Hi Wade
from the recon-all.log it looks like you never ran autorecon3. Is there a
reason for this? Usually we run all the way through autorecon3 before
running the T2pial stuff
cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:
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Hi all,
I’m trying to run –autorecon2 on 3 subjects (I already ran –autorecon1 on them
with no errors.) and I’m
getting an error after the –final_surfs part saying that lh.white does not
exits (and it doesn’t, I
checked for it). I have run about 10 other subjects, and they all ran fine and
contain ?h.white
files. I saw 2 other strings in the archive with this same issue, but there
was no resolution to them.
This error just started happening, and I didn’t change anything. Here’s the
command I’ve been using:
recon-all –subjid <my subject #> -T2 <name of t2.nii file> -T2pial -autorecon2
Here’s the error output:
MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/analysis_files/ANG_1034/surf/lh.wh
ite): could not open file
I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c on a
virtual machine running Red
Hat Enterprise Linux Workstation 7.6
I’ve attached the recon-all.log file
Thanks!
----
Wade A. Weber, MS
Psychiatry Research Program Coordinator
Dell Medical School | The University of Texas at Austin
o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
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