I see, and I agree that would be better
cheers
Bruce
On Sat, 17 Aug 2019, Tim Schäfer wrote:
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Hi Bruce,
yes, but to clarify, I was referring to something else:
If a subject is missing a fold of an atlas, I somehow expected there would
still be an entry for the fold in the atlas stats file (which would list 0
vertices and NaNs for the mean thickness and other measurements), but the whole
entry is missing instead.
That's fine, you just have to be aware of it.
Tim
On August 16, 2019 at 4:02 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Tim
I think that is the nature of the parcellation - there are some small
folds that don't occur in all subjects.
cheers
Bruce
On Thu, 15 Aug 2019, Tim Schäfer
wrote:
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Another interesting thing I noticed, which may be of interest to anybody
parsing label data: in the ABIDE data (5.x), labels without any assigned
vertices are not listed at all for subjects.
So if you want to find all label names of an atlas, you cannot just take a
random subject and read them from its ?h.aparc.a2009s.annot file: the subject
you chose may be lacking some of them. (That's why I went for fsaverage, which
was a bad idea as well.)
Tim
On August 15, 2019 at 9:37 AM Tim Schäfer <ts...@rcmd.org> wrote:
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Yes, this has indeed also caused me some confusion.
I took the label names from fsaverage (and thus from my v6 installation),
parsed ABIDE structural data (5.x) and wondered why there was no data in there
for most atlas labels. I was quite sure it was an issue with the fact that '%'
is a special character at first (as a programmer I smell trouble immediately
when seeing special characters), but at some point understood that the labels
had simple been renamed. oO
On August 14, 2019 at 9:47 PM Jyrki Ahveninen <jy...@nmr.mgh.harvard.edu> wrote:
Hi guys,
I (and probably others) have noticed the aparc.a2009s label naming convention has changed
in recons starting from 6.0. “_and_” has become “&”, such as in lh.G&S_subcentral.
It is fixable, but it may become a bit confusing for those who use fsaverage vs.
individually segmented labels in a study that uses the different versions of 6.0 and
beyond (e.g., those interested in using the subpmillmeter recon option). And & is also
a special character, too.
It is completely fixable, of course, but I just thought to bring this up,
because it might cause confusion in some users. (For me, it was just a “why the
xxxx does not my mris_divide_parcellation splittable” moment.)
Thankfully,
Jyrki
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Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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