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'''Index'''
<<TableOfContents>>


= Name =
[[isxconcat-sess]] 
 
= 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 =
FsFast

= Methods Description =
??

= References =
none

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

= Author/s =
DougGreve