External Email - Use Caution
Hmm, it looks like the command `mri_binarize` isn't recognizing the
`--noverbose` flag. I tested this in my env, and I'm not getting that
("ERROR: Option --noverbose unknown") error.
Could it be that $FREESURFER_HOME is pointing to an older version of
FreeSurfer? What does `mri_binarize --version` return?
You can also try running the failed command in isolation:
```
mri_binarize --match 2 41 --count
/home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.count.txt
--i
/home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.nii.gz
--noverbose
```
-Paul
On Thu, Jul 1, 2021 at 11:41 AM Fernanda Hansen P. de Moraes <
fernandahmor...@gmail.com> wrote:
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I am trying to process some newborn subjects including the segfile. In
> both situations, including the mask file and using the --forceskullstrip
> flag I get the following error (log file attached):
>
>
>
> *lta_convert successful./home/fernanda/Documentos/dHCP/freesurfer1ERROR:
> Option --noverbose unknown*
>
> This is the exact command I am running:
> *infant_recon_all --s sub-CC00060XX03 --age 0 --segfile
> sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz
> --forceskulltrip --force*
>
> How can I overcome this? Thank you very much.
> Fernanda Hansen P. de Moraes
>
> fernandahmor...@gmail.com
> Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1RRuTHG5D-H3NaGVFWgZfL1Bi77ULGHojbbVDmyqhVH2jSGexGYRUk5ZmgP-V0QkO9mi_tPvV3mncwWruLkyPW12PPF63_AVMPQg0xvBzcEs8PZCWNJUJojvIB8EfaZkUZ6skvO5H42CnSA1nHM8ayFmmTUNpO0ob1BODwMW-VjE0XocS5wNjWZ7jVTM0RcpovsKqBJiq5tQTo-HaD04p-iBGksME2a4NfHS59qKgSgVGuKsiCSyzspUBq0YrVlL7U5tTDPvAsHzaMnlsC8ElLw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
