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
>
>
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