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 matthieuvanhoutte@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 <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%3...
- aseg.mgz (230.42 KiB) <
http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=41rb99vxdza%3...
- aparc.a2009s+aseg.mgz (406.09 KiB) <
http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=b68kofegemp%3...
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.
Hello,
Does anybody have an idea ?
Thanks in advance !
Best regards, Matthieu
2016-01-08 16:59 GMT+01:00 Matthieu Vanhoutte matthieuvanhoutte@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 <matthieuvanhoutte@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 < 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
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.
freesurfer@nmr.mgh.harvard.edu
-
Matthieu Vanhoutte