Assemble the Data (isxconcat-sess) (Volume)

The first step in the group analysis is to "assemble" the data. This means creating a single 4D file with where the 4th "time" dimension is actual all the subjects concatenated together in a common space.

To run the volume-based concatenation, run the command below. This program resamples a group of FS-FAST first-level analyses into a common space and concatenates all the sessions together into one multi-frame file suitable for use with mri_glmfit.

isxconcat-sess -sf <sessid> -analysis <analysis name> -c <contrast name> -o <output dir>

In the output directory, you will see a series of files that start with "tal":

- tal.meanfunc.nii is a stack where each "time point" is the mean functional image of each subject sampled in the MNI305 space.
- tal.masks.nii are the binary masks for all the subjects
- tal.fsnr.nii are the functional SNR maps from each subject.
- tal.mask.nii is a single binary mask made from the intersection of the individuals.
- ffxdof.dat is the fixed-effects DOF across all subjects.
- sessid.txt is the list of sessions, the corresponding freesurfer subject name, and the DOF contributed by each subject.

In the new contrast name folder, you will see:

- tal.ces.nii - the contrast maps for each of the subjects
- tal.cesvar.nii are the variance of the contrast for each subject (i.e., the square of the standard error). This variance is needed for fixed-effects and weighted random-effects analysis.

Group GLM Analysis (Volume)

When you perform a group analysis, you are looking for effects of the task across the population. Now decide if you are running a Random Effects or Weighted Random Effects or Fixed Effects Analysis.

Random Effects (RFx, OLS) (Volume) This is a program for intersubject averaging using a random-effects model, by computing one number for each subject (at each voxel) based on the contrast matrix.

Weighted Random Effects (WRFx, WLS) (Volume) In a real experiment, some subjects are noisier than others, and it is a good idea to take this into account since we have information about how noisy a subject is through the lower-level analysis. In weighted least squares (WLS), this is handled by weighting each subject by the inverse of their noise (i.e., noisier subjects get lower weight). The first-level noise variances (tal.cesvar.nii) are passed with the --wls option.

Fixed Effects (FFx) (Volume) This is a program for intersubject averaging using a fixed effects model, where data from all subjects are treated as if they came from a single subject.

Correction for Multiple Comparisons/Cluster Analysis (Volume)

With so many voxels in fMRI maps, it is very likely that many voxels will appear to be active purely by random chance (ie, a false positive). The is known as the "Problem of Multiple Comparisons". One way around this is to do a cluster analysis in which active voxels are eliminated unless they appear in a cluster, the idea being that false positives will not appear next to each other.

This program (mri_volcluster) will find clusters in a volume. A cluster is a set of contiguous voxels which meet a threshold criteria. The set may also have to reach a certain minimum number of voxels to be considered a cluster. The results can be saved in four ways: (1) a text summary file, (2) a new volume which is same as the input volume but with all the voxels that do not belong to a cluster set to zero, (3) a volume with each voxel's value equal to the cluster number in the summary file to which the voxel belongs, and (4) one cluster can be saved as a label file. The search space within the volume can be restricted to be within a mask. Two voxels are considered contiguous if they share a common row, column, or slice (except for --allowdiag).