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Hello,
I recently updated to Freesurfer 7.4.1 (previously running 7.2.0) and am trying
to get my full workflow to run. I am getting the following error when I try to
run “surfreg –s test –t fsaverage_sym –lh –xhemi –no-annot”:
#CMD# mris_convert --center --vol-geom
/usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
centering surface
error: mghRead(/usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz, -1): could
not open file
It looks as if there is a typo in the path to “orig.mgz”, where
“freesurfer/subjets” should be “freesurfer/subjects”.
I’ve not found anything searching for “surfreg” in the message board that
points to a corrected surfreg binary.
1. Freesurfer version:
freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460
2. Platform: python:3.9-debian Docker image
3. uname -a: Linux 828abe00572a 6.5.0-1024-gcp #26~22.04.1-Ubuntu SMP Fri
Jun 14 18:48:45 UTC 2024 x86_64 GNU/Linux
4. Full terminal dump attached
Thanks and cheers.
Suzanne T. Witt, PhD
Scientific Solutions Engineer
suzannew...@flywheel.io<mailto:suzannew...@flywheel.io>
she/her
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root@828abe00572a:/flywheel/v0# surfreg --s test --t fsaverage_sym --lh
--no-annot --xhemi
Tue Dec 3 16:21:45 UTC 2024
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /flywheel/v0
/usr/local/freesurfer/bin/surfreg --s test --t fsaverage_sym --lh --no-annot
--xhemi
Linux 828abe00572a 6.5.0-1024-gcp #26~22.04.1-Ubuntu SMP Fri Jun 14 18:48:45
UTC 2024 x86_64 GNU/Linux
#@# lh Tue Dec 3 16:21:45 UTC 2024
#CMD# mris_register -curv -threads 1
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.sphere
/usr/local/freesurfer/subjects/fsaverage_sym/lh.reg.template.tif
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
using smoothwm curvature for final alignment
cwd /flywheel/v0
cmdline mris_register -curv -threads 1
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.sphere
/usr/local/freesurfer/subjects/fsaverage_sym/lh.reg.template.tif
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
0 inflated.H
1 sulc
2 smoothwm (computed)
7.4.1
7.4.1
reading surface from /usr/local/freesurfer/subjects/test/xhemi/surf/lh.sphere...
reading template parameterization from
/usr/local/freesurfer/subjects/fsaverage_sym/lh.reg.template.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=828ab, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0
tol=5.0e-01, sigma=0.0, host=828ab, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
tol=1.0e+00, sigma=0.5, host=828ab, nav=1024, nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = 0.000, std = 5.555
curvature mean = 0.040, std = 0.799
curvature mean = 0.011, std = 0.866
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
new MRISrigidBodyAlignGlobal_findMinSSE min @ (10.00, -3.00, -6.50) sse =
255888.2, elapsed since starting=0.4827 min
MRISrigidBodyAlignGlobal() done 0.48 min
curvature mean = 0.019, std = 0.805
curvature mean = 0.005, std = 0.948
curvature mean = 0.018, std = 0.817
curvature mean = 0.003, std = 0.979
curvature mean = 0.018, std = 0.820
curvature mean = 0.001, std = 0.992
2 Reading smoothwm
curvature mean = -0.018, std = 0.269
curvature mean = 0.033, std = 0.166
curvature mean = 0.055, std = 0.380
curvature mean = 0.030, std = 0.177
curvature mean = 0.030, std = 0.581
curvature mean = 0.030, std = 0.188
curvature mean = 0.015, std = 0.726
curvature mean = 0.030, std = 0.194
curvature mean = 0.005, std = 0.830
MRISregister() return, current seed 0
-01: dt=0.0000, 11 negative triangles VmPeak 507676
111: dt=0.9900, 11 negative triangles
112: dt=0.9900, 10 negative triangles
113: dt=0.9900, 9 negative triangles
114: dt=0.9900, 11 negative triangles
115: dt=0.9900, 9 negative triangles
116: dt=0.9900, 9 negative triangles
117: dt=0.9900, 9 negative triangles
118: dt=0.9900, 11 negative triangles
119: dt=0.9900, 8 negative triangles
120: dt=0.9900, 10 negative triangles
121: dt=0.9900, 9 negative triangles
122: dt=0.9900, 9 negative triangles
123: dt=0.9900, 10 negative triangles
124: dt=0.9900, 10 negative triangles
125: dt=0.9900, 9 negative triangles
126: dt=0.9900, 10 negative triangles
127: dt=0.9900, 6 negative triangles
128: dt=0.9900, 10 negative triangles
129: dt=0.9900, 5 negative triangles
130: dt=0.9900, 1 negative triangles
131: dt=0.9900, 5 negative triangles
132: dt=0.9900, 3 negative triangles
133: dt=0.9900, 1 negative triangles
writing registered surface to
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg...
registration took 0.16 hours
#VMPC# mris_register VmPeak 507676
FSRUNTIME@ mris_register 0.1581 hours 1 threads
#CMD# mris_convert --center --vol-geom
/usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
/usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
centering surface
error: mghRead(/usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz, -1): could
not open file
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