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Hello again
I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening?
By the way the option description is not super clear, could you please give some extra details?
Best
Antonin
[cid:6517702D-5283-43A2-9829-E5FA475ABA23@erasme.ulb.ac.be][cid:BD0A0CE3-A403-4733-9BDC-B38AEED75225@erasme.ulb.ac.be]
[Hôpital Erasme]
Lien vers Disclaimerhttp://www.erasme.ulb.ac.be/email-disclaimer
Hi Antonin
hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes.
cheers Bruce
On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use Caution
Hello again
I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening?
By the way the option description is not super clear, could you please give some extra details?
Best
Antonin
[IMAGE][IMAGE]
Hôpital Erasme
Lien vers Disclaimer
External Email - Use Caution
Hey
So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation is completely wrong so I really think there something wrong in the file….
Best
Antonin
Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be
Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On 3 Sep 2019, at 15:55, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antonin
hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes.
cheers Bruce
On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHello again I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening? By the way the option description is not super clear, could you please give some extra details? Best Antonin [IMAGE][IMAGE] Hôpital Erasme Lien vers Disclaimer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp site? On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHey
So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation is completely wrong so I really think there something wrong in the file….
Best
Antonin
Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be
Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On 3 Sep 2019, at 15:55, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antonin
hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes.
cheers Bruce
On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHello again I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening? By the way the option description is not super clear, could you please give some extra details? Best Antonin [IMAGE][IMAGE] Hôpital Erasme Lien vers Disclaimer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hello
I think there is a problem with the dicom files. I could not see it on the images before mri_convert -conform but there’s definitely something weird in there. I suspect it comes from some software that misexported the data. Running reconall on properly imported dicom data show not problem at all…
Never mind then!
Best
Antonin
Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be
Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On 3 Sep 2019, at 16:57, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp site? On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHey
So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation is completely wrong so I really think there something wrong in the file….
Best
Antonin
Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be
Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On 3 Sep 2019, at 15:55, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antonin
hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes.
cheers Bruce
On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHello again I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening? By the way the option description is not super clear, could you please give some extra details? Best Antonin [IMAGE][IMAGE] Hôpital Erasme Lien vers Disclaimer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
glad to hear it worked out (and it wasn't our fault!)
cheers Bruce On Wed, 4 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHello
I think there is a problem with the dicom files. I could not see it on the images before mri_convert -conform but there’s definitely something weird in there. I suspect it comes from some software that misexported the data. Running reconall on properly imported dicom data show not problem at all…
Never mind then!
Best
Antonin
Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be
Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On 3 Sep 2019, at 16:57, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp site? On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHey
So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation is completely wrong so I really think there something wrong in the file….
Best
Antonin
Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be
Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On 3 Sep 2019, at 15:55, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antonin
hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes.
cheers Bruce
On Tue, 3 Sep 2019, Rovai Antonin wrote:
External Email - Use CautionHello again I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening? By the way the option description is not super clear, could you please give some extra details? Best Antonin [IMAGE][IMAGE] Hôpital Erasme Lien vers Disclaimer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The conform option resamples the data into 256^3, 1mm3 space that is aligned with the scanner (not voxel space). This means that if the person's head is rotated sharply in the scanner, then it can look a little funny. Check the corronal view.
On 9/3/2019 6:56 AM, Rovai Antonin wrote:
External Email - Use Caution
Hello again
I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening?
By the way the option description is not super clear, could you please give some extra details?
Best
Antonin
[cid:part1.35C8C5F9.03644DF5@mgh.harvard.edu][cid:part2.0CF25301.64CF6D9A@mgh.harvard.edu]
[Hôpital Erasme]
Lien vers Disclaimerhttp://www.erasme.ulb.ac.be/email-disclaimer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Rovai Antonin