Hello Fresurfer admin!
I was looking for the v6 beta and it looks like it still hasn't been
released after it was pulled down the last time. I would like to know what
is the expected ETA for the beta. Last I remember it was mentioned it was
on the verge of release about two weeks ago.I'm looking f
Dear freesurfer people,
I haven’t noticed that computing geodesic distance between two points across
hemispheres is not a trivial as I thought.
There are many implementations of Dijkstra algorithm publicly available to
compute geodesic distance on a triangular mesh, but it’s a bit tricky to dea
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Monday, May 2, 2016 3:49 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] no recon
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
> It opens a box that says "voxel edit" This allows me to edit the images
> accordingly, however I read in the email forum that this may create some
> issues further on down the line?
>
> ___
It opens a box that says "voxel edit" This allows me to edit the images
accordingly, however I read in the email forum that this may create some issues
further on down the line?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
what happens when you click on the button with the pencil in it? The one
just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf
Can you send a snapshot of your Freeview window? The Recon Edit button
looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it
says to use the recon edit button to man
Thank you Douglas. However, in the tutorial for editing output, it says to use
the recon edit button to manually perform edits. After this step, I use the
command line and recon-all. How do I do the manual edits without this button. I
do see a voxel edit button.
https://surfer.nmr.mgh.harvard.e
freeview does not have a recon button. You have to run recon-all from
the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem,
but I see no answers to their queries. I have version 1.0 (5/13/2013)
of Freeview for
Hi Domenico
check out read_annotation.m and write_annotation.m. YOu should be able to
create your own .annot file and write it out from matlab to be displayed
in freeeview.
cheers
Bruce
On Mon, 2 May 2016,
Domenico Zacà wrote:
Dear FS experts,
I dumped the average cortical thickness val
Dear FreeSurfer Users,
I would like to know if we can do brainstem segmentation as described in the
recent publication
http://www.sciencedirect.com/science/article/pii/S1053811915001895
Author as well as FreeSurfer website mention that this feature is only
available in FreeSurfer 6.0 and
Hello,
I searched the mail list and saw that others have had this problem, but I see
no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for
Linux. I have no recon button. What should I do?
Thank you
___
Freesurfer mailing list
glad it worked out
Bruce
On Mon, 2 May 2016, Jesu Kiran Jk wrote:
Thank you very much for your patient help. I could load the surfaces,
Have a nice day!
Kind Regards,
Jesu
On Mon, May 2, 2016 at 5:40 PM, Bruce Fischl wrote:
those aren't surfaces, they are scalar fields over the surface
Thank you very much for your patient help. I could load the surfaces,
Have a nice day!
Kind Regards,
Jesu
On Mon, May 2, 2016 at 5:40 PM, Bruce Fischl
wrote:
> those aren't surfaces, they are scalar fields over the surface. Load
> lh.inflated then load lh.area as an overlay.
>
> Also, please c
those aren't surfaces, they are scalar fields over the surface. Load
lh.inflated then load lh.area as an overlay.
Also, please cut and paste text in directly instead of sending us images of
text.
thanks
Bruce
On Mon, 2 May 2016, Jesu Kiran
Jk wrote:
Thanks for the reply, I could now load
Dear FS experts,
I dumped the average cortical thickness values of 68 ROI using
aparcstats2table into a spreadsheet, then generated a set of CT networks
measures in matlab for each ROI. Now how can I visualize the results back
in FreeSurfer?
Thanks
Domenico Zacà, PhD
MR Lab Research Fellow
Ce
Hi Jesu
can you send su the full command line and screen output?
cheers
Bruce
On Mon, 2 May 2016,
Jesu Kiran Jk wrote:
> Dear Freesurfer Experts,
> I wish to load wm.mgz, brain.mgz volumes with freeview. But it is giving me
> an error 'Failed to load MRI'. Why is it giving me
> this error and
Dear Freesurfer Experts,
I wish to load wm.mgz, brain.mgz volumes with freeview. But it is giving me
an error 'Failed to load MRI'. Why is it giving me this error and how could
I correct this? Please help.
Kind Regards,
Jesu
___
Freesurfer mailing list
then you will need to create those too. Why not just run recon-all and
avoid all this trouble?
On Mon, 2 May 2016, Muhammad Razib wrote:
Dear Fischl,
No I don't have the white and the inflated ones.
On Mon, May 2, 2016 at 10:01 AM, Bruce Fischl
wrote:
you need the white surfae I believe
Dear Fischl,
No I don't have the white and the inflated ones.
On Mon, May 2, 2016 at 10:01 AM, Bruce Fischl
wrote:
> you need the white surfae I believe and the inflated. Do you have those?
>
>
>
> On Mon, 2 May 2016, Muhammad Razib wrote:
>
> Dear Fischl,
>> Thank you so much for your reply. I
you need the white surfae I believe and the inflated. Do you have those?
On
Mon, 2 May 2016, Muhammad Razib wrote:
Dear Fischl,
Thank you so much for your reply. I don't have all the files that have been
created by recon-all. For the surfaces I just have the .pial files. Is there
a way to ge
Dear Fischl,
Thank you so much for your reply. I don't have all the files that have been
created by recon-all. For the surfaces I just have the .pial files. Is
there a way to generate .sphere files from .pial files? Or we need the
original volume files and then run recon-all to reconstruct them?
Hi Muhammad
are you using recon-all? It should create everything, including both pial
and sphere. I think the spheres are create earlier in the recon process
than the pial these days
cheers
Bruce
On Mon, 2 May 2016, Muhammad Razib wrote:
Hi,
I have some (freesurfer generated) pial surfac
Dear freesurfer experts,I have a question regarding correction of cortical
measures or global measures (ICV, total surface area). As I understand from
literature and the freesurfer wiki, a model for thickness should not be
corrected for ICV (since thickness does not scale with total brain vol
24 matches
Mail list logo
