Hi again,
I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions!
Thank you, Tudor
On 12 July 2013 16:03, Tudor Popescu tudor3@gmail.com wrote:
Thanks Bruce. So the massive chunks that appear as missing in freeview, e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces don't exist there. If I mouse above that area, brainmask.mgz intensities (which seem to be always identical to T1.mgz ones) seem quite normal to me, i.e. they're not all 0 but vary in a range centred around ~100.
As for the segmentation (aseg) - not quite sure where I need to look for that. I attach here the main volumes & surfaces of this subject. Could my "-wsthresh 35" recon not have replaced the existing one?
Many thanks again! Tudor
PS: why does freeview show the coordinates in the order [x z y] instead of [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle coordinate to decrease, rather than the third one.
PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to do with conformity and intensity correction, just like the difference between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would be a binary image (a mask consisting of 0s and 1s), rather than a regular (skull-stripped) structural.
On 11 July 2013 21:40, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tudor
can you cc the list so others can answer? What are the intensities in the excluded right temporal wm in the brainmask.mgz? What is the aseg like there? Looks like an intensity normalization failure, but I'm not sure why. If you want to upload the subject I'll take a look Bruce
On Thu, 11 Jul 2013, Tudor Popescu wrote:
Hi Bruce,
Sorry, wasn't sure whether you'd seen my previous message. So in the meantime, after the following command for subject C06 (whose artefactual skull strip I previously included as a screenshot) completed without error,
recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06
..the volumes&surfaces still look bad (see screenshot and recon log attached).
C06 is just one of several subjects for which this has happened. Is there anything else I can try? Thanks!
Tudor
On 9 July 2013 13:33, Tudor Popescu tudor3@gmail.com wrote: Thanks for clarifying this Doug!
Please let me know if anyone has suggestions about my other questions below, re skull stripping. Cheers! T On 8 July 2013 18:01, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz If you only have one run, then 001 and raw are the same orig.mgz is the first conformed volume doug On 07/08/2013 12:38 PM, Tudor Popescu wrote: > Thanks Bruce. I have looked at that part of the wiki but I was > wondering whether the screenshots at all suggest that all artefacts > are likely to be the result of the same problem, and that e.g. > re-running recon for all subjects with a watershed>25 and with the > -no-wsgcaatlas flag might be the thing to do in this case, rather than > manually editing slices in tkmedit. > > So after making these corrections to all affected subjects, before > proceeding to analyses, is a visual inspection in freeview of the > brain.mgz of all subjects enough? It seems like some of these > skull-stripping errors are quite subtle and can be easily missed (as I > have, in fact, when I checked the output after my first recon-all). > > the T1.mgz is intensity corrected and conformed (the orig.mgz is > just conformed). > > So are both derived from 001.mgz? Otherwise, what is the difference > between 001.mgz and orig.mgz? > > Thanks! > Tudor > >______________________________**_________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ 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.
Dear Bruce,
Could you please let me know whether my message of last week, in which I uploaded the subject's vols&surfs, have reached the list? I haven't received a reply about those questions and was wondering whether that email maybe got rejected due to the large size of the attachments. The questions should be visible in plaintext below, please let me know if I should upload the files on a sharing server
Thanks! Tudor
On 15 July 2013 19:51, Tudor Popescu tudor3@gmail.com wrote:
Hi again,
I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions!
Thank you, Tudor
On 12 July 2013 16:03, Tudor Popescu tudor3@gmail.com wrote:
Thanks Bruce. So the massive chunks that appear as missing in freeview, e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces don't exist there. If I mouse above that area, brainmask.mgz intensities (which seem to be always identical to T1.mgz ones) seem quite normal to me, i.e. they're not all 0 but vary in a range centred around ~100.
As for the segmentation (aseg) - not quite sure where I need to look for that. I attach here the main volumes & surfaces of this subject. Could my "-wsthresh 35" recon not have replaced the existing one?
Many thanks again! Tudor
PS: why does freeview show the coordinates in the order [x z y] instead of [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle coordinate to decrease, rather than the third one.
PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to do with conformity and intensity correction, just like the difference between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would be a binary image (a mask consisting of 0s and 1s), rather than a regular (skull-stripped) structural.
On 11 July 2013 21:40, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tudor
can you cc the list so others can answer? What are the intensities in the excluded right temporal wm in the brainmask.mgz? What is the aseg like there? Looks like an intensity normalization failure, but I'm not sure why. If you want to upload the subject I'll take a look Bruce
On Thu, 11 Jul 2013, Tudor Popescu wrote:
Hi Bruce,
Sorry, wasn't sure whether you'd seen my previous message. So in the meantime, after the following command for subject C06 (whose artefactual skull strip I previously included as a screenshot) completed without error,
recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06
..the volumes&surfaces still look bad (see screenshot and recon log attached).
