Hey,Bruce, yes WM is already classified as 110 in the regions, but grey matter is still being excluded.MattOn Tue, Aug 12, 2014 at 2:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi MattNot really. Is the white matter in those regions already 110?BruceHey Bruce,Is there anyway I can make edits to the grey matter to help with the segmentation errors (i.e reclassify grey matter in the brainmask with voxel edit so they are included in the pial layer). Even with the addition of control points and wm edits I'm still not getting a proper segmentation, especially in areas like the temporal lobes and central grey matter where signal is lower.Thanks,MattOn Thu, Aug 7, 2014 at 1:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Matt
the young age is probably why you are having to do extra work - incomplete myelination.
cheers
Bruce
On Thu, 7 Aug 2014, Walton, Matt wrote:
Thanks for your help. It is most appreciated.
I thought I would mention that these subjects are quite young (3-4 years
old). I've read a few posts that free surfer is not ideal for analyzing
young subjects, so I am wondering if this might be causing some errors.
Maybe there is a way to register to a paediatric template, or something?
As well the raw T1w images always have an intensity bias in the occipital
lobe. I'm not sure if this is from the coil itself (32 channel phased
array), or just from the young subject age. Do you think ramping up the
normalization procedures in freesurfer would result in an improvement?
Thought I would just let you know this, incase it helps you.
Matt
On Thu, Aug 7, 2014 at 10:12 AM, Tirrell, Lee <LTIRRELL@mgh.harvard.edu>
wrote:
Hi Matt,
Overall, I've made the following changes that have led to some
improvements:
- Remove excess dura from the brainmask that hasn't been
stripped away
- Erasing voxels from wm in areas where white matter should be,
even if the voxels don't show up as what on the wm mask. (If you
view the wm volume with the heat color map, and lower the mid
parameter to zero, areas that you have deleted show up in red)
- Control points to push out the pial surface
Specifically for the case I sent you, I added control points
near 115, 89, 82 (+/- a few slices in the sagittal view) to move
the pial surface out further. The wm intensity is decreasing as
it moves out along that strand, so adding control points in
these areas will increase the values to help Freesurfer
recognize it as part of the white matter surface.
Also, near 141, 116, 45 (sagittal view) there is a problem with
the wm surface. I tried deleting wm voxels as mentioned above,
but I don't think I was aggressive enough on the first attempt
so it didn't help much. I will try this again to see if it
leads to further improvements.
Best,
Lee
On 08/06/2014 11:54 AM, Walton, Matt wrote:
Hey Bruce,
Thanks so much. If it would help, I could upload another
subject, perhaps one with worse segmentation in the occipital
lobe. I could also upload a raw T1 image sequence (Nifiti)
Matt
On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee
<LTIRRELL@mgh.harvard.edu> wrote:
Hi Matt,
I've taken a look at the subject that you uploaded.
I initially deleted portions of the skull from the
brainmask that weren't removed from coronal slices
101-109 (see screenshot), which led to some
improvement. I also edited the wm volume by
deleting areas that were obviously not white matter,
even if it didn't effect the white matter surface.
However, this didn't lead to much improvement. The
segmentation isn't as bad in this subject as in the
screenshot that you sent originally, so this
strategy may help in worse cases.
I am going to take another look at it now to try to
improve the segmentation further.
Best,
Lee
On 07/30/2014 12:21 PM, Walton, Matt wrote:
Hey Bruce,
I uploaded a subject that you requested a few days
ago (problems with segmentation in the occipital
lobe). I just wanted to make sure the file
transferred successfully, and if you have had a
change to analyze.
Thanks,
Matt
On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt
<mt.walton@alumni.uleth.ca> wrote:
Hey Bruce.
I've sent one of my subjects in which I
noticed the segmentation problems in the
occipital lobe. Sagittal slice 115 provides a
good example. I've also noticed that with my
subjects I frequently have problems with
segmentation of the temporal lobes, although
adding control points usually fixes this quite
well.
Thanks for your help
Matt
On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
Hi Matt
there are instructions on our
wiki. You can either ftp or use
the filedrop, although ftp is
probably best if you are uploading
an entire subject
cheers
Bruce
On Mon, 28 Jul 2014, Walton, Matt
wrote:
Hey Bruce.
Thanks for the
response. How do I go
about uploading the
subject?
On Monday, July 28,
2014, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Matt
certainly
something is wrong,
but it's hard to tell
why from the
single slice.
You have big
topological defects
that are being
fixed
incorrectly. Can you
upload the subject and
we will take a
look?
cheers
Bruce
On Mon, 28 Jul
2014, Walton, Matt
wrote:
Hello
Freesurfer team,
I've used
freesurfer to segment
(recon-all)
approximately 30
different
subjects
from a study. I've
noticed that a large
number of
these subjects
have a
misclassification of
the white and pial
boundaries
in the occipital
lobe (such
that grey matter is
being classified as
white
matter). I believe
this
problem is originating
from my scanner and
original
data. I'm acquiring
a T1W
BRAVO sequence on a GE
Discovery 750w 3T
scanner,
using a 32 channel
phased
array head coil. For
many subjects, this
acquistion
gives intensity
inhomogeneity in the
occipital lobe. I've
begun
using a GE
based correction
technique
(PURE) on the images,
and it appears to
improve
the intensity in
the
occipital lobe, but
Freesurfer is still
frequently
misclassifying.
I'm
wondering what would
be the best way to
edit the
data. I've
often tried
to edit
the wm.vol, but this
doesn't seem to fix
anything.
For the most
part, the
wm.vol is correct to
begin with, but the
wm cutting
line isn't
segmenting
with the wm.vol. I've
also tried to add
control
points but this
doesn't
seem to improve
anything either.
I've
attached an image
which I hope will
further
explain my
problems.
Thanks for
any help
_______________________________________________
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 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 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
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 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer