Hi Alex,
it's hard to tell from just the one slice. Is there a topological defect
there? You can look at the orig.nofix/inflated.nofix to see. If not, you
could try changing the intensity thresholds in mris_make_surfaces with
the export opts (and look in the recon-all to see what they are set to
When you said to process it with the -notal-check to skip the talairach
checkam I supposed to add that in the first recon all or add it to the
recon all base command?
On 10/2/09 1:15 PM, "Martin Reuter" wrote:
Looks like the talairach check failed. Check the talairach.xfm (as you
would do
Only to the runs, where the check fails (if the transform looks OK). So
in your case the -base run.
Good luck, Martin
On Mon, 2009-10-05 at 10:01 -0400, Weisinger, Brian (NIH/OD) [E] wrote:
> When you said to process it with the -notal-check to skip the talairach
> checkam I supposed to add
Hi Nick,
Below is Bruce's response to a problem I'm having with the gray/white
segmentation. (Pasted below, you can see the brainmask.mgz volume and
surfaces--the entire brain is labeled as white matter). I could use
some guidance in carrying out his advice. He says to adjust the
intensity
Hey Doug - first of all, thanks for the reply. second -
1. I'm afraid i didn't get the explanation. what is the FIR, and what does it
mean "two samples in the FIR" ?
2. ok, thanks. isn't it strange though? how do researches jitter the ISI than?
manually?
3. thanks.
Hi, there,
I am looking at the volume size of front pole .
In lh.aparc.stats, this volume is 590,
while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610,
which one is accurate?
Thanks a lot!
BTW:
In FreeSurfer Tutorial : Process Flow
(http://surfer.nmr.mgh.harvard.edu/fs
the aparc
On Mon, 5 Oct 2009, Guang Zeng wrote:
>
> Hi, there,
>
> I am looking at the volume size of front pole .
> In lh.aparc.stats, this volume is 590,
> while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610,
> which one is accurate?
>
> Thanks a lot!
>
> BTW:
>
> In FreeS
Dana,
First I would run:
recon-all -s subid -clean
to remove any prior control points and edits.
Then I would open nu.mgz:
tkmedit subjid nu.mgz
and *sparingly* put control points well into white matter areas on a few
different slices. you only need a half dozen or so. to add control
points
Guang,
You are correct in noticing that the segstats stage appears to run
during -autorecon3. It was moved to run during that stage, but the
flags to enable it exist in -autorecon2, so that needs to be updated for
the next freesurfer release.
Nick
On Mon, 2009-10-05 at 17:47 -0500, Guang Zeng
Dear freesurfer experts,I would like to use freeview to check the pial surface and label with annotation file. how to do it ?thanks your helpbestJL--- 本郵件來自HiNet WebMail ---___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.ha
Hi,
Annotation option is not available in the stable release version. If you
are able to run the development version, you can load annotation file
from the Surface control panel on the left. Or you can load it from the
command-line like:
freeview -f surface_filename:annot=annotation_filename
Bes
Hello,
I am running FS 3 and am having problems with auto-recon1, in particular the
mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my
nu.mgz image has intensities all below 20. I am having errors further down the
line, but I think they are all due to this step. C
Dear all,
It seems that freesurfer's source code is open.
But I couldn't find any link for source code or cvs id and password.
Could anybody tell me whether the source code is available to external people
for academic purpose?
If it's available, where can I download the source code?
Please tell
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