Hi,
I ave noticed fmriprep produced a couple of surf.gii in the anat folder for each subject.
From my understanding these images are in the native space.
Is it possible to average these images to get a group template?
I guess it will require some sort of normalization in template space. How could I do that?
Is freesurfer the best tool to develop this pipeline? Are there good tools in python as well?
Best,
Simon
Hi @simon.thibault,
In FreeSurfer:
USAGE: make_average_surface
Required Arguments
--subjects <subj1> <subj2> ... <subjN>
: or declare subjects in SUBJECTS env var
--fsgd fsgdfile : get subject list from fsgd
Optional Arguments
--out <average subject name> : default name is 'average'
--sdir <SUBJECTS_DIR to use instead of the one in the env>
--sd : same as --sdir
--sd-out topdir : put data here
--xform <transform_fname> : filename of transform file
--ico <number> : specify icosahedron number, default is 7 (ic7.tri)
--surf-reg <surface name> : alternative registration surface
--lh : only do left hemi (default is to do both)
--rh : only do right hemi (default is to do both)
default: sphere.reg
--force : overwrite existing average subject data
--annot-template : use annotation when making tif
--template-only : useful when creating iterative atlases
--no-template-only : turns off --template-only
--no-annot : do not create average annotations (does not affect use with template)
--no-cortex-label : do not create ?h.cortex.label
--annot annotname <--annot annotname > : supply list of annots to use (default )
--meas measname <--meas measname > : supply list of meass to use (default )
--no-surf2surf : use old parametric surface method (may give big faces at the poles)
--help : short descriptive help
--no-symlink : do not use symbolic links (just copy files)
--no-lik : same as --no-symlink
--version : script version info
--echo : enable command echo, for debug
--debug : same as --echo
See also: recon-all, make_final_surfaces, morph_subject
Version: FreeSurferEnv.csh 7.4.1
Creates average surfaces and curvatures from a set of subjects.
Calls mris_average_curvature, mris_make_average_surface, mris_smooth,
mris_inflate, and mris_curvature.
EXAMPLE
make_average_surface --out avgsubject --subjects subj1 subj2 subj3 subj4
will create $SUBJECTS_DIR/avgsubject with average surfaces for orig,
white, pial, inflated for each hemi.
SEE ALSO
make_average_subject, make_average_volume
GETTING HELP
Run recon-all --help for extensive text on the reconstruction process.
Or, send email to freesurfer@nmr.mgh.harvard.edu.
Also see http://surfer.nmr.mgh.harvard.edu.
Best,
Steven
Thanks,
I guess the use of this function requires to make sure each template is in the same space (my surf.gii images are in native space).
That is something I am not sure how to do it in freesurfer or with any other software.
Best,
Simon