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The "-o" indicates the output file name, so you probably want to label this with the test parameters (e.g., -o L_Hipp_vertexMNI_2sample_rand_F3 for the suggested options).
Examples
Refer to table in randomise guide for files that are created (randomise User Guide).
[user@localhost temp]$ randomise -i L_Hipp_vertexMNI_2sample.nii.gz -m L_Hipp_vertexMNI_2sample_mask.nii.gz -o L_Hipp_vertexMNI_2sample_rand -d des_2sample.mat -f des_2sample.fts --fonly -D -F
[user@localhost temp]$ randomise -i L_Hipp_vertexMNI_2sample.nii.gz -m L_Hipp_vertexMNI_2sample_mask.nii.gz -o L_Hipp_vertexMNI_2sample_rand -d des_2sample.mat -f des_2sample.fts --fonly -D -x
[user@localhost temp]$ randomise -i L_Hipp_vertexMNI_2sample.nii.gz -m L_Hipp_vertexMNI_2sample_mask.nii.gz -o L_Hipp_vertexMNI_2sample_rand -d des_2sample.mat -f des_2sample.fts --fonly -D --T2x
[user@localhost temp]$ randomise -i L_Hipp_vertexMNI_2sample.nii.gz -m L_Hipp_vertexMNI_2sample_mask.nii.gz -o L_Hipp_vertexMNI_2sample_rand -d des_2sample.mat -f des_2sample.fts --fonly -D -
F 3
Probably Incorrect Example: t-tests
...
S 3
[user@localhost temp]$ randomise -i L_Hipp_vertexMNI_2sample.nii.gz -m L_Hipp_vertexMNI_2sample_mask.nii.gz -o L_Hipp_vertexMNI_2sample_rand -d
...
des_2sample.mat -
...
Note: the T option can include a threshold (e.g., "-T 2" for t-statistic threshold of 2), but this is optional.
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f des_2sample.fts --fonly -D -F 3
Each analysis will generate a number of files, one for each contrast
...
. There are maps of
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f statistics, p values, and corrected p values,
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regions that are significantly different based on the threshold if one was included (
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F statistic
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> 3 in the
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last example):
