Closed vferat closed 5 years ago
@vferat This happens if your fsaverage6
and PT02
are not in the $SUBJECTS_DIR
.
You need to first create a symbolic link for fsaverage6
in your $SUBJECTS_DIR
(it should be the folder contain PT02
)
ln -s your_freesurfer_dir/freesurfer/5.3.0/subjects/fsaverage6
Hey @rubykong , thanks for you answer Both subject (PT02 and fsaverage) are in the same folder. I only downloaded the fsaverage6 folder available in this repo, but there is no lh.sphere or lh.sphere.reg here. Do I have to download the full fsaverage6 folder ( this one ? ) and overwrite files with the ones of this repo ?
@vferat You might need to replace this fsaverage6
folder with the one from freesurfer: freesurfer/5.3.0/subjects/fsaverage6
Perfect @rubykong it's working ! Thanks a lot. 👍
Last question : To use thesurf2surf
with the fsaverage6
provided , does my subject need to be registered to the average.curvature.filled.buckner40.tif
default template ?
@vferat I am actually not super sure. We normally just run the standard recon-all pipeline. I think you can check with the freesurfer mailing list. You can also load the individual surface mesh (e.g. PT02/surf/lh.inflated) and the mri_surf2surf output (i.e. PT02/lh.Schaefer2018_1000Parcels_17Networks_order.annot) in freeview to visually check if it looks okay.
I ran parcellation using both mris_ca_label
(with the .gcs files) and surf2surf
for the100 labels 7 networks and fond a 2% difference in voxel labels between both files, so I assume the method works correctly. If I found more information, I'll keep you inform.
Thanks again for your help
I'm trying to follow this example in order to parcellate an individual brain. However whenI try to run mri_surf2, it raises an error saying it does not find the lh.sphere.reg ( not provided in the repo) Do I have to manually create this file ? If yes can you explain me the different steps to achieve that ?
Actual situation
mri_surf2surf: could not read surface .../fsaverage6/surf/lh.sphere.reg No such file or directory Return code: 255
Steps to reproduce the issue (optional)
Run the following command:
Thanks for all yur work, Victor