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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
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>>>
>>
>
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