External Email - Use Caution
Dear Freesurfer experts,
Hi. Hoping someone can give me some
guidance in how to proceed with this error in recon-all (at
the moment, was running autorecon-wm, but not sure that’s
relevant). Just pasting the last few commands which were
successfully run, can send the whole recon-all.log file if
needed. Nothing obvious in terms of the T1 or T2 images.
Thanks!
#===============================
mri_surf2surf
--s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg --surfreg
woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf
Reading header
for orig.mgz
Source
registration surface changed to woT2.pial.rawavg
Target
registration surface changed to woT2.pial.rawavg
7.3.2
setenv
SUBJECTS_DIR
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
mri_surf2surf
--s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg --surfreg
woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf
sysname Linux
hostname
cpu-771.cluster.local
machine x86_64
user
mwagshul
srcsubject =
sub-XXX
srcval =
(null)
srctype =
trgsubject =
sub-XXX
trgval =
woT2.pial.rawavg.conf
trgtype =
srcsurfreg =
woT2.pial.rawavg
trgsurfreg =
woT2.pial.rawavg
srchemi = rh
trghemi = rh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src =
(null)
label-trg =
(null)
OKToRevFaceOrder
= 1
UseDualHemi = 0
Reading source
surface reg
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg
Loading source
data
Reading surface
file
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg
Applying linear
registration transform
1.00000
0.00000 0.00000 -0.40000;
0.00000
1.00000 0.00000 0.00000;
0.00000
0.00000 1.00000 0.39999;
0.00000
0.00000 0.00000 1.00000;
INFO: trgsubject
= srcsubject
Saving target
data
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
Tue Nov 21
17:49:18 EST 2023
#===============================
bbregister --s
sub-XXX --mov orig/T2raw.mgz --lta transforms/T2raw.auto.lta
--init-coreg --t2 --surf white.preaparc --proj-abs 1.5
--threads 1
tmp
transforms/tmp.bbregister.3166191
Log file is
transforms/T2raw.auto.log
Tue Nov 21
17:49:18 EST 2023
setenv
SUBJECTS_DIR
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
/public/apps/freesurfer/7.3.2/bin/bbregister
--s sub-XXX --mov orig/T2raw.mgz --lta
transforms/T2raw.auto.lta --init-coreg --t2 --surf
white.preaparc --proj-abs 1.5 --threads 1
bbregister 7.3.2
Linux
cpu-771.cluster.local 4.18.0-477.13.1.el8_8.x86_64 #1 SMP
Thu May 18 10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME
/public/apps/freesurfer/7.3.2
mri_convert
orig/T2raw.mgz
transforms/tmp.bbregister.3166191/template.nii
mri_convert
orig/T2raw.mgz
transforms/tmp.bbregister.3166191/template.nii
reading from
orig/T2raw.mgz...
TR=2500.00,
TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0,
0)
j_ras = (0, 1,
0)
k_ras = (0, 0,
1)
writing to
transforms/tmp.bbregister.3166191/template.nii...
