Dear Freesurfers,
I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well?
The wm.mgz before and after manual editing are shown on the left and right panels of the attachment.
Thank you very much!
Sincerely, Ye
Nope, it won't matter Cheers Bruce
On Jul 12, 2013, at 7:50 PM, ye tian tianye730@gmail.com wrote:
Dear Freesurfers,
I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well?
The wm.mgz before and after manual editing are shown on the left and right panels of the attachment.
Thank you very much!
Sincerely, Ye <before_after.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Nope, it won't matter Cheers Bruce
On Jul 12, 2013, at 7:50 PM, ye tian tianye730@gmail.com wrote:
Dear Freesurfers,
I deleted some extra dura that was included in the pial surface. I
recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well?
The wm.mgz before and after manual editing are shown on the left and
right panels of the attachment.
Thank you very much!
Sincerely, Ye <before_after.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear Bruce and freesurfers,
I still don't fully understand how deleting a few voxels in brainmask.mgz affects the assignment of the white matter.
The troubleshooting tutorial has a similar example to the attached image below, where we were instructed to delete the extra voxels in wm.mgz. In the attached example, I just deleted the dura in brainmask.mgz and re-ran using autorecon-pial and it seemed to work, too. Would it make a difference if I edited wm.mgz and re-run using -autorecon2-wm -autorecon3?
I guess I fundamentally don't understand what each of autorecon-pial and autorecon2-wm does.
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 3:37 PM, ye tian tianye730@gmail.com wrote:
Dear Bruce,
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Nope, it won't matter Cheers Bruce
On Jul 12, 2013, at 7:50 PM, ye tian tianye730@gmail.com wrote:
Dear Freesurfers,
I deleted some extra dura that was included in the pial surface. I
recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well?
The wm.mgz before and after manual editing are shown on the left and
right panels of the attachment.
Thank you very much!
Sincerely, Ye <before_after.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
if the edits are aimed at only correcting the pial surface you don't need to run autorecon2-wm. Sometimes the pial is incorrect because the white is also wrong, then you need to run them both
cheers Bruce
On Mon, 15 Jul 2013, ye tian wrote:
Dear Bruce and freesurfers, I still don't fully understand how deleting a few voxels in brainmask.mgz affects the assignment of the white matter.
The troubleshooting tutorial has a similar example to the attached image below, where we were instructed to delete the extra voxels in wm.mgz. In the attached example, I just deleted the dura in brainmask.mgz and re-ran using autorecon-pial and it seemed to work, too. Would it make a difference if I edited wm.mgz and re-run using -autorecon2-wm -autorecon3?
I guess I fundamentally don't understand what each of autorecon-pial and autorecon2-wm does.
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 3:37 PM, ye tian tianye730@gmail.com wrote: Dear Bruce, Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Nope, it won't matter Cheers Bruce
On Jul 12, 2013, at 7:50 PM, ye tian <tianye730@gmail.com> wrote: > Dear Freesurfers, > > I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well? > > The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. > > Thank you very much! > > Sincerely, > Ye<before_after.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear Bruce,
Thank you very much!
In my experience, autorecon-pial does seem to alter white matter assignment, which seems to contradict the statement that autorecon-pial "regenerates all final surfaces".
Sincerely, Ye
On Mon, Jul 15, 2013 at 12:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
if the edits are aimed at only correcting the pial surface you don't need to run autorecon2-wm. Sometimes the pial is incorrect because the white is also wrong, then you need to run them both
cheers Bruce
On Mon, 15 Jul 2013, ye tian wrote:
Dear Bruce and freesurfers,
I still don't fully understand how deleting a few voxels in brainmask.mgz affects the assignment of the white matter.
The troubleshooting tutorial has a similar example to the attached image below, where we were instructed to delete the extra voxels in wm.mgz. In the attached example, I just deleted the dura in brainmask.mgz and re-ran using autorecon-pial and it seemed to work, too. Would it make a difference if I edited wm.mgz and re-run using -autorecon2-wm -autorecon3?
I guess I fundamentally don't understand what each of autorecon-pial and autorecon2-wm does.
