Name

Synopsis

isxconcat-sess sf <subjectfilename> -df <srchdirfile> -analysis <your_analysisname> -c <your_contrastname> -o <outdir>

Arguments

Required Arguments:

-analysis <your_analysisname>	session-level functional analysis name
-sf <subjectfilename>	text file list of subjects
-df <srchdirfile>	text file list of directories where subjects can be found
-d <srchdir>	use instead of df if specifying only one dir
-c <your_contrast_name>	use instead of df if specifying only one dir
-o <outdir>	top group output directory

Optional Arguments:

Volume-based options:

-talres res

1 or 2 mm (default 2)

Surface-based options:

-hemis	surface-based, both lh and rh
-hemi <hemisphere>	for surface-based analysis (lh or rh)
-subject <subject>	sample to subject's surface (default fsaverage)

Outputs

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

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

In the your_contrast_name folder, you will see:

tal.ces.nii (the contrast maps for each of the subjects)
tal.cesvar.nii (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.)
"osgm" directory (one-sample-group-mean corresponds to a group design matrix that is
- simply a column of 1s. This will be used later in group analysis (i.e. in mri_gmfit))

Description

This command will go through each session in the sessid file and find the your_contrastname contrast in the your_analysisname analysis. It will use the register.dat for that session to resample to MNI305/fsaverage space. Then concatenate all subjects' data into one file.

General Description

Resamples a group of FS-FAST first-level analyses into a common space,either volume- or surface-based, and concatenates all the sessions together into one multi-frame file suitable for use with mri_glmfit.

Bugs

none

Links

FsFast

Methods Description

References