The “Group” indicator in FSL

In FSL, when we create a design using the graphical interface in FEAT, or with the command Glm, we are given the opportunity to define, at the higher-level, the “Group” to which each observation belongs. When the design is saved, the information from this setting is stored in a text file named something as “design.grp”. This file, and thus the group setting, takes different roles depending whether the analysis is used in FEAT itself, in PALM, or in randomise.

What can be confusing sometimes is that, in all three cases, the “Group” indicator does not refer to experimental or observational group of any sort. Instead, it refers to variance groups (VG) in FEAT, to exchangeability blocks (EB) in randomise, and to either VG or EB in PALM, depending on whether the file is supplied with the options -vg or -eb.

In FEAT, unless there is reason to suspect (or assume) that the variances for different observations are not equal, all subjects should belong to group “1”. If variance groups are defined, then these are taken into account when the variances are estimated. This is only possible if the design matrix is “separable”, that is, it must be such that, if the observations are sorted by group, the design can be constructed by direct sum (i.e., block-diagonal concatenation) of the design matrices for each group separately. A design is not separable if any explanatory variable (EV) present in the model crosses the group borders (see figure below). Contrasts, however, can encompass variables that are defined across multiple VGs.

The variance groups not necessarily must match the experimental observational groups that may exist in the design (for example, in a comparison of patients and controls, the variance groups may be formed based on the sex of the subjects, or another discrete variable, as opposed to the diagnostic category). Moreover, the variance groups can be defined even if all variables in the model are continuous.

In randomise, the same “Group” setting can be supplied with the option -e design.grp, thus defining exchangeability blocks. Observations within a block can only be permuted with other observations within that same block. If the option --permuteBlocks is also supplied, then the EBs must be of the same size, and the blocks as a whole are instead then permuted. Randomise does not use the concept of variance group, and all observations are always members of the same single VG.

In PALM, using -eb design.grp has the same effect that -e design.grp has in randomise. Further using the option -whole is equivalent to using --permuteBlocks in randomise. It is also possible to use together -whole and -within, meaning that the blocks as a whole are shuffled, and further, observations within block are be shuffled. In PALM the file supplied with the option -eb can have multiple columns, indicating multi-level exchangeability blocks, which are useful in designs with more complex dependence between observations. Using -vg design.grp causes PALM to use the v– or G-statistic, which are replacements for the t– and F-statistics respectively for the cases of heterogeneous variances. Although VG and EB are not the same thing, and may not always match each other, the VGs can be defined from the EBs, as exchangeability implies that some observations must have same variance, otherwise permutations are not possible. The option -vg auto defines the variance groups from the EBs, even for quite complicated cases.

In both FEAT and PALM, defining VGs will only make a difference if such variance groups are not balanced, i.e., do not have the same number of observations, since heteroscedasticity (different variances) only matter in these cases. If the groups have the same size, all subjects can be allocated to a single VG (e.g., all “1”).

6 thoughts on “The “Group” indicator in FSL

  1. Dear Anderson,

    I am using PALM for inference on a number of brain networks. I decided to save time by launching multiple PALM threads in parallel: one for each network. However, I ran into the limitations of memory and ended up having a couple of the threads quit unexpectedly, at about 50% completion.

    I’d like to be able to restart them after the remaining threads finish, but because the process is time consuming, I want to restart were I left off, not from the very beginning, as I am forced to do by using the “palm prefix_palmconfig.txt” option. How could I accomplish that?

    Thank you,
    ~ Sergey

    • Hi Sergey,

      Unfortunately it isn’t possible to restart from the middle (that would imply storing intermediate results, which don’t currently happen). That said, there should be workarounds to avoid memory issues. What exactly are the options you are using? Could you post the contents of the _palmconfig.txt file and/or give further details about the size of the input files? Thanks.

      All the best,


  2. Here is the content of my palmconfig.txt :

    # Configuration file for PALM.
    # Version alpha105, running in MATLAB (R2016a).
    # 18-Jun-2017 10:26:59

    -i /data/Sergey/dual_regression/dr_stage2_ic0012.nii
    -d /data/Sergey/designs/glm_2x2_ANOVA.mat
    -t /data/Sergey/designs/glm_2x2_ANOVA.con
    -m /data/Sergey/dual_regression/mask.nii
    -C 2.3
    -Cstat mass
    -n 10000
    -o /data/Sergey/dual_regression/palm_out_np10000/dr_stage3_ic0012
    -eb /data/Sergey/Documents/MATLAB/EB.csv

    The size of the input file is 317.2 MB
    Memory capacity on my machine 8 GB
    I attempted to run 6 threads – not knowing that each of them would take ~1.5 GB (according to my Activity Monitor). Then, # 6 went down throwing the following exception (“disk space” is an unlikely issue, because I am saving the output on the cluster.):

    Saving file: /data/Sergey/dual_regression/palm_out_np10000/dr_stage3_ic0012_vox_tstat_c4
    Error using mat2file
    Problem writing data (could be a disk space or quota issue).

    Error in file_array/subsasgn>subfun (line 164)

    Error in file_array/subsasgn (line 85)

    Error in nifti/subsasgn>fun (line 74)
    val = subsasgn(obj.dat,subs(2:end),val);

    Error in nifti/subsasgn (line 20)
    obji = fun(obji,subs,val);

    Error in palm_miscwrite (line 98)
    nii.dat(:,:,:) =,:,:);

    Error in palm_quicksave (line 163)

    Error in palm_core (line 1562)

    Error in palm (line 81)

    • Hi Sergey,
      This really looks like a problem with saving the results. Are you sure you have enough disk space to write the results?
      All the best,

  3. Dear Anderson,

    Hi, I’m trying to build a matrix for mixed effects (flame), I was wondering if I can set a subgroup in my design.grp, like those images which belong to placebo but the first session. Thanks :)

    • Hi Melanie,

      I’m not sure I understand the question. Sounds like you have a longitudinal study, and two groups, is this right? Variance groups can be used in FEAT, only make sure that the design is “separable” as indicated in the article. Perhaps if you provide more details…

      All the best,


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