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 3:37 PM, ye tian tianye730@gmail.com wrote: Dear Bruce, Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Nope, it won't matter Cheers Bruce
On Jul 12, 2013, at 7:50 PM, ye tian <tianye730@gmail.com> wrote: > Dear Freesurfers, > > I deleted some extra dura that was included in the pial surface.I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well? > > The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. > > Thank you very much! > > Sincerely, > Ye
<before_after.png> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/**compliancelinehttp://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.
it does recreate the white and pial surfaces, but not all steps, and not the segmentation step that creates the wm.mgz and hence the lh.orig and rh.orig files. Erasing dura for example shouldn't require rerunning autorecon2-wm (since the wm.mgz isn't expected to change)
cheers Bruce
On Mon, 15 Jul 2013, ye tian wrote:
Dear Bruce, Thank you very much!
In my experience, autorecon-pial does seem to alter white matter assignment, which seems to contradict the statement that autorecon-pial "regenerates all final surfaces".
Sincerely, Ye
On Mon, Jul 15, 2013 at 12:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if the edits are aimed at only correcting the pial surface you don't need to run autorecon2-wm. Sometimes the pial is incorrect because the white is also wrong, then you need to run them both
cheers Bruce On Mon, 15 Jul 2013, ye tian wrote: Dear Bruce and freesurfers, I still don't fully understand how deleting a few voxels in brainmask.mgz affects the assignment of the white matter. The troubleshooting tutorial has a similar example to the attached image below, where we were instructed to delete the extra voxels in wm.mgz. In the attached example, I just deleted the dura in brainmask.mgz and re-ran using autorecon-pial and it seemed to work, too. Would it make a difference if I edited wm.mgz and re-run using -autorecon2-wm -autorecon3? I guess I fundamentally don't understand what each of autorecon-pial and autorecon2-wm does. Thank you very much! Sincerely, Ye On Sat, Jul 13, 2013 at 3:37 PM, ye tian <tianye730@gmail.com> wrote: Dear Bruce, Thank you very much! Sincerely, Ye On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Nope, it won't matter Cheers Bruce On Jul 12, 2013, at 7:50 PM, ye tian <tianye730@gmail.com> wrote: > Dear Freesurfers, > > I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well? > > The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. > > Thank you very much! > > Sincerely, > Ye > <before_after.png> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Dear Bruce,
Thank you very much!
Sincerely, Ye
On Mon, Jul 15, 2013 at 12:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
it does recreate the white and pial surfaces, but not all steps, and not the segmentation step that creates the wm.mgz and hence the lh.orig and rh.orig files. Erasing dura for example shouldn't require rerunning autorecon2-wm (since the wm.mgz isn't expected to change)
cheers Bruce
On Mon, 15 Jul 2013, ye tian wrote:
Dear Bruce,
Thank you very much!
In my experience, autorecon-pial does seem to alter white matter assignment, which seems to contradict the statement that autorecon-pial "regenerates all final surfaces".
Sincerely, Ye
On Mon, Jul 15, 2013 at 12:09 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: if the edits are aimed at only correcting the pial surface you don't need to run autorecon2-wm. Sometimes the pial is incorrect because the white is also wrong, then you need to run them both
cheers Bruce On Mon, 15 Jul 2013, ye tian wrote: Dear Bruce and freesurfers, I still don't fully understand how deleting a few voxels in brainmask.mgz affects the assignment of the white matter. The troubleshooting tutorial has a similar example to the attached image below, where we were instructed to delete the extra voxels in wm.mgz. In the attached example, I just deleted the dura in brainmask.mgz and re-ran using autorecon-pial and it seemed to work, too. Would it make a difference if I edited wm.mgz and re-run using -autorecon2-wm -autorecon3? I guess I fundamentally don't understand what each of autorecon-pial and autorecon2-wm does. Thank you very much! Sincerely, Ye On Sat, Jul 13, 2013 at 3:37 PM, ye tian <tianye730@gmail.com> wrote: Dear Bruce, Thank you very much! Sincerely, Ye On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Nope, it won't matter Cheers Bruce On Jul 12, 2013, at 7:50 PM, ye tian <tianye730@gmail.com> wrote: > Dear Freesurfers, > > I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well? > > The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. > > Thank you very much! > > Sincerely, > Ye > <before_after.png> > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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<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
-
Bruce Fischl -
ye tian