I am having a problem with @SUMA_Make_Spec_FS that I hope you can help me with.
I have noticed that after running the command (from the base of the relevant FreeSurfer output directory):
@SUMA_Make_Spec_FS -sid p1032
that some of the files in the SUMA directory that is created (e.g., “T1.nii”) are out of alignment with the “p1032_SurfVol+orig” file in that directory (when viewed in AFNI).
There are some (non-fatal) errors that are logged during the execution of @SUMA_Make_Spec_FS that are likely to be related - for example:
mri_convert -ot nii mri/T1.mgz /sci/anat/db_ver1/p1032/./SUMA/T1.nii $Id: mri_convert.c,v 126.96.36.199 2012/09/05 21:55:16 mreuter Exp $ reading from mri/T1.mgz... TR=2730.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -9.18154e-14, 0) j_ras = (0, 0, -1) k_ras = (-2.18714e-14, 1, 0) writing to /sci/anat/db_ver1/p1032/./SUMA/T1.nii... Error: base brick /p1032_SurfVol+orig not found.
It all works fine when using the “-NIFTI” flag to “@SUMA_Make_Spec_FS”.
This is with:
Precompiled binary linux_openmp_64: May 29 2021 (Version AFNI_21.1.09 'Domitian')
Thanks for any help!