Hello,
I am running recon-all for several subjects’ 7T data using Freesurfer version 6.0 and currently trying to ensure appropriate skull stripping and pial/wm surface generation. For a few participants that needed some control points added and for which I reran them through the –autorecon2-cp option, I was unable to open the pial surfaces for review. I’ve seen on some of the other posts that you guys recommend running “recon-all –make all” to rebuild the files. I’ve tried to run the -make all command but have been running into the same error in the “Jacobian white lh” step:
#@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018 /bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts
mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
reading surface from ../surf/lh.white.preaparc… mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match ../surf/lh.white.preaparc
No such file or directory mrisReadTriangleFile failed.
No such file or directory mris_jacobian: could not read target surface ../surf/lh.sphere.reg No such file or directory
recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018
All of the output in the log file up until this point appears to have finished without error. I can now open the surfaces for review, but am wondering what is affected by –make all not finishing completely.
Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnweis@uwm.edu