on one group of subjects i ran "recon-all -all -clean -wsthresh n", which
according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes
what "-clean-bm" does.
on the other group i ran "recon-all -all -wshthresh n" after deleting
everything and converting them from raw invol da
Thanks, Andreas. That clears it up.
There was no attachment though. Can you send me the screenshots?
--
On Tue, 13 Apr 2010, Andreas Berger wrote:
> on one group of subjects i ran "recon-all -all -clean -wsthresh n", which
> according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFla
Hi all,
I'm a new user of freesurfer.
It's a simple question.
I want to convert ?h.smoothwm and ?h.smoothwm.nofix to .mgz as binary volume
(foreground/background = 1/0).
So I found mri_surf2vol command, but the command I used could be problem.
> mri_surf2vol --template ./orig/001.mgz --volreg reg
thank you for replying,
i reattached the screenshots. they were in my first mail but i think i broke
the thread by replying to the wrong adress once, sorry. screenshot 1 is result
of "recon-all -all", screenshot 2 is result of "recon-all -all -wsthresh 0".
what's weird is that next to the left
Your surfaces look fine (at least in that slice). Why do you feel you need
to strip away more skull?
--
On Tue, 13 Apr 2010, Andreas Berger wrote:
> thank you for replying,
>
> i reattached the screenshots. they were in my first mail but i think i broke
> the thread by replying to the wrong a
try using mris_fill.
cheers
Bruce
On Tue, 13 Apr 2010, Jerald Zhao wrote:
> Hi all,
> I'm a new user of freesurfer.
> It's a simple question.
>
> I want to convert ?h.smoothwm and ?h.smoothwm.nofix to .mgz as binary volume
> (foreground/background = 1/0).
> So I found mri_surf2vol command, but th
Hi,
I post this message once again because I didn't get
any reply.
On an Intel Mac the "Edit Voxels Tool" in tkmedit does
not work, contrary to a PPC Mac.
This applies both to version v4.3.1 and v4.5.0.
Ed
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There's not a volume that the surface was created from, but there is a
volume that more-or-less matches.
Just look in $FREESURFER_HOME/subjects/fsaverage/mri. You can use any
of the volumes there.
doug
Ritobrato Datta wrote:
> Hello All,
>
> Which is the volumetric version of the fsaverage bra
Hi everyone,
I am using freesurfer version 4.5.0, and have just gotten an error message that
I have never received before. The end of the recon-all script is pasted
below. what does this mean?
#...@# Skull Stripping Mon Apr 5 15:06:52 EDT 2010
/home/fs01/kab2003/FS/133_S_0525/mri
mri_water
try adding -nowsgcaatlas to the end of the recon-all command.
n.
On Tue, 2010-04-13 at 18:59 +, Dana W. Moore wrote:
> Hi everyone,
>
> I am using freesurfer version 4.5.0, and have just gotten an error
> message that I have never received before. The end of the recon-all
> script is pasted
Hi Bruce,
I found some comments from your deep in the archive on converting
distance measured on the sphere to distance on the folded surface:
http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/msg00251.html
Is this still the case? And, will loading the ?h.area file in matlab
and
Hi Mike,
I think that's still correct, but it's been a long time since I messed
with it.
Bruce
On Tue, 13 Apr 2010, Michael Waskom wrote:
> Hi Bruce,
>
> I found some comments from your deep in the archive on converting
> distance measured on the sphere to distance on the folded surface:
> http
Thanks, that should be helpful.
Is there a way to use mris_anatomical_stats on the .annot file that the cluster
correction creates within the qdec analysis folder, or do I need to map the
annotation to a subject in order to use mris_anatomical_stats? If I try to run
mris_anatomical_stats on th
Job Announcement: Research Assitant in Brain Imaging
Boston, MA, USA
Full time research assistant positions are available in structural and
functional imaging of several clinical conditions including degenerative
brain changes in individuals with neurological diseases, traumatic brain
injury,
i was going to have you link wm.mgz to T1.mgz as a hack to get
mris_anatomical_stats to dump the colortable, but i see that
mris_anatomical_stats complains about running against fsaverage. so
rather than add a hack on a hack, i'll just update mris_info to dump the
colortable of a .annot file.
Thank you. I succeeded to convert it, but the label is completely incorrect.
Actually, I can not understand how exactly it can work: when I make an
opposite direction with mri_label2vol I pass the registrer.dat file;
however, in mri_cor2label there is no such option. How then this
transformation ca
Hi Nick,
I should have mentioned that this actually was done with the -no-wsgcaatlas
option. The results I sent you were obtained using that command.
Thanks,
Dana
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Tuesday, April 13, 2010 3:09 PM
To: Dana W
Hi, there,
I have a question about mri_robust_template,
I have a binary brainmask for each time point, I'd like to create a binary
norm_template.mgz using mri_robust_template command.
Has mri_robust_template an option to do nearest interpolation ?
Thanks!
Guang
Hi Bruce
Thank you for the quick answer. We already considered using
mris_divide_parcellation. Unfortunately the result is a strip shaped
parcellation scheme, which is not suitable for our aim. Therefore we
would rather use mris_make_face_parcellation. Is there no other way to
get the MNI C
Hi FSusers,
I am engaging to map automatic segmentation image (eg.
aparc.a2009s+aseg.mgz) to raw functional space. According to the
instructions from the FreeSurfer website, I found that there were two ways
below to do it. However, the results from both methods are different and
attached. Let me s
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