Re: [Freesurfer] recon-all error - MRISlabel2Mask()

Douglas N. Greve Wed, 22 Nov 2023 10:18:50 -0800

yes, sending the full log file will be helpful. My guess is that thesurfaces got out of synch (eg, if you had done edits).


On 11/21/2023 8:15 PM, Mark Wagshul wrote:

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Dear Freesurfer experts,
Hi. Hoping someone can give me some guidance in how to proceed withthis error in recon-all (at the moment, was running autorecon-wm, butnot sure that’s relevant). Just pasting the last few commands whichwere successfully run, can send the whole recon-all.log file ifneeded. 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 --ltatransforms/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 --movorig/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 ThuMay 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 --movtransforms/tmp.bbregister.3166191/template.nii --regdattransforms/tmp.bbregister.3166191/reg.init.dat --regtransforms/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 --movtransforms/tmp.bbregister.3166191/template.nii --regdattransforms/tmp.bbregister.3166191/reg.init.dat --regtransforms/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 0.00001.0000 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 1.100000.00000 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 0.0000000.000000 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 0.059354540.04330484 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 --regtransforms/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-regtransforms/tmp.bbregister.3166191/bbr.pass1.dat --subsamp-brute 100--subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surfwhite.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-regtransforms/tmp.bbregister.3166191/bbr.pass1.dat --subsamp-brute 100--subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surfwhite.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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Re: [Freesurfer] recon-all error - MRISlabel2Mask()

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