mri_coreg --s
sub-XXX --mov transforms/tmp.bbregister.3166191/template.nii
--regdat transforms/tmp.bbregister.3166191/reg.init.dat
--reg transforms/tmp.bbregister.3166191/mri_coreg.lta
--nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01
$Id:
mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
cmdline
mri_coreg --s sub-XXX --mov
transforms/tmp.bbregister.3166191/template.nii --regdat
transforms/tmp.bbregister.3166191/reg.init.dat --reg
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1
--dof 6 --sep 4 --ftol .0001 --linmintol .01
sysname Linux
hostname
cpu-771.cluster.local
machine x86_64
user
mwagshul
dof 6
nsep 1
cras0 1
ftol 0.000100
linmintol
0.010000
bf 1
bflim
30.000000
bfnsamp 30
SmoothRef 0
SatPct
99.990000
MovOOB 0
optschema 1
Seed 53
Reading in mov
transforms/tmp.bbregister.3166191/template.nii
Reading in ref
brainmask.mgz
Reading in and
applying refmask aparc+aseg.mgz
Setting cras
translation parameters to align volume centers
Creating random
numbers for coordinate dithering
Performing
intensity dithering
Performing
intensity dithering on mov with computed dither
Init matrix
params -0.1000 0.1000 -0.9000 0.0000 0.0000 0.0000
1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
Initial
parameters to be opt -0.1000 0.1000 -0.9000 0.0000
0.0000 0.0000
Separation list
(1): 4 min = 4
DoSmoothing 1
DoCoordDither 1
DoIntensityDither
1
nitersmax 4
ftol 1.000e-04
linmintol
1.000e-02
SatPct 99.990000
Hist FWHM
7.000000 7.000000
nthreads 1
movsat =
278136.6250
mov gstd 1.9140
1.9140 1.9140
Smoothing mov
refsat =
116.0000
ref gstd 1.8914
1.8914 1.8914
Smoothing ref
COREGpreproc()
done
Testing if mov
and target overlap
Init cost
-1.0792090127
nhits = 110749
out of 16777216, Percent Overlap: 42.2
Initial
RefRAS-to-MovRAS
1.00000
0.00000 0.00000 -0.10000;
0.00000
1.00000 0.00000 0.10000;
0.00000
0.00000 1.00000 -0.90000;
0.00000
0.00000 0.00000 1.00000;
Initial
RefVox-to-MovVox
1.25000
0.00000 0.00000 -46.37500;
0.00000
0.00000 1.25000 -23.87500;
0.00000
-1.25000 0.00000 272.37500;
0.00000
0.00000 0.00000 1.00000;
sep = 4
-----------------------------------
COREGoptBruteForce()
30 1 30
Turning on
MovOOB for BruteForce Search
#BF# sep= 4
iter=0 lim=30.0 delta=2.00 -0.10000 0.10000 1.10000
0.00000 0.00000 0.00000 -1.0539398
Turning MovOOB
back off after brute force search
---------------------------------
Init Powel
Params dof = 6: -0.099998 0.099998 1.099998 0.000000
0.000000 0.000000
Starting
OpenPowel2(), sep = 4
InitialCost
-1.0792208910
#@# 4 188
-0.10000 0.10000 1.10000 0.00000 0.00000 0.00000
-1.0792209
fs_powell::minimize
nparams 6
maxfev 4
ftol
0.000100
linmin_xtol_
0.010000
powell nthiter
0: fret = -1.079221
#@# 4 195
-0.08162 0.10000 1.10000 0.00000 0.00000 0.00000
-1.0792221
#@# 4 196
-0.07162 0.10000 1.10000 0.00000 0.00000 0.00000
-1.0792230
#@# 4 210
-0.07162 0.10000 -0.51804 0.00000 0.00000 0.00000
-1.0806090
#@# 4 211
-0.07162 0.10000 -0.05384 0.00000 0.00000 0.00000
-1.0815350
#@# 4 215
-0.07162 0.10000 0.06935 0.00000 0.00000 0.00000
-1.0815829
#@# 4 217
-0.07162 0.10000 0.05935 0.00000 0.00000 0.00000
-1.0815856
#@# 4 245
-0.07162 0.10000 0.05935 0.00000 0.00000 0.01140
-1.0815859
#@# 4 246
-0.07162 0.10000 0.05935 0.00000 0.00000 0.02140
-1.0815865
powell nthiter
1: fret = -1.081586
#@# 4 259
-0.03311 0.10000 0.05935 0.00000 0.00000 0.02140
-1.0815872
#@# 4 261
-0.05124 0.10000 0.05935 0.00000 0.00000 0.02140
-1.0815881
#@# 4 269
-0.05124 0.03905 0.05935 0.00000 0.00000 0.02140
-1.0816078
#@# 4 270
-0.05124 0.00179 0.05935 0.00000 0.00000 0.02140
