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func2sph-sess -analysis (analysisname) -sf subjectfilename -d . func2sph-sess -analysis <analysisname> -sf <subjectfilename> -d <subjects_dir>
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["othercommand1"], ["othercommand2"] ["func2tal"],

Index TableOfContents


func2sph-sess - resamples functional data from native space to spherical space


func2sph-sess -analysis <analysisname> -s <subjecname> or -sf <subjectfilename> -d <subjects_dir>


Positional Arguments


Required Flagged Arguments

-analysis analysisname

session-level functional analysis name

-sf sessidfile ...

-df srchdirfile ...

Optional Flagged Arguments

-hemi hemilist

lh, rh, or <lh rh>

-surf surfacename

resample onto surfacename <white>

-surfreg surfacename

use surfacename for registration <sphere.reg>

-trgsubject subjectname

resample onto subject instead of ico

-icoorder order

icosahedron order 0-7 <7>

-mapmethod method

<nnfr> or nnf

-float2int method

tkreg, floor, round

-projfrac fraction

resample fraction of thickness into gray


save data to spacedir (sph)

-umask umask

set unix file permission mask


print version and exit

-fwhm fwhm

smooth the volume before resampling (good with -synth)


synthesize volume with white gaussian noise


This will create a subdirectory called "sph" under the bold/analysisname directory for each session. Within this directory, two new volumes will be created with stems "h" and "h-offset". These are where the hemodynamic averages are stored.


Spatial normalization is the process through which two or more subjects' brains are aligned or registered based on anatomical information. This is so that when the subjects' functional data are averaged together on a voxel-by-voxel basis, the voxels represent the same anatomical location in each subject. The Talairach transform is the traditional spatial normalization technique. However, the spherical transform (for cortical surfaces) is also supported in the standard stream. Henceforth, the term space will be used to refer to the way in which the functional data has been spatially normalized (or resampled). There are three spaces that are supported in the standard stream: native (no resampling), Talairach, and spherical. Resampling is always done on data averaged in an analysis (ie, not the raw data).


Example 1

func2sph-sess -analysis <analysisname> -sf <subjectfilename> -d <subjects_dir>



See Also



FreeSurfer, FsFast

Methods Description



Reporting Bugs

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


DougGreve, PhD

func2sph-sess (last edited 2008-04-29 11:45:26 by localhost)