Dear Bruce,
Did you get my email with the link for our problematic data?
Best Regards,
Gabor
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The information in this e-mail is in
it would change for example the volume of the ventricle or white matter
in each hemi (taking from one and giving to the other)
On Wed, 27 Sep 2017,
Antonin Skoch wrote:
> Bruce, Gabor,
>
> may I ask, does it ever matter where the midline surface lies? I thought that
> this does not affect
> an
Bruce, Gabor,
may I ask, does it ever matter where the midline surface lies? I thought that
this does not affect anything in the analysis.
Antonin
hmmm, if you tar, gzip and upload the subject I'll take a look.
Bruce
On Tue, 26
Sep 2017, Gabor Perlaki wrote:
> I've already corrected a
great, we will take a look and get back to you
Bruce
On Wed, 27 Sep 2017, Gabor
Perlaki wrote:
> Dear Bruce,
>
> I sent you a link for our subject's data by email.
>
> Best regards,
> Gabor
>
>
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Dear Bruce,
I sent you a link for our subject's data by email.
Best regards,
Gabor
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hmmm, if you tar, gzip and upload the subject I'll take a look.
Bruce
On Tue, 26
Sep 2017, Gabor Perlaki wrote:
> I've already corrected aseg.presurf.mgz and the left and right lateral
> ventricles are now correct in
> the final aseg.mgz. However the pial surface is almost the same as earlier:
I've already corrected aseg.presurf.mgz and the left and right lateral
ventricles are now correct in the final aseg.mgz. However the pial surface
is almost the same as earlier:
https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM
https://mega.nz/#!XRRHna7Q!vaeSLG5Cv-fGW-0xdEJlgF
yes, Gabor already pointed this out to me :)
thanks to both of you
Bruce
On Tue, 26 Sep 2017, Antonin Skoch
wrote:
Dear Bruce, Gabor,
while reading this thread, I think that there is misunderstanding.
-noaseg flag of recon-all indeed disables using aseg.presurf,
whereas -autorecon2-noas
oh, sorry, you are correct. I guess you need to edit the aseg.presurf.mgz
since that is what mri_fill is given as a segmentation. Sorry for the
mistake
Bruce
On Tue, 26 Sep 2017, Gabor Perlaki wrote:
> If I accurately understand the recon-all script, then -noaseg sets UseAseg=0,
> but
> "auto
Dear Bruce, Gabor,
while reading this thread, I think that there is misunderstanding.
-noaseg flag of recon-all indeed disables using aseg.presurf,
whereas -autorecon2-noaseg does the same thing as -autorecon2-cp
(at least in dev version, looking at the recon-all code).
Antonin Skoch
Hi Ga
If I accurately understand the recon-all script, then -noaseg sets
UseAseg=0, but "autorecon2-noaseg" is a different flag, which only sets the
following things.
case "-autorecon2-cp":
case "-autorecon2-noaseg":
case "-autorecon2-wm":
set DoNormalization2 = 1;
set DoSegment
no, I don't think that is the case. -noaseg sets UseAseg=0, which stops
things like mri_fill from using the aseg, which is not what you want
cheers
Bruce
On Tue,
26 Sep 2017, Gabor Perlaki wrote:
> Dear Bruce,
>
> From the recon-all script it seems to me that autorecon2-noaseg,
> autorecon2-w
Dear Bruce,
>From the recon-all script it seems to me that autorecon2-noaseg,
autorecon2-wm and autorecon2-cp are totally equivalent (the same flags are
defined to be true in all three cases). Could you confirm this?
Best regards,
Gabor
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Hi Gabor
you don't want to specify -noaseg. That tells recon-all not to use the
aseg. I think autorecon2-cp and autorecon3 should do the trick
cheers
Bruce
On Tue, 26 Sep 2017, Gabor Perlaki wrote:
> Dear Bruce,
>
> I've corrected the lateral ventricles in the aseg.presurf.mgz and ran
> "reco
Dear Bruce,
I've corrected the lateral ventricles in the aseg.presurf.mgz and ran
"recon-all -autorecon2-noaseg -autorecon3 -subjid". Although the labels in
aseg.mgz is fine the surfaces (and midline cut) remained bad. Any other
idea how to correct this type of error?
Best Regards,
Gabor
I'll try your suggestion. Thank you very much.
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addressed
Hi Gabor
if you fix the aseg labels I think it should correct the midline problem
(rerun autorecon2-wm autorecon3 I think)
cheers
Bruce
On Mon, 25 Sep 2017, Gabor
Perlaki wrote:
Here are links to images showing the bad midline cut.
Could anybody help me how to solve this issue? The main c
https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM
https://mega.nz/#!XRRHna7Q!vaeSLG5Cv-fGW-0xdEJlgFTNRPm7qGHOlShYh7y5z1g
2017-09-25 13:50 GMT+02:00 Gabor Perlaki :
> Here are links to images showing the bad midline cut.
> Could anybody help me how to solve this issue? The ma
Here are links to images showing the bad midline cut.
Could anybody help me how to solve this issue? The main cause seems to be
asymmetric lateral ventricles.
Best,
Gabor
2017-09-23 8:18 GMT+02:00 Gabor Perlaki :
> Dear all,
> Here is my question again. Somehow, it didn't appear on the Freesurfe
Dear all,
Here is my question again. Somehow, it didn't appear on the Freesurfer
forum. I'm resending it without the attachments.
> I've a subject, where the midline cut is bad (see the attached pictures),
> therefore the segmented left lateral ventricle also includes considerable
> number of vo
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