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 < fernandahmoraes@gmail.com> wrote:
External Email - Use CautionDear 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
fernandahmoraes@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-H3NaGVFWgZfL1Bi77ULGHojbbVDmyqhVH2jSG...