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I am a researcher currently working with the Freesurfer 7.1.1 version for a research project. I have encountered an issue while trying to compute the local gyrification index (LGI).
We have pre-existing Freesurfer analysis results, and we want to use the mris_compute_lgi script to calculate the LGI values. However, we are facing difficulties in the first step of running the mris_fill command to generate the ?h.pial.filled.mgz file. After the command completes, we are unable to read the generated ?h.pial.filled.mgz file, and we receive the following error:
reading filled volume... /bin/bash: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh for reading ERROR: loading lh.pial.filled.mgz as MGH Dot indexing is not supported for variables of this type. Error in make_outer_surface (line 25) volume=vol.vol;
We have also tried to read the lh.pial.filled.mgz file generated by mris_fill using the load_mgh function individually, but we are still unable to read it successfully.
Could you please provide us with some guidance on how to resolve this issue?