Hi Anderson,
Unfortunately, the command you have given me is producing the same error that I was having when trying to generate an f-stat map. When I include -f and -fonly, I get no images in my outputs. But when I remove the -fonly, I get two t-stat images.
Just to clarify, my design.mat has 4 columns and 18 rows. My design.con is [1 0 0 0] and my design.fts is simply [1], so I just want to get an f-stat map for EV1 in my design.mat, which is my dummy EV - the other 3 EVs that are zeroed out in the design.con are confounds. When I include both the -f and -fonly flags, the palm outputs to terminal don't include "Doing maths for -evperdat before model fitting:", just skips to the end. When I exclude -fonly flag, the two t-statistic maps output are identical (and they include both positive and negative values, so definitely not f-statistics). I am indeed also including the -t flag. To try clarify further, I'll copy below the terminal outputs to screen for my commands. They are the same command as the one you've given me, only with 1 permutation to save time to suss out this issue. However, the same thing happens when I ask for 2000 permutations, as you had in your original command. Any help would be greatly appreciated.
Cheers,
Luke.
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\ \:\/:/ \ \:\/:/__\/ \ \:\ /:/ \ \:\~~\__\/
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=======================================================================
Permutation Analysis of Linear Models
=======================================================================
Running PALM alpha111 using MATLAB 9.4.0.813654 (R2018a) with the following options:
-i Y.nii.gz
-d design.mat
-t design.con
-f design.fts
-fonly
-evperdat X.nii.gz 1 1
-m mask.nii.gz
-n 1
-nouncorrected
-approx tail
-demean
-noniiclass
-saveglm
-logp
-o output/palm
Found FSL in /usr/local/fsl
Reading input 1/1: Y.nii.gz
Reading EV per datum 1/1: X.nii.gz
Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 2.69047 seconds.
Elapsed time with permutations: ~ 0.000280452 seconds.
Computing p-values.
Saving p-values (uncorrected, and corrected within modality and within contrast).
Elapsed time generating and saving results: ~ 0.132578 seconds.
Overall elapsed time: ~ 2.82333 seconds.
PALM finished at 10-Sep-2018 14:37:12.
=======================================================================
___ ___ ___
/ /\ / /\ /__/\
/ /::\ / /::\ | |::\
/ /:/\:\ / /:/\:\ ___ ___ | |:|:\
/ /:/~/:/ / /:/~/::\ /__/\ / /\ __|__|:|\:\
/__/:/ /:/ /__/:/ /:/\:\ \ \:\ / /:/ /__/::::| \:\
\ \:\/:/ \ \:\/:/__\/ \ \:\ /:/ \ \:\~~\__\/
\ \::/ \ \::/ \ \:\/:/ \ \:\
\ \:\ \ \:\ \ \::/ \ \:\
\ \:\ \ \:\ \__\/ \ \:\
\__\/ \__\/ \__\/
=======================================================================
Permutation Analysis of Linear Models
=======================================================================
Running PALM alpha111 using MATLAB 9.4.0.813654 (R2018a) with the following options:
-i Y.nii.gz
-d design.mat
-t design.con
-f design.fts
-evperdat X.nii.gz 1 1
-m mask.nii.gz
-n 1
-nouncorrected
-approx tail
-demean
-noniiclass
-saveglm
-logp
-o output/palm
Found FSL in /usr/local/fsl
Reading input 1/1: Y.nii.gz
Reading EV per datum 1/1: X.nii.gz
Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 2.6748 seconds.
Doing maths for -evperdat before model fitting: [Design 1/1, Contrast 1/2] (may take several minutes)
Doing maths for -evperdat before model fitting: [Design 1/1, Contrast 2/2] (may take several minutes)
Number of possible permutations is 6.40237e+15 = 18!.
Generating 1 shufflings (permutations only).
Building null distribution.
50% [Design 1/1, Contrast 1/2, Shuffling 1/1, Modality 1/1]
Saving file: output/palm_vox_cope_c1
Saving file: output/palm_vox_varcope_c1
Saving file: output/palm_vox_cohen_c1
Saving file: output/palm_vox_cfvar_c1
Saving file: output/palm_vox_tstat_c1
Number of possible permutations is 6.40237e+15 = 18!.
Generating 1 shufflings (permutations only).
Building null distribution.
100% [Design 1/1, Contrast 2/2, Shuffling 1/1, Modality 1/1]
Saving file: output/palm_vox_cope_c2
Saving file: output/palm_vox_varcope_c2
Saving file: output/palm_vox_cohen_c2
Saving file: output/palm_vox_cfvar_c2
Saving file: output/palm_vox_tstat_c2
Elapsed time with permutations: ~ 19.3284 seconds.
Computing p-values.
Saving p-values (uncorrected, and corrected within modality and within contrast).
Saving file: output/palm_vox_tstat_fwep_c1
Saving file: output/palm_vox_tstat_fwep_c2
Elapsed time generating and saving results: ~ 0.33872 seconds.
Overall elapsed time: ~ 22.342 seconds.
PALM finished at 10-Sep-2018 14:34:02.
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