I am trying to transfer Yeo2011 parcellations to a subject’s surface after I fixed an issue with the wm surface and reran recon. The recon had no errors and the surface is fixed. However, when I tried to run mri_surf2surf I got “MRISreadAnnotationIntoArray: vertex index out of range” and the output is clearly wrong (see attached), despite it working before the recon edits. Any help would be much appreciated!

 

This is the re-run of recon on the edited subject:

recon-all -autorecon2-wm -subjid 200614

 

This is the mri_surf2surf on the edited subject:

mri_surf2surf --srcsubject fsaverage --trgsubject 200614 --hemi lh --sval-annot fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval 200614/label/lh.Yeo2011_7Networks_N1000.annot

 

This is the output:

sysname  Linux

hostname c0012

machine  x86_64

user     snolin

srcsubject = fsaverage

srcval     = (null)

srctype    =

trgsubject = 200614

trgval     = 200614/label/lh.Yeo2011_7Networks_N1000.annot

trgtype    =

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

srchemi    = lh

trghemi    = lh

frame      = 0

fwhm-in    = 0

fwhm-out   = 0

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder  = 1

UseDualHemi = 0

Reading source surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/lh.sphere.reg

Loading source data

Reading surface file /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/lh.orig

reading colortable from annotation file...

colortable with 8 entries read (originally MyColorLUT)

Reading target surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/200614/surf/lh.sphere.reg

Done

Using surf2surf_nnfr()

Mapping Source Volume onto Source Subject Surface

surf2surf_nnfr: building source hash (res=16).

Surf2Surf: Forward Loop (136080)

 

Surf2Surf: Dividing by number of hits (136080)

INFO: nSrcLost = 54959

nTrg121 = 136080, nTrgMulti =     0, MnTrgMultiHits = 0

nSrc121 = 87475, nSrcLost = 54959, nSrcMulti = 76367, MnSrcMultiHits = 0.636466

Saving target data

Converting to target annot

Saving to target annot 200614/label/lh.Yeo2011_7Networks_N1000.annot

 

mri_surf2surf --srcsubject fsaverage --trgsubject 200614 --hemi rh --sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval 200614/label/rh.Yeo2011_7Networks_N1000.annot

 

sysname  Linux

hostname c0012

machine  x86_64

user     snolin

srcsubject = fsaverage

srcval     = (null)

srctype    =

trgsubject = 200614

trgval     = 200614/label/rh.Yeo2011_7Networks_N1000.annot

trgtype    =

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

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 /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/rh.sphere.reg

Loading source data

Reading surface file /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/rh.orig

reading colortable from annotation file...

colortable with 8 entries read (originally MyColorLUT)

Reading target surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/200614/surf/rh.sphere.reg

Done

Using surf2surf_nnfr()

Mapping Source Volume onto Source Subject Surface

surf2surf_nnfr: building source hash (res=16).

Surf2Surf: Forward Loop (137933)

 

Surf2Surf: Dividing by number of hits (137933)

INFO: nSrcLost = 54189

nTrg121 = 137933, nTrgMulti =     0, MnTrgMultiHits = 0

nSrc121 = 87617, nSrcLost = 54189, nSrcMulti = 76225, MnSrcMultiHits = 0.660098

Saving target data

Converting to target annot

Saving to target annot 200614/label/rh.Yeo2011_7Networks_N1000.annot

 

subject = 200614

annotation = 200614/label/rh.Yeo2011_7Networks_N1000.annot

hemi = rh

outdir = 200614/label/Yeolabels

surface   = white

 

Reading surface

 /data/project/vislab/raw/HCP_900sub/subjects_reconall/200614/surf/rh.white

Loading annotations from 200614/label/rh.Yeo2011_7Networks_N1000.annot

MRISreadAnnotationIntoArray: vertex index out of range: 137425 i=00010101, in_array_size=137425

    annot file: 200614/label/rh.Yeo2011_7Networks_N1000.annot

MRISreadAnnotationIntoArray: vertex index out of range: 137426 i=00010101, in_array_size=137425

    annot file: 200614/label/rh.Yeo2011_7Networks_N1000.annot

MRISreadAnnotationIntoArray: vertex index out of range: 137427 i=00010101, in_array_size=137425

    annot file: 200614/label/rh.Yeo2011_7Networks_N1000.annot