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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"] ["selxavg3-sess"] ["mri_glmfit"] |
[[mkanalysis-sess -gui]] [[selxavg3-sess]] [[mri_glmfit]] |
Index
Contents
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
See Also
mkanalysis-sess -gui selxavg3-sess mri_glmfit
Links
Methods Description
??
References
none
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>