helpful in identifying clusters in my data at the p < .001 uncorrected level and yields T statistics for peaks, but I'm not sure how to generate or find FWE-corrected p values.

I have been using the peak_nii script from the following webpage (https://www.nitrc.org/projects/peak_nii), but I would be very grateful if you could point me in the direction of an updated script or an additional option I should use to generate FWE-corrected p values.

Many thanks,

Monica

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[Monica Leslie]

Hi Donald,

I just wanted to follow up to see if you've had a chance to see what might be causing the "Too Many Output Arguments" issue with peak_nii? Unfortunately I still haven't found a way around it on my end.

Kind Regards,

Monica

[MCLAREN, Donald]

Hi Monica,

[voxels voxelstats clusterstats sigthresh regions map parameters UID] 

should be

[voxels voxelstats clusterstats sigthresh regions mapparameters UID] 

sigthresh has the threshold values in them.

voxelstats column 1 should have the FWE-corrected values. This requires that you provide the FWHM of the image. This can be found in the SPM.mat file.

I'm also attaching an updated version of peak_nii.m

Let me know if this doesn't work and I can look again.

Best Regards, 

Donald McLaren, PhD

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