C06 is just one of several subjects for which this has happened. Is there anything else I can try? Thanks!
Tudor
On 9 July 2013 13:33, Tudor Popescu tudor3@gmail.com wrote: Thanks for clarifying this Doug!
Please let me know if anyone has suggestions about my other questions below, re skull stripping. Cheers! T On 8 July 2013 18:01, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz If you only have one run, then 001 and raw are the same orig.mgz is the first conformed volume doug On 07/08/2013 12:38 PM, Tudor Popescu wrote: > Thanks Bruce. I have looked at that part of the wiki but I was > wondering whether the screenshots at all suggest that all artefacts > are likely to be the result of the same problem, and that e.g. > re-running recon for all subjects with a watershed>25 and with the > -no-wsgcaatlas flag might be the thing to do in this case, rather than > manually editing slices in tkmedit. > > So after making these corrections to all affected subjects, before > proceeding to analyses, is a visual inspection in freeview of the > brain.mgz of all subjects enough? It seems like some of these > skull-stripping errors are quite subtle and can be easily missed (as I > have, in fact, when I checked the output after my first recon-all). > > the T1.mgz is intensity corrected and conformed (the orig.mgz is > just conformed). > > So are both derived from 001.mgz? Otherwise, what is the difference > between 001.mgz and orig.mgz? > > Thanks! > Tudor > >______________________________**_________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ 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.
Hi Tudor,
yes, it got through. It's on our list of things to get to, we just haven't gotten there yet Bruce On Wed, 17 Jul 2013, Tudor Popescu wrote:
Dear Bruce,
Could you please let me know whether my message of last week, in which I uploaded the subject's vols&surfs, have reached the list? I haven't received a reply about those questions and was wondering whether that email maybe got rejected due to the large size of the attachments. The questions should be visible in plaintext below, please let me know if I should upload the files on a sharing server
Thanks! Tudor
On 15 July 2013 19:51, Tudor Popescu tudor3@gmail.com wrote: Hi again,
I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions! Thank you, Tudor On 12 July 2013 16:03, Tudor Popescu <tudor3@gmail.com> wrote: Thanks Bruce. So the massive chunks that appear as missing in freeview, e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces don't exist there. If I mouse above that area, brainmask.mgz intensities (which seem to be always identical to T1.mgz ones) seem quite normal to me, i.e. they're not all 0 but vary in a range centred around ~100. As for the segmentation (aseg) - not quite sure where I need to look for that. I attach here the main volumes & surfaces of this subject. Could my "-wsthresh 35" recon not have replaced the existing one? Many thanks again! Tudor PS: why does freeview show the coordinates in the order [x z y] instead of [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle coordinate to decrease, rather than the third one. PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to do with conformity and intensity correction, just like the difference between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would be a binary image (a mask consisting of 0s and 1s), rather than a regular (skull-stripped) structural. On 11 July 2013 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Tudor can you cc the list so others can answer? What are the intensities in the excluded right temporal wm in the brainmask.mgz? What is the aseg like there? Looks like an intensity normalization failure, but I'm not sure why. If you want to upload the subject I'll take a look Bruce On Thu, 11 Jul 2013, Tudor Popescu wrote: Hi Bruce, Sorry, wasn't sure whether you'd seen my previous message. So in the meantime, after the following command for subject C06 (whose artefactual skull strip I previously included as a screenshot) completed without error, recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06 ..the volumes&surfaces still look bad (see screenshot and recon log attached). C06 is just one of several subjects for which this has happened. Is there anything else I can try? Thanks! Tudor On 9 July 2013 13:33, Tudor Popescu <tudor3@gmail.com> wrote: Thanks for clarifying this Doug! Please let me know if anyone has suggestions about my other questions below, re skull stripping. Cheers! T On 8 July 2013 18:01, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz If you only have one run, then 001 and raw are the same orig.mgz is the first conformed volume doug On 07/08/2013 12:38 PM, Tudor Popescu wrote: > Thanks Bruce. I have looked at that part of the wiki but I was > wondering whether the screenshots at all suggest that all artefacts > are likely to be the result of the same problem, and that e.g. > re-running recon for all subjects with a watershed>25 and with the > -no-wsgcaatlas flag might be the thing to do in this case, rather than > manually editing slices in tkmedit. > > So after making these corrections to all affected subjects, before > proceeding to analyses, is a visual inspection in freeview of the > brain.mgz of all subjects enough? It seems like some of these > skull-stripping errors are quite subtle and can be easily missed (as I > have, in fact, when I checked the output after my first recon-all). > > the T1.mgz is intensity corrected and conformed (the orig.mgz is > just conformed). > > So are both derived from 001.mgz? Otherwise, what is the difference > between 001.mgz and orig.mgz? > > Thanks! > Tudor > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Tudor Popescu