Hi! Sorry for a multi-question post but since they are related I felt bad posting several separate posts.
I have tried the different approaches to apply multiple comparisons error corrections and ran into some questions:
- Approach1: 3dFWHMx + 3dClustSim. Detrend?
To use 3dFWHMx -acf -mask GM+tlrc. with our without -detrend does, according to the documentation depend on if your data has been de-trended during pre-proc or not. So a data-set that has been detrended (I think via 3ddespike) does not have to be de-trended, and if you do it anyway it should not make a big difference.
When I run (on detrended data, as far as I know)
a) 3dFWHMx -ACF NULL -mask GM+tlrc -input errts.sjb*.fanaticor+tlrc and
b) 3dFWHMx -detrend -ACF NULL -mask GM+tlrc -input errts.sjb*.fanaticor+tlrc and
The acf-parameters become:
a) 0.5581857308 3.1542607692 10.8851776923 (no detrend)
b) 0.7097887692 3.1102161538 11.3432861538 (detrend)
Why would the difference of acf parameters be so big? b) has a much higher first value, while the second two values are bit lower. The average of the 3 values is higher for the detrended data). This affect the 3dClustSim output (see below)
- 3dClustSim: different ACF params
If I use the two different ACF-sets above I obviously get different tables. What we see is more conservative table values (you need bigger clusters for a given p-value) for the acf with the average lower values. Is this reasonable? Aren’t high acf values representing higher spatial smoothness / autocorrelations giving a higher risk for false positives and would then give a more conservative table? Or do I think about it wrong? The 4th ACF value (not showed) is a bit lower for the -detrended data.
Output (bi-sided, NN=1, but same trend for all settings):
No Detrend
3dClustSim -acf 0.5581857308 3.1542607692 10.8851776923 -mask DMN_network_anat_bool_fit+tlrc
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 101.4 121.6 154.5 183.0
0.020000 45.4 55.4 69.4 81.1
0.010000 28.0 33.8 42.4 49.4
0.005000 18.3 22.1 27.6 32.4
0.002000 11.1 13.6 17.2 19.6
0.001000 8.0 9.7 12.2 14.4
0.000500 5.8 7.2 9.1 10.6
0.000200 3.9 4.9 6.3 7.5
0.000100 3.0 3.8 4.9 5.7
Detrend
3dClustSim -acf 0.7097887692 3.1102161538 11.3432861538 -mask DMN_network_anat_bool_fit+tlrc.
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 72.1 87.4 105.4 125.2
0.020000 33.8 39.9 48.7 56.5
0.010000 21.4 25.3 30.7 34.9
0.005000 14.4 16.9 20.6 23.6
0.002000 9.2 11.0 13.2 15.3
0.001000 6.8 8.1 9.8 11.1
0.000500 5.1 6.1 7.8 9.0
0.000200 3.7 4.5 5.5 6.4
0.000100 2.8 3.5 4.4 5.1
Should not the higher acf-values give a more conservative threshold since the smoothness is higher? It’s just the first value that is higher for detrend, but that is where the biggest difference is.
-
What thresholds to use:
I’m I right that even though the 3dClustsim gives a cluster size for e.g. p > 0.05 you should not use that. You should only use the p-values < 0.002 (ideally 0.001) with this approach? -
I also want to use ETAC but I don’t get the expected output.
my command
3dttest++ -paired -prefix AvP_opt_anaticor -mask $mask_anat -ETAC -ETAC_blur 4 6 -ETAC_opt NN=1:hpow=0:sid=1:pthr=0.01,0.05,0.002,0.01:name=robin \
a) what is the meaning of hpow? Did not understand the manual.
b) According to the manual I should get
P+tlrc.HEAD normal 3dttest++ output from input datasets
P.B4.0.nii 3dttest++ output from blurred datasets
P.B7.0.nii (4 and 7 mm, respectively)
Px.B4.0.5percent.txt voxel-wise threshold list for a variety
Px.B7.0.5percent.txt of global FPRs, for blurs 4 and 7
Px.N.ETAC.mthresh.B4.0.5perc.nii Multi-threshold datasets for blur=4 and =7,
Px.N.ETAC.mthresh.B7.0.5perc.nii for overall 5% global false positive rate
Px.N.ETACmask.2sid.5perc.nii.gz Binary (0 or 1) mask of 'active voxels'
PX.N.ETACmaskALL.2sid.5perc.nii.gz Multi-volume mask showing which ETAC
But I don’t get the Px files, I get a lot of TT, files (70 files of this kind TT.c7xJqG0BM99.0000.minmax.1D) and these:
AvP_opt_anaticor.B4.0.nii
AvP_opt_anaticor.B6.0.nii
AvP_opt_anaticor+tlrc.BRIK
AvP_opt_anaticor+tlrc.HEAD
globalETAC.mthresh.TT.c7xJqG0BM99.robin.ETAC.B4.0.5perc.niml
globalETAC.mthresh.TT.c7xJqG0BM99.robin.ETAC.B6.0.5perc.niml
TT.c7xJqG0BM99.robin.ETACmaskALL.global.1neg.5perc.nii.gz
TT.c7xJqG0BM99.robin.ETACmaskALL.global.1pos.5perc.nii.gz
TT.c7xJqG0BM99.robin.ETACmask.global.1pos.5perc.nii.gz
Is that expected?
c) If I want to see if get any clusters surviving the 5% FDR limit, which file should I check? I get the files 1neg 1pos… Should I cluster or is that included in the masks?
Thanks a bunch! feel free to just anser any of the sub-questions.
and just make a script that extracts the acf from each and average them.