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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(a)einsteinmed.org<mailto:mark.wagshul@einsteinmed.org>
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