The Schaefer2018 atlas is provided in fsaverage format (FreeSurfer version 5.3).
I would like to use the Schaefer2018 atlas instead of an atlas already provided in freesurfer, for commands such as:
mris_anatomical_stats -a $SUBJECTS_DIR/bert/label/lh.aparc.annot -b bert lh
Assuming recon-all is already run, how can I get this to work in FreeSurfer (using version 7.4.1)?
I think I should do something like the following to get the atlas into subject space (using bert and built in atlas for example):
mri_surf2surf --srcsubject fsaverage --trgsubject bert --hemi lh --sval $FREESURFER_HOME/subjects/fsaverage/label/lh.aparc.annot --tval ./test.annot
But I get this error (on multiple computers):
Reading source surface reg /usr/local/freesurfer/7.4.1/subjects/fsaverage/surf/lh.sphere.reg
Loading source data
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Converting source to float
Reading target surface reg /usr/local/freesurfer/7.4.1/subjects/bert/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (135579)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (163842)
Reverse Loop had 46849 hits
Surf2Surf: Dividing by number of hits (135579)
INFO: nSrcLost = 0
nTrg121 = 95365, nTrgMulti = 40214, MnTrgMultiHits = 2.16499
nSrc121 = 146909, nSrcLost = 0, nSrcMulti = 16933, MnSrcMultiHits = 2.09762
Saving target data
Copying ctab from source
NOT Copying ctab from source
Saving to ./test.annot
error: MRIwriteType(): code inconsistency (file type recognized but not caught)
ERROR: writing ./test.annot