are you just running gcut or all of recon-all? If all of recon-all, please send the recon-all.log file
On 12/2/2021 2:43 PM, Vishal Mohanty wrote:
External Email - Use Caution
Hi
This is Vishal Mohanty, a Research Assistant at the CNS Lab https://secure-web.cisco.com/15W4gGDirofYO8-hxBJZzt-0Z-M9nlsafkwxgoE1yBXcR-yRlpi4hSdJy1Rmabv3CgdHVnnVbW4HOgzr58sGmHpdvzKHyuauJORmQfXplg2hzvu1LZTBlXu1II7iZPKUsfRW5vvjtsnhq_IOlApnYs9tUrlKIiLbP-0WMhESr5HmRsaK9Cyt8rXS2kYTvEZHd4SjHX6RDQgV1VdJ9jPs6wlF9addGZ8LDyTmipJ62kaLJ_B_Li-7hzloE_jMFxWqCL0NOe8EXqFqxqqXru4g33l5sqh0KfC1XOWLinkm65w_S0SRbJB3IriH8nP34c3-y/https%3A%2F%2Fcnslab.stanford.edu%2F at Stanford which is headed by Prof. Kilian Pohl http://secure-web.cisco.com/1SZ4eEoYf_E7omrj4INdi5GjmRCw5BV-qQfn2PUzBkhAmhzg9o1EOsGNK10NZRw5SfnL5bJkYZTQTHkzenh--uXslAATvtFTmJ7NjUOLDiJgSRVSzTnG2joPBK5ngvrDs2nDg10edlZPsdBg8V2evhOrlAj3Q8Y5a0Icw4wH7DIGgCTlSngFLkK8lmTLGTZYNpQgHETNcLNfQRaksY2HB0VRu5tPFk6EkeR6apvPAEghUfHILOUPInGPn3UEANagA637xp9HAtEEnxJ5HWTuwmBKT9wxePBfm6qL0NgWGhNIu2oUNzc8odvM5B4ZVmJgU/http%3A%2F%2Fcnslab.stanford.edu%2Fpersonal%2Fkilian-pohl.html. We are running Freesurfer commands for processing of our MRI data on Sherlock https://secure-web.cisco.com/1ELFOu5r8C0zuhwJthCGAIpaL-g9geTHv3j06pTTPK06DKUjl_FsABCbwv_YEB4NiLvPf5WaIymCbVGgy_N3zr1m0bbHiNHuZq1bQLIxhcthpMYEvxKVOI7F4PKk__J43FiQjajODDvS-plsHLwSjaI2vOA4RHGzU8KzuWGfhUG79R_7PEQjfaRe-fzF4cN41C4kadb7hcxPD6pusNG3Ciuq5HM_UH1n1HzwAtyKIDAB4f4PynteNw0qdQAIRDg7Ha_-vHwFAnwduc3MwdAT0tmsVCxmifNpM3GnYRbr4YMi-9wBCy1llPqh_XXxN3OlV/https%3A%2F%2Fwww.sherlock.stanford.edu%2F which is the HPC cluster at Stanford. We are seeing some errors in running *mri_gcut* of the type:
CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain.nii.gz
========================================================================
error: No such file or directory
error: Could not set locale^@
I'm attaching the full log file. Could you please help me understand what's the issue and how to fix it. Do let me know what other information would be needed from my end.
Thanks and Regards
Vishal Mohanty MS CS Candidate (2023) Stanford University
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer