Not sure what is going on here. Can you run it without the -parallel flag?
On 12/19/2021 3:37 AM, Atsushi Yamaguchi wrote:
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Hello FreeSurfer Developers,
I'm attempting to run recon-all on structural MRI data of Human Connectome Project (ex. T1w.nii.gz from folder"102109_3T_Structural_preproc"), but I get the following error :
ERROR: From recon-all.log.
cp rh.white.preaparc.K rh.white.K
cp: cannot stat 'rh.white.preaparc.K': No such file or directory
I've searched the list and no similar errors have been reported.
Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
- FreeSurfer
version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Platform: Linux-generic-Ubuntu SMP
uname -a: Linux l4n 5.4.0-91-generic #102-Ubuntu SMP Fri Nov 5
16:31:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
- recon-all.log: see attached
total integrated curvature = 10.482*4pi (131.726) --> -9 handles
ICI = 191.0, FI = 2265.8, variation=34649.724
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.
rm -f rh.white.H
cp rh.white.preaparc.H rh.white.H
cp: cannot stat 'rh.white.preaparc.H': No such file or directory
rm -f rh.white.K
cp rh.white.preaparc.K rh.white.K
cp: cannot stat 'rh.white.preaparc.K': No such file or directory
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
245 vertices thresholded to be in k1 ~ [-0.20 0.44], k2 ~ [-0.08 0.05]
total integrated curvature = 0.489*4pi (6.143) --> 1 handles
ICI = 1.6, FI = 11.7, variation=193.559
152 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
189 vertices thresholded to be in [-0.11 0.21]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.023
done.
PIDs (30184 30187 30190 30193 30196 30199 30202 30205 30208 30211 30214 30217) completed and logs appended.
Linux l4n 5.4.0-91-generic #102-Ubuntu SMP Fri Nov 5 16:31:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 102019 exited with ERRORS at Sun Dec 19 09:54:10 JST 2021
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