Hello, Does anybody have an idea ?
Thanks in advance ! Best regards, Matthieu 2016-01-08 16:59 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > 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 . > > So I checked the aseg at the anterior end of the calcarine and see if it > incorrectly labeled some voxels there as ventricle. I corrected the aseg > and rerun from there with this command : > > > > *recon-all -all -sd ${SUBJECTS_DIR} -subjid ${SUBJECT_ID} > -nuintensitycor-3T -make all* > However, this command exited with errors (please find attached > recon-all_log.txt). > > Thanks in advance far any helping ! > > Best regards, > Matthieu > > 2016-01-08 10:14 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com > >: > >> 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 < >> matthieuvanhou...@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 <fis...@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, matthieuvanhou...@gmail.com wrote: >>>> >>>> Matthieu (matthieuvanhou...@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 >>>>> >>>>> >>>>> >>>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >> >
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