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["isxconcat-sess"] –sf <subjectfilename> -df <srchdirfile> -analysis <your_analysisname> -c <your_contrastname> -o <outdir> [[isxconcat-sess]] –sf <subjectfilename> -df <srchdirfile> -analysis <your_analysisname> -c <your_contrastname> -o <outdir>
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["mkanalysis-sess -gui"]
[[mkanalysis-sess -gui]]





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


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:


surface-based, both lh and rh

-hemi <hemisphere>

for surface-based analysis (lh or rh)

-subject <subject>

sample to subject's surface (default fsaverage)


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))


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.



See Also

mkanalysis-sess -gui selxavg3-sess mri_glmfit



Methods Description




Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>



isxconcat-sess (last edited 2008-04-29 11:46:24 by localhost)