Okay, I've uploaded them as cdluna_whitematter_002.img and *.hdr.
Thanks,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute
for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Tue, Aug 9, 2011 at 11:02 PM, Bruce Fischl <[email protected]>
wrote:
Eek, that looks awful! Can you upload this subject so we can figure out
what is going on?
On Aug 9, 2011, at 4:09 PM, Christopher Luna <[email protected]> wrote:
Hello,
On this topic again, we tried fixing the coordinate system (we flipped A/P) as
much as we could until we heard back from our
colleagues.
And we also altered the white matter thresholds from mri_segment in case the
missing white matter was due to some strange qualities
in the original IMG files.
Unfortunately, this didn't work. I've attached some example pictures of what we
end up with even after tinkering with the white
threshold.
Are we going to have to add in this missing white matter by hand?
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute
for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 3:04 PM, Christopher Luna <[email protected]> wrote:
Hi Bruce,
Thank you very much! We'll get in contact with them.
Best,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute
for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 2:52 PM, Bruce Fischl <[email protected]> wrote:
Hi Chris,
they are front/back reversed (a/p), which is why everything fails. I
don't know how you are ever going to know left
from right though. You should talk to whoever got you this data and see
if they have some way to tell.
cheers
Bruce
On Mon, 1 Aug 2011, Christopher Luna wrote:
I've uploaded the IMG and HDR files, they are named after my email
address.
Thank you kindly,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute
for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 12:40 PM, Bruce Fischl <[email protected]>
wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange?highlight=%28ftp%29
On Mon, 1 Aug 2011, Christopher Luna wrote:
Ah, I forgot about the left/right orientation. Where should I upload these
files?
Thanks,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern
Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 12:23 PM, Bruce Fischl <[email protected]>
wrote:
how do you know left/right is correct? In any case, if you
upload the subject we'll take a look. Things very rarely fail
that badly
On Mon, 1 Aug 2011, Christopher Luna wrote:
Hi Bruce,
The orientations are correct - they weren't at first so I
had to do a lot of work in tkregister2 to get the
orientations correct. Unfortunately I only have access to
the
*.IMG and sometimes the *.HDR file for each subject.
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab,
McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 12:16 PM, Bruce Fischl
<[email protected]> wrote:
Hi Christopher,
are you sure that the orientations are correct? That is,
when you bring the orig.mgz up in tkmedit does the coronal view
actually show the brain coronally? Img
is a dangerous format to use as it doesn't contain
orientation info. Do you have access to the data in some other
format before it was convered to img?
Bruce
On Mon, 1 Aug 2011, Christopher Luna wrote:
Hello Freesurfers,
I'm putting *.IMG files into the program and after correcting
talaraich transformations for them, I notice that when the
reconstructions have completed, that
there are
entire lobes of white matter absent from the surfaces detected
and from the wm.mgz file. I went through my hand at first to
manually fill in the missing white
matter for
the first case, but after seeing how many were affected, I
figured there was some setting I may be missing or some contrast
level that may be off.
I had tried using control points, but after following the WIKI
instructions on regenerating surfaces after placing them, I
found no significant difference in
white matter
detection.
How do I ensure all of the white matter in my converted IMGs is
identified?
Thank you kindly,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab,
McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
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.
<example1a.png>
<example1b.png>
<example2a.png>
<example2b.png>
<example3a.png>
<example3b.png>
