Dear Freesurfer experts, I'm trying to run *mris_make_surfaces* with a FLAIR.mgz file as input. I used the same command as used if I run autorecon3, in order to make a pial refinement. Here is the command:
mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR subject_name rh However, when I try to run this command individually I always get this error: ... smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning cortical surface to gray/csf boundary. repositioning pial surface locations using ../mri/FLAIR.mgz *mghRead(../mri/FLAIR.mgz, -1): could not open file* *mris_make_surfaces: could not load flair volume ../mri/FLAIR.mgz* The problem is that the output of mghRead is type NULL, and then the program exits with this error, as it can be seen in mri_make_surfaces.c: [image: Imágenes integradas 3] I have set up the same enviroment (SUBJECTS_DIR, etc) as if I run with autorecon3, so I can't understand why is this error happening. The FLAIR file mgz is not corrupted as I checked with tkmedit and mri_info. Could you give me some idea? Thanks in advance, Best, Marc
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