Hi Bruce,

I erased the false ventricle signal and re-run with -make all option.

However, Recon-all exited with errors:

---------------------------------------------------
#@# 1/1 Hallaert_Beatrice_M0_2010-12-15 Thu Jan  7 19:46:56 CET 2016 --------------
-----------------------
mri_surf2surf --srcsubject Hallaert_Beatrice_M0_2010-12-15 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.16394/Hallaert_Beatrice_M0_2010-12-15.1.mgh --sval /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
srcsubject = Hallaert_Beatrice_M0_2010-12-15
srcval     = /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume
srctype    = curv
trgsubject = fsaverage
trgval     = ./tmp.mris_preproc.16394/Hallaert_Beatrice_M0_2010-12-15.1.mgh
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
Reading source surface reg /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.sphere.reg
Loading source data
Reading curvature file /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume
ERROR: number of vertices in /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume does not match surface (124822,125094)
ERROR: reading curvature file
Linux toto 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s Hallaert_Beatrice_M0_2010-12-15 exited with ERRORS at Thu Jan  7 19:46:57 CET 2016

Please find attached the logs.

Moreover, I visualized aparc.a2009.annot and there's still unknown label in calcarine.

Best regards,

Matthieu

2016-01-07 17:52 GMT+01:00 Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>:

Hi Bruce,

Thank you I erased false ventricle and rerun recon-all with option -make all.

Is there any mean to prevent this problem ?

Best regards,

Matthieu

-------------------------------------
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France
http://www.ci2c.fr

2016-01-07 16:21 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

it's the bit of ventricle at e.g. 150, 117, 76 in the aseg. This should be unknown instead. You can erase it all from the aseg.mgz, then rerun recon-all -make all I think

Bruce
On Thu, 7 Jan 2016, matthieuvanhoutte@gmail.com wrote:

Matthieu (matthieuvanhoutte@gmail.com) has uploaded some files for you at the Martinos Center FileDrop:

+ T1.mgz (3.89 MiB) <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=1qg3sxihniv>
+ aseg.mgz (230.42 KiB) <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=41rb99vxdza>
+ aparc.a2009s+aseg.mgz (406.09 KiB) <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=b68kofegemp>

Also, they left this message for you:
Hi Bruce,

I couldn't see what you've explained to me. I attached the T1 and aseg files, could you please give me coordinates of this phenomen ?

Once problem have been seen, what is the process to follow for correcting aseg labels and re-run recon-all at which step ?

Thanks in advance !

Best regards,
Matthieu


Hi Matthieu

check the aseg at the anterior end of the calcarine and see if it
incorrectly labels some voxels there as ventricle. The bit of WM that
separates ventricle from calcarine at the posterior horn of the ventricle
is thin and sometimes quite dark, and if we lose that the ventricle label
can extend incorrectly into calcarine, in which case we think it isn't
cortex. If you correct the aseg and rerun from there it should fix it.

cheers
Bruce


On Thu, 7 Jan 2016,
Matthieu Vanhoutte wrote:

Dear FS's experts,

Projecting volumic data onto native surface (brain mask:
"Unknown_S_calcarine_ROI_mask.jpg"), I observed that a thin region in the
S_calcarine was set to 0.

I loaded then the inflated left surface and the l.aparc.a2009s.annot
("Unknown_S_calcarine_ROI_annot.jpg") and took into account that this region
inside the S_calcarine was set as "unknown" in the parcellation file .

What does it mean and is this possible to correct for this ?

Best regards,
Matthieu

Please be aware, your upload will expire on December 31st. If you'd like to download these files, feel free to use the link below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q

Cheers,
The Martinos Center Web Team

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