Re: [Freesurfer] Cortical parcellation showing dots

2024-03-07 Thread Douglas N. Greve
And how does the parcellation look on the surface? On 3/7/2024 9:53 AM, Hyunchul Lee wrote: External Email - Use Caution Yes, it looks fine to me Those dots seem to lie on the pial surface On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve wrote: Have you looked at the actual

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

2024-03-07 Thread Huang, Yujing
Hi Brian, Since there is no output, I’m wondering if it passed reading lh.cortex.label. Some questions: 1. how did you generate lh.cortex.label? It needs to have the format described here - https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles 2. what is your SUBJECTS_DIR? ‘echo

Re: [Freesurfer] Cortical parcellation showing dots

2024-03-07 Thread Hyunchul Lee
External Email - Use Caution Yes, it looks fine to me Those dots seem to lie on the pial surface On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve wrote: > Have you looked at the actual surface? > > On 3/7/2024 2:29 AM, Hyunchul Lee wrote: > > External Email - Use Caution

Re: [Freesurfer] Cortical parcellation showing dots

2024-03-07 Thread Douglas N. Greve
Have you looked at the actual surface? On 3/7/2024 2:29 AM, Hyunchul Lee wrote: External Email - Use Caution Hello, I'm using Freesurfer recon-all to create reconstructions to use with MNE-python for source estimation of SEEG data. My work relies on having correct labeling of

Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

2024-03-07 Thread Douglas N. Greve
Yujing, you can just send Taylor a binary that can be put in the local version of $FREESURFER/bin On 3/6/2024 11:45 AM, Huang, Yujing wrote: Hi Taylor, Thanks for sharing the data. I see the problem now.  The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as