check the talairach to see if it is value, and also make sure that the
T1.mgz white matter intensities are close to 110 almost everywhere.
On Mon, 31 Jul 2006 [EMAIL PROTECTED] wrote:
I keep getting this error when trying to skullstrip a scan...
*WATERSHED*
Hello,
I was wondering if there is a Freesurfer command for getting neuroanatomical
labels for the output clusters of mri_volcluster.
thank you very much for your help,
paymon
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Hi all,
I was wondering if fs-fast implements slice time correction at any point
during processing? if so does it default to correction for either
interleaved or linear acquisition and can this be modified?
Thanks,
Cameron
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Does running it with --label not work?
On Mon, 31 Jul 2006, Paymon Hosseini wrote:
Hello,
I was wondering if there is a Freesurfer command for getting neuroanatomical
labels for the output clusters of mri_volcluster.
thank you very much for your help,
paymon
_
You can run it with stc-sess (this is a frontend for FSL's
slicetimer). You can pick the slice order with -so. If it's
interleaved and from a siemens scanner, then just specify "siemens" as
the slice order. Run it with -help for more info.
doug
On Mon, 31 Jul 2006 [EMAIL PROTECTED] wrote:
doug
i think he's asking about what you were thinking of implementing with
a similar flag to the --annot one that you added to mri_surfcluster.
frida
On Jul 31, 2006, at 5:34 PM, Doug Greve wrote:
Does running it with --label not work?
On Mon, 31 Jul 2006, Paymon Hosseini wrote:
Hello,
Oh, no that does not exist yet. There are some issues as to whether
it's really valid as the volumetric analysis that preceeds
mri_volcluster is linear whereas the aseg.mgz is produced with a
nonlinear registration. I'm looking into something intermediate that
could give you something close to th
Hello,
I have seen a list of 40 freesurfer-segmented
subcortical objects with their respective intensity
values somewhere in the documentation, but not able to
locate it now. Could somebody help me please.
Thanks
Shahab
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After a recon, there will be a file called subject/stats/aseg.stats
with a list of structures, their volumes, and the mean intensity. Is
this what you mean?
doug
On Mon, 31 Jul 2006, Shahabuddin Ansari wrote:
Hello,
I have seen a list of 40 freesurfer-segmented
subcortical objects with t
I have just changed the way that DEV version recon-all creates the
aseg.stats file. Previously, it would report everything that it found
in FreeSurferColorLUT.txt. This included a lot of stuff that would
never be in the subcortical segmentation, and this made the aseg.stats
file very messy.
The
Hi,
So where can I download this update?
Would I have to download the whole version of freesurfer?
Thanks,
HweeLing
On 8/1/06 10:09 AM, "Doug Greve" <[EMAIL PROTECTED]> wrote:
>
> I have just changed the way that DEV version recon-all creates the
> aseg.stats file. Previously, it would report
I should have mentioned one more thing. If you want to re-run
recon-all so that it only re-creates the stats/aseg.stats table, then run
recon-all -s subject -segstats
doug
On Mon, 31 Jul 2006, Doug Greve wrote:
I have just changed the way that DEV version recon-all creates the
aseg.stats f
Hi Hwee Ling!
In general, we typically post a new stable update on our website every few
weeks, and you can check
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
to see what bugs/fixes/changes have been made to each release.
For this change, Doug may be able to make something specific av
I think we'd have to get nick to cut a new dev version and put it on
the web site.
doug
On Mon, 31 Jul 2006, Jenni Pacheco wrote:
Hi Hwee Ling!
In general, we typically post a new stable update on our website every few
weeks, and you can check
https://surfer.nmr.mgh.harvard.edu/fswiki/Rele
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