Hi FreeSurfer experts,
When I specify fwhm=15 to analyze area, mri_surfcluster said that it cannot
find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/...
This did not happen when I used FreeSurfer 5.3.0
I am wondering if FreeSurfer 6.0.0 pre-smooths the surface area?
Thanks,
Daniel
Hi list,using FS-FAST I have obtained a map reporting - Red_positive cluster
shows difference for FC of group A > FC of group B- Blue_negative cluster shows
difference for FC of group B < FC of group A
Because I would like to extract the value of cortical thickness from each
cluster, I have save
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
Try mri_cor2label
On 09/26/2017 04:11 PM, Fereshte wrote:
> Dear Experts,
> Is it possible to convert aseg file to individual lables ( except the
> one introduced by Jared Tanner) ?
> Thank you!
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.
Dear Experts,
Is it possible to convert aseg file to individual lables ( except the one
introduced by Jared Tanner) ?
Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
Well i think there are some by making comparisons between surfaces( pial
and white) and the segmentation before topology correction ( i could see
some holes still existed) . I'm going to check the mris_euler_number to see
the result.
Thank you.
On Tue, Sep 26, 2017 at 5:30 PM Bruce Fischl
wrote:
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
ructing geometrically accurate and topologically correct models of
> >> the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
> >>
> >> Florent S?gonne,Eric GrimsonBruce Fischl, 2003. Topological Correction
> of
> >> Subcortical
Dear All,
We are pleased to announce the 0.8.0 release of PySurfer, a Python-based
package for visualizing Freesurfer data. This release includes bugfixes and
multiple enhancements, including:
- The surface geometry that is displayed can now be changed after
initializing a Brain instance with e.
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
___
Freesurfe
If you are using the Different Offset Different Slope (DODS) model,
then, by default, it tests at age=0. If you want to test at age=8, just
subtract 8 from all the ages
On 09/26/2017 01:57 PM, Eryilmaz, H. Hamdi wrote:
> Dear all,
>
> We are modeling changes in cortical thickness over time usin
Dear all,
We are modeling changes in cortical thickness over time using a cross-sectional
design. We have two groups of participants, age 8 to 18. In the cortical
regions that interest us, there is generally a linear decline in thickness with
age. Each group can be fitted to a best-fit line.
Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 1001_Baseline.long.longbase and 1001_Followup.long.lon
Hi Daniel
you might try asking the MNE developers about this, but I don't think
this is correct. What would a volume version of the sphere.reg be? A filled
in sphere?
cheers
Bruce
On Tue, 26 Sep 2017, Daniel van de Velden wrote:
Dear Freesurfer Team,
I am using your reconstruction pipelin
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
why do you think there are defects? If you have run recon-all there are
pretty much guaranteed not wo be any. You can't really see this visually,
but mris_euler_number will tell you if there are any
cheers
Bruce
On Tue, 26 Sep 2017,
Fereshte wrote:
Dear Experts,
I checked the topology corre
Dear Freesurfer Team,
I am using your reconstruction pipeline for my study. Since I need to
morph all my subjects to an average subject (using mne-python for this)
for upcoming a Volume Source Analysis I deeply looked into the whole
source-code of both software packages. Narowing down the probl
Dear Experts,
I checked the topology corrected surfaces in recon-all pipeline however i
found it didn't do well as still there are many topology defects in the
pial surfaces. I know how to correct them manually in freeview but are
there any commands to recorrect these topological defects with for e
24 matches
Mail list logo
