Dear all,
Continue with my previous question in "To use the file thickness.mgh outside
Freesurfer". Thanks for Doug's recommedation to use the mri_surf2vol program to
convert mgh files into image format, such as NIFTI.
But I failed due to wrong setting on several arguments:
1, '--volreg': I do
Hi all,
I wonder if there are any plans to support CUDA on Mac platform. I see there
are libraries available for the platform.
Thanks a lot for feedback,
Martin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu
Hi,
One quick question: In the aparc+aseg file I suppose we have two volumes
(one for aparc and other for aseg). Are those volumes overlapped or one
after another?
thanks
PPJ
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de
Hi Pedro Paulo,
The aparc+aseg file describes a single volume with parcellation and
segmentation information combined.
--Lilla
On Wed, 15 Dec 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
Hi,
One quick question: In the aparc+aseg file I suppose we have two volumes
(one for aparc a
i use nohup with recon-all remotely, with:
nohup recon-all -s subj -all >& /dev/null &
notice the >& /dev/null, which redirects stdout and stderr to null.
i've found this is necessary. note that recon-all output still goes to
its log. after launching this way, you can close the terminal, and
r
this is a problem that will be fixed in the upcoming 5.1 release
(*hopefully* by the end of the year).
the workaround is to run mri_nu_correct.mni adding the -nofloat flag.
n.
On Wed, 2010-12-15 at 02:57 -0500, Thomas, Adam (NIH/NIMH) [E] wrote:
> Bruce et al,
>
>
>
> Did you ever get to t
another option is to convert the thickness file to gifti format. see
mris_convert --help.
n.
On Wed, 2010-12-15 at 01:26 -0800, qizhu wu wrote:
> Dear all,
>
> Continue with my previous question in "To use the file thickness.mgh
> outside Freesurfer". Thanks for Doug's recommedation to use the
yes, its in the works for the next release.
n.
On Wed, 2010-12-15 at 11:34 +0100, Martin Kavec wrote:
> Hi all,
>
> I wonder if there are any plans to support CUDA on Mac platform. I see
> there are libraries available for the platform.
>
> Thanks a lot for feedback,
>
> Martin
> _
Bruce and Allison,
Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct
solution. I just need the labeled WM boundary (ribbon) to seed my fiber
tracking. So basically I will have to compute the boundary from wmparc.mgz. Is
there anything that does that already?
Thanks,
M
Dear List,
I installed version 5.0 of freesurfer on my Linux machine, when I tried to
run tkmedit I got the attached error. Do you have any suggestion?
Kind regards,
Paola
---
SOSTIENI ANCHE TU LA RICERCA DEL SAN
Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz
is uchar. However, I found that the places surrounding the brain which have
0 grayscale values in the a.mgz
Hi Madhura,
I'm not sure I understand. The ?h.white is the boundary. If you want to
create a voxel representation of it you can use mris_fill
cheers
Bruce
On Wed, 15 Dec
2010, Ingalhalikar, Madhura wrote:
> Bruce and Allison,
> Thanks for your prompt reply. For me wmparc.mgz is not entirely th
Hi Bruce,
Thank you.
I did try
mri_convert -i a.mgz conformed_a.mgz --conform -ns 1
the pixels with 0 grayscale in a.mgz are still turned into pixels with 108
grayscale in conformed_a.mgz.
Yang
On Wed, Dec 15, 2010 at 11:11 AM, Bruce Fischl
wrote:
> specify -ns 1 (for no scaling)
>
>
> On W
specify -ns 1 (for no scaling)
On Wed, 15 Dec 2010, Yang Liu wrote:
> Hello all,
>
> I am converting one .mgz file to another like this:
>
> mri_convert -i a.mgz -o conformed_a.mgz --conform
>
> The data type of a.mgz is float. After the conversion, The conformed_a.mgz
> is uchar. However, I foun
Bruce,
I agree that ?h.white is a boundary. But it is labeled based on cortical
labels? If yes, that is exactly what I need.
Let me know,
Thanks for your response.
Madhura
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wed 12/15/2010 11:05 AM
To: Ing
Bruce,
Please ignore my earlier email.
Let me explain what I exactly need.
The wmparc.mgz gives me WM parcellation based on cortical parcellation. What I
need is just the boundary voxels from wmparc.mgz, such that each voxel in my
output has a neighbor in GM and other WM voxels are set to 0.
I am having trouble with the interface between freesurfer and matlab. When I
run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the
script does not finish.) When I force it to quit, I get the error "-display:
Command not found." In both mkcontrast and selxavg3-sess, the co
yes, the cortical labels in the .annot files apply the ?h.white surfaces
cheers
Bruce
On
Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:
>
> Bruce,
> I agree that ?h.white is a boundary. But it is labeled based on cortical
> labels? If yes, that is exactly what I need.
> Let me know,
>
> Thanks
Hi,
I found that some of the voxels in my original a.mgz are negative.
I think that caused some strange behaviors in the float to uchar conversion.
Are there methods in Freesurfer to modify the voxel values ?
Yang
On Wed, Dec 15, 2010 at 11:11 AM, Bruce Fischl
wrote:
> specify -ns 1 (for no
Hi everybody,
I am working towards multi-modal integration of BOLD data. For some of
my data, the entire brain was not recorded (in this case, I have 12
slices covering the superior half of the brain). I have been working to
align this data using bbregister and have had very inconsistent result
Hi,
We installed freesurfer on a mac computer but could not find where to paste the license code, thus have difficulty getting the freesurfer running.
Can anyone help, please.
Nisser
___
Freesurfer mailing list
Freesurfer@nmr.mg
Hi Nisser,
put it in a file named $FREESURFER_HOME/.license
cheers
Bruce
On Thu, 16 Dec 2010, Nisser ali
umar wrote:
> Hi,
>
> We installed freesurfer on a mac computer but could not find where to
> paste the license code, thus have difficulty getting the freesurfer
> running.
>
> Can anyon
If you're having trouble pasting it in there, try:
pico /$FREESURFER_HOME/.license
(Press Crt-X to save)
If there are permission problems, manually go to the folder info and
change permissions at the bottom.
On Wed, Dec 15, 2010 at 8:11 PM, Bruce Fischl
wrote:
>
> Hi Nisser,
>
> put it in a fi
Hi Thomas,
you need to create that file.
cheers
Bruce
On Wed, 15 Dec 2010, Obisesan, Thomas O.
wrote:
> Thanks Bruce,
>
> Unfortunately, we are unable to locate any such file. Any directives on how
> to locate the file will be helpful. Additionally, we are unable to paste into
> the Xterminal
Hi everybody,
I am interested in doing sub-sampling of functional data for some new
analyses. Just about the only reference I can find to sub-sampling of
data in FreeSurfer is in mri_surf2surf, which has an optional flag
trgicoorder. The comment for this flag is:
"This specifies the size of
Yes, that seems reasonable
Bruce
On Dec 15, 2010, at 1:57 PM, "Ingalhalikar, Madhura"
wrote:
> Bruce,
>
> Please ignore my earlier email.
> Let me explain what I exactly need.
> The wmparc.mgz gives me WM parcellation based on cortical parcellation. What
> I need is just the boundary vox
26 matches
Mail list logo
