[Freesurfer] recon-all error - MRISlabel2Mask()

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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@einsteinmed.orgmailto:mark.wagshul@einsteinmed.org

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