-1.0816091
#@# 4 271
-0.05124 0.01441 0.05935 0.00000 0.00000 0.02140
-1.0816101
#@# 4 288
-0.05124 0.01441 0.05935 0.04330 0.00000 0.02140
-1.0816138
#@# 4 298
-0.05124 0.01441 0.05935 0.04330 0.01983 0.02140
-1.0816160
#@# 4 301
-0.05124 0.01441 0.05935 0.04330 0.04002 0.02140
-1.0816177
#@# 4 311
-0.05124 0.01441 0.05935 0.04330 0.04002 0.03140
-1.0816185
Powell done
niters total = 1
OptTimeSec 8.5
sec
OptTimeMin 0.14
min
nEvals 315
Final optimized
parameters -0.05123561 0.01440958 0.05935454
0.04330484 0.04001505 0.03140411
Final matrix
parameters -0.0512 0.0144 0.0594 0.0433 0.0400 0.0414
1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
Final cost
-1.081618519399467
---------------------------------
Final
RefRAS-to-MovRAS
1.00000
0.00055 0.00070 -0.05124;
-0.00055
1.00000 0.00076 0.01441;
-0.00070
-0.00076 1.00000 0.05935;
0.00000
0.00000 0.00000 1.00000;
Final
RefVox-to-MovVox
1.25000
0.00087 -0.00069 -46.46457;
0.00069
-0.00094 1.25000 -23.93044;
0.00087
-1.25000 -0.00095 273.60037;
0.00000
0.00000 0.00000 1.00000;
Final matrix
parameters -0.0512 0.0144 0.0594 0.0433 0.0400 0.0314
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Final opt
parameters -0.0512 0.0144 0.0594 0.0433 0.0400 0.0314
nhits = 110715
out of 16777216, Percent Overlap: 42.2
mri_coreg
RunTimeSec 75.3 sec
To check run:
tkregisterfv
--mov transforms/tmp.bbregister.3166191/template.nii --targ
brainmask.mgz --reg
transforms/tmp.bbregister.3166191/mri_coreg.lta --s sub-XXX
--surfs
mri_coreg done
mri_segreg --mov
transforms/tmp.bbregister.3166191/template.nii --init-reg
transforms/tmp.bbregister.3166191/reg.init.dat --out-reg
transforms/tmp.bbregister.3166191/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3
--brute -4 4 4 --surf white.preaparc --gm-proj-abs 1.5
--gm-gt-wm 0.5
7.3.2
setenv
SUBJECTS_DIR
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
mri_segreg --mov
transforms/tmp.bbregister.3166191/template.nii --init-reg
transforms/tmp.bbregister.3166191/reg.init.dat --out-reg
transforms/tmp.bbregister.3166191/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3
--brute -4 4 4 --surf white.preaparc --gm-proj-abs 1.5
--gm-gt-wm 0.5
sysname Linux
hostname
cpu-771.cluster.local
machine x86_64
user
mwagshul
movvol
transforms/tmp.bbregister.3166191/template.nii
regfile
transforms/tmp.bbregister.3166191/reg.init.dat
subject sub-XXX
dof 6
outregfile
transforms/tmp.bbregister.3166191/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign -1
PenaltySlope
0.500000
PenaltyCenter
0.000000
surfname
white.preaparc
GMProjAbs
1.500000
WMProjAbs
2.000000
lhcostfile
(null)
rhcostfile
(null)
interp
trilinear (1)
frame 0
TolPowell
0.000100
nMaxItersPowell
36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed
1701112546
TransRandMax
0.000000
RotRandMax
0.000000
Translations
0.000000 0.000000 0.000000
Rotations
0.000000 0.000000 0.000000
Input reg
1.00000
0.00055 0.00070 -0.04753;
-0.00070
-0.00076 1.00000 0.07289;
0.00055
-1.00000 -0.00076 -0.02905;
0.00000
0.00000 0.00000 1.00000;
Loading mov
ExcludeZeroVoxels
1
Reading in targ
vol
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri/orig.mgz
Projecting LH
Surfs
Loading
lh.white.preaparc surf
GM Proj: 0
0.500000 1.500000
WM Proj: 0
0.500000 2.000000
Projecting RH
Surfs
Loading
rh.white.preaparc surf
Projecting RH
Surfs
Using
lh.cortex.label
ERROR:
MRISlabel2Mask(): label vertex 150145 is >= nvertices
150145
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email:
mark.wagshul@einsteinmed.org
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