Dear FSers,
Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance!
Tudor
On 5 July 2013 17:26, Tudor Popescu tudor3@gmail.com wrote:
Hi everyone
The skull-stripping step of recon-all must have gone bad for my sample, because I noticed that there are artefacts (chips) in the brain-extracted structurals of several of my subjects. Since I ran recon-all on all my sample without having noticed this initially, this of course also lead to the surfaces being created wrongly, i.e. following the wrong volumetric information.
I attach screenshots showing some of the more obvious artefactual skull extractions, corresponding to subjects 04, 06 and 17, and also the brain.mgz and T1.mgz for subject 17.
FSL's BET extracted the skull with no problems from the same original structurals, so I'm guessing it's maybe the case that I need to override some parameters in recon-all in order for the initial recon-all to produce good brain extractions?
And by the way, I noticed that, in any one subject's folder, the images /mri/T1.mgz, /mri/orig.mgz and /mri/orig/001.mgz all seem to contain the subject's original structural scan. Why does this exist in 3 separate copies, which also seem to be of different file sizes? The only difference I can see between them is in terms of brightness correction...
Many thanks!
Tudor
Hi Tudor
the T1.mgz is intensity corrected and conformed (the orig.mgz is just conformed). Have you read the documentation on fixing skull strip problems on the wiki?
cheers Bruce On Mon, 8 Jul 2013, Tudor Popescu wrote:
Dear FSers,
Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance!
Tudor
On 5 July 2013 17:26, Tudor Popescu tudor3@gmail.com wrote: Hi everyone
The skull-stripping step of recon-all must have gone bad for my sample, because I noticed that there are artefacts (chips) in the brain-extracted structurals of several of my subjects. Since I ran recon-all on all my sample without having noticed this initially, this of course also lead to the surfaces being created wrongly, i.e. following the wrong volumetric information. I attach screenshots showing some of the more obvious artefactual skull extractions, corresponding to subjects 04, 06 and 17, and also the brain.mgz and T1.mgz for subject 17. FSL's BET extracted the skull with no problems from the same original structurals, so I'm guessing it's maybe the case that I need to override some parameters in recon-all in order for the initial recon-all to produce good brain extractions? And by the way, I noticed that, in any one subject's folder, the images /mri/T1.mgz, /mri/orig.mgz and /mri/orig/001.mgz all seem to contain the subject's original structural scan. Why does this exist in 3 separate copies, which also seem to be of different file sizes? The only difference I can see between them is in terms of brightness correction... Many thanks! Tudor
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
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
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
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