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Cheers,Thaks in advanceHi Bruce,I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surface segmentation in some subjects (as this that i send to you) was incorrect.
https://drive.google.com/open?id=11xcWuDlWzGeLLV4MvW-bJK3-rrlsIA8Q2018-05-01 16:26 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:why don't you tar and gzip the whole subject dir and upload it to our ftp site and we will take a look
cheers
Bruce
On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote:
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Hi Bruce,
The problem is that the reconstruction of the pial surface is incorrect. I tried to put control
points on some voxels but did a wrong reconstruction because in this region there is no voxel with
an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case
extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I
could not understand very well how to modify the statistics that FreeSurfer does in the
mri_make_surfaces.
Hi Saum
it is, but you need to figure out why it isn't getting out far enough. The easiest way is to
override the intensity statistics that are computed automatically in mris_make_surfaces. You can see
them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the
pial surface is too high, then it will settle too far in
Thanks,
Cheers,
2018-04-29 17:33 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes
significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial
temporal lobe is WM or GM. Try putting some control points in regions where the
intensity is in say [95, 110) and see if that helps
cheers
Bruce
On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote:
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Hi guys,
I have the same problem as Saum, I executed the recon-all in several
subjects and I did not obtain a
completely correct segmentation of the pial surface. To solve this error
could I use the control
points? When I use the control points, will I also be able to correct the
white matter segmentation?
I send you a image if you want
to check it.
Thank you very much!
Cheers,
[IMAGE]
2018-04-27 21:28 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
Hi Saum
it is, but you need to figure out why it isn't getting out far enough.
The easiest way
is to override the intensity statistics that are computed
automatically in
mris_make_surfaces. You can see them if you look in your
recon-all.log. For example if
the lowest value gm is allowed to be at the pial surface is too high,
then it will
settle too far in
cheers
Bruce
On Fri, 27 Apr 2018, Saum Naderi wrote:
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Hi guys,
I'm having some trouble extending the pial surface of my bm
volume. I am
aware that the general
procedure for extending the pial is to extend the wm first and
the pial will
follow. However, is it
possible to extend the pial surface without affecting the wm
boundary?
Thanks,
Saum
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--
Miguel Ángel Rivas Fernández
_______________________________________________
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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.
--Miguel Ángel Rivas Fernández