Pål,
the log file also says:
Original Data has (0.546875, 0.546875, 12) mm size and (512, 512, 41)
voxels.
is this a structural volume? it only has 41 slices.
Nick
On Fri, 2009-03-27 at 07:57 -0400, Bruce Fischl wrote:
> wow, is it really that big or did you zero-pad it?
> On Fri, 27 Mar 200
Thomas,
It's created if you include the -localGI flag with recon-all. You must
have matlab installed for this to work. See also:
http://surfer.nmr.mgh.harvard.edu/fswiki/LGI
Nick
On Thu, 2009-03-26 at 16:57 -0700, ox...@yahoo.com wrote:
> Sorry to bother with such a trivial question, but I lo
Pedro Paulo,
Hi! Sita noticed that the file has a FOV > 256. We have found this to
be a problem in processing, so beginning in v4.2.0, we exit with an
error if it detects this. Normally he solution is simply to include the
flag -cw256 on the recon-all command line. This crops the image to a
F
Thank you Bruce. I haven't thought about it specifically. But, if I can
uniformly subdivide them, it would be very helpful to me.
Best wishes,
Sungeun
On Fri, Mar 27, 2009 at 4:55 PM, Bruce Fischl wrote:
> Hi Sungeun,
>
> Koen Van Leemput (ccd) have some prototypes for doing this in hippocampu
Hi Sungeun,
Koen Van Leemput (ccd) have some prototypes for doing this in hippocampus,
but we haven't written anything for elsewhere. What specifically were you
thinking about? Just a uniform subdivision? Along the major eigendirection
for example?
cheers,
Bruce
On Fri, 27 Mar 2009, Sungeu
I agree. At some point the high resolution actually makes things much
harder. For example, we are treating cortical gray matter as a single
class, but at high enough resolution you start to see relatively large
differences in signal intensity between deep and superficial gray,
particularly wher
yes, the thickness is independent of these. I think the only issue are
the spots in the aparc+aseg, which I think we've fixed. You should be able
to just rerun the very last (Fast) steps to regenerate them.
cheers,
Bruce
On Fri, 27 Mar 2009,
Ryan Scotton wrote:
Hi guys,
Does this mean th
Hello,
I am looking for any automated method to sub-divide segmented subcortical
structures by FreeSurfer. Is there anyone who knows how to do this?
Thanks in advance.
--
Sungeun Kim.
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Nasim,
Can you update to the newest Freesurfer? I think that bug has been
fixed.
Nick
On Thu, 2009-03-26 at 11:05 -0400, Nasim Maleki wrote:
> Dear Freesurfers,
>
> I get the following error message in Qdec (1.1) when I choose ?
> h.aparc.a2005s.thickness on the tutorial data:
>
> Loading d
Dave,
Doug will be able to give you a better answer when he returns, but it
seems like you should be able to perform the monte-carlo analysis on
volume data. see mri_glmfit-sim --help. that has volume-based info.
you would use mri_concat to concatenate volume data together. The
simulation treat
Rosa,
The recon-all.log file indicates that it failed the tailarich_avi step
because your system does not have libg2c.dylib. Can you update to a
newer version of freesurfer?
You will still have problems getting your hi-res data to be processed by
the recon-all stream. I am sorting out those pro
Falk,
Is it possible to send me an example hires volume that you are working
with? I'd like to send it through the stream myself so that I can fix
the problems encountered (with using hires data) first-hand. You can
upload the dicom or the 001.mgz file to me here:
https://www.nmr.mgh.harvard.ed
Hi,
I'm getting an NAN value for some surfaces but not for others. Any
ideas? Both surfaces below were generated using an identical process.
[yi...@schnook sph_sm20]$ pwd
/autofs/space/ventzl_001/users/SUBJECTS_DIR/mano010/bold/EMexec3/sph_sm20
[yi...@schnook sph_sm20]$ mris_fwhm --i e001-rh.b
Hi guys,
Does this mean that the measurements are probably solid, but the
aparc+aseg.mgz volume inaccurately represents these measurements, or will I
need to recompute the last two steps (aparc2aseg and wmparc) in order to
attain accurate cortical thickness values? It doesn't like that way, since
Hello,
Using tkmedit-sess I get this error
ERROR: cannot determine format for stem
./group-fsfast_ASD/bold/ana_FaceSCR/tal-rfx/h-offset
What does this message mean ? And how can I solve the problem ?
Thank you,
Nils
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Hi Ryan,
I think a lot of the spottyness you are seeing is a bug in FS3 that was
fixed. Try using the new FS to just regenerate the aparc+aseg and see if
it looks better.
Bruce
On Fri, 27 Mar 2009, Nick Schmansky wrote:
Ryan,
Be sure to have a look at ribbon.mgz, as that is a volume file c
Ryan,
Be sure to have a look at ribbon.mgz, as that is a volume file created
using the white and pial surfaces (from mris_volmask), and would be the
most accurate of the volume files in regards to gm segmentation.
Nick
On Fri, 2009-03-27 at 10:53 -0400, Ryan Scotton wrote:
> Hi Bruce,
>
> I've
ok, we'll take a look
On Fri, 27 Mar 2009, Ryan Scotton wrote:
Hi Bruce,
I've uploaded an example of a case with fairly accurate white and pial
boundries when viewed on top of the wm.mgz volume, and GM areas that are not
segmented and others
which have a very fuzzy/noisy boundary within the apa
Hi Bruce,
I've uploaded an example of a case with fairly accurate white and pial
boundries when viewed on top of the wm.mgz volume, and GM areas that are not
segmented and others
which have a very fuzzy/noisy boundary within the aparc+aseg.mgz volume.
Also, I'm not sure what email client you're u
I think you mean FreeSurfer?
You can find this in aseg.stats inside stats directory in each subject.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
On Fri
Hello,
How can I calculate the GM using the FSL?
Thanks, Kelly
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wow, is it really that big or did you zero-pad it?
On Fri, 27 Mar 2009,
Pedro Paulo de Magalhães Oliveira Junior wrote:
I think you have a problem in the voxel size.
*The physical sizes are (280.00 mm, 280.00 mm, **492.00 mm**), which cannot
fit in 256^3 mm^3 volume.*
can you send us the output of recon-all?
On Fri, 27 Mar 2009, Pål Gunnar
Larsson wrote:
I problem with a MRI set that stops recon-all very early in the process. There is a
warning before : "If you find problems, please let us know", but I don't think
that text is related to the error.
Sugges
I think you have a problem in the voxel size.
*The physical sizes are (280.00 mm, 280.00 mm, **492.00 mm**), which cannot
fit in 256^3 mm^3 volume.*
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
---
I problem with a MRI set that stops recon-all very early in the process. There
is a warning before : "If you find problems, please let us know", but I don't
think that text is related to the error.
Suggestions?
Regards
Pål G. Larsson
Freesurferproblem
Description: Freesurferproblem
_
Thomas,
?h.pial.outer.smoothed surface is created as a part of the local
gyrification index computation and represent the envelope of the brain
(hull). It is computed using morphological closing of the sulci (see
the validation publication in IEEE TMI and the lGI wiki page).
Marie
Quot
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