Hi Freesurfer Experts,
I have a question about the use of mri_surf2surf. Can I use this command to
convert the sphere of a surface to its native space? To be specific, we can
get a sphere if we do inflation and other steps to the white surface , can
we transform the sphere back to the orginal whit
The error msg asks you to look at transforms/talairach_avi.log. Have you
and does it reveal anything?
doug
Dana W. Moore wrote:
Hi all,
I get the following error message during recon-all:
ERROR: 'imgreg_4dfp
/usr/local/freesurfer/average/711-2C_as_mni_average_305
/usr/local/freesurfer/aver
Hi all,
I get the following error message during recon-all:
ERROR: 'imgreg_4dfp
/usr/local/freesurfer/average/711-2C_as_mni_average_305
/usr/local/freesurfer/average/711-2B_as_mni_average_305_mask
talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283'
failed! status=254
ERROR: m
$>mris_calc -o combined.mgz vol1.mgz add vol2.mgz
(i.e. combined.mgz = vol1.mgz + vol2.mgz)
--Original Message--
From: xfore...@ucla.edu
Sender: freesurfer-boun...@nmr.mgh.harvard.edu
To: 'Freesurfer Mailing List'
Subject: [Freesurfer] merging 2 .mgz files?
Sent: Jun 29, 2009 16:57
Dear
Zhang
In the wiki page there's a feature to check the previous version of each page.
-- Pedro Paulo Jr
E71 Nokia
-Msg original-
De: Bruce Fischl
Enviada: 29/06/2009 17:30:10
Para: Zhang, Xiaochu (NIH/NIDA) [F]
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Assunto: Re: [Freesurfer] Where can I
Dear Freesurfer Experts,
I was wondering if its possible to combine 2 mgz files?
the 2 files don't have overlaps..
sincerely,
Andy
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Sure. Since that release was on 11-25-06, I will send you the last edited
version of that page before that date (on 8-22-06) unless I find the
latest version without all the changes.
Allison
--
On Mon, 29 Jun 2009, Bruce Fischl wrote:
I'm not sure we have it so easily. Does anyone know?
On M
Thanks for the tip! The problem is that if I simply change black pixels to
white, the edge of the surface is not so nice, that's why I asked for a
built-in solution. Fortunately, this is a minor issue.
Attila
On Mon, Jun 29, 2009 at 3:38 PM, Rudolph Pienaar <
rudo...@nmr.mgh.harvard.edu> wrote:
>
I'm not sure we have it so easily. Does anyone know?
On Mon, 29 Jun 2009,
Zhang, Xiaochu (NIH/NIDA) [F] wrote:
The freesurfer I am using now is this version,
"freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4". I knew there is much improved in the
current version.However, I have about 80 par
The freesurfer I am using now is this version,
"freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4". I knew there is much
improved in the current version.However, I have about 80 participants done in
this old version. I only want to add several new participants and do some group
anlaysis. Today
If you are thinking about capturing screenshots for publication (with a
white background), you can save a picture of interest to a tiff from
tksurfer (with a black background), and then use 'convert' (part of
ImageMagick and standard on most Linux distros) to change the black
background to whit
What have you tried so far? You might try mri_aparc2aseg. I think the
only requirement is that the segs for cortex and white matter have the
same index number as they have in aseg.mgz
doug
xfore...@ucla.edu wrote:
Dear Freesurfer Experts,
I am trying to combine aparc.annot with aseg.mgz for
Hi Andy,
I'm not sure this makes sense, as the aseg labels are not cortical, and
thus won't be close to the surface. Why did the combo not work? You can
use mris_sample_parc to sample the asegs onto the surface, but I don't
think that will get you where you want to go.
cheers
Bruce
On Mon, 2
Dear Freesurfer Experts,
I am trying to combine aparc.annot with aseg.mgz for a Vervet monkey brain,
the Aseg.mgz is hand made, not generated by freesurfer.
so far I have no luck with it, So i've decided to go with a different
approach,
which is to add the Aseg (subcortical structures labels)
I don't think there is an easy way to do this, sorry
On Jun 29, 2009, at 12:46 PM, Krajcsi Attila wrote:
Hi,
Is there any possibility in tksurfer to change the background color
from black to white?
Thanks,
Attila
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Fr
ok
On Mon, 29 Jun 2009, Falk Lüsebrink wrote:
I could do that, but not before wednesday.
- Original Message - From: "Bruce Fischl"
To: "Falk Lüsebrink"
Cc:
Sent: Monday, June 29, 2009 6:53 PM
Subject: Re: [Freesurfer] Bad aseg
do you want to send us the subject?
On Mon, 29 Jun
I could do that, but not before wednesday.
- Original Message -
From: "Bruce Fischl"
To: "Falk Lüsebrink"
Cc:
Sent: Monday, June 29, 2009 6:53 PM
Subject: Re: [Freesurfer] Bad aseg
do you want to send us the subject?
On Mon, 29 Jun 2009, [UTF-8] Falk
Lüsebrink wrote:
Yes, the s
Yes, the skull stripping looks nice.
- Original Message -
From: "Bruce Fischl"
To: "Falk Lüsebrink"
Cc:
Sent: Monday, June 29, 2009 6:19 PM
Subject: Re: [Freesurfer] Bad aseg
Did you check the skull stripping?
On Jun 29, 2009, at 3:54 AM, Falk Lüsebrink wrote:
do you want to send us the subject?
On Mon, 29 Jun 2009, [UTF-8] Falk
Lüsebrink wrote:
Yes, the skull stripping looks nice.
- Original Message - From: "Bruce Fischl"
To: "Falk Lüsebrink"
Cc:
Sent: Monday, June 29, 2009 6:19 PM
Subject: Re: [Freesurfer] Bad aseg
Did you check th
Hi,
Is there any possibility in tksurfer to change the background color from
black to white?
Thanks,
Attila
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Did you check the skull stripping?
On Jun 29, 2009, at 3:54 AM, Falk Lüsebrink wrote:
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Hi Freesurfer experts,
I want to use the old freesurfer version. However, I read the wiki today and
found the manual has been changed. I need read the "GroupAnalysis" in the old
version. Who can help me?
Thanks a lot!
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
Nation
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