Hi all,
I want to try Freesurfer in object with a physical
sizes are (310.00 mm, 310.00 mm, 310.00 mm) but I have a segmentation fault
when running the recon-all, precisely, in stage 2 when running:
mri_em_register -mask brainmask.mgz nu.mgz
/home/samba/user/douiri/dev/freesurfer
just make sure that the window shows as you want it (you may need to
redraw it before hitting save).
On Wed, 12 Jul 2006, Chacko Cherian wrote:
when i want to print-out the outputs using "Save TIFF
as" it isn't giving me any results.Is there something
else that I need to do to save the output
we are currently limited to 256^3, which fits pretty much every brain
I've ever seen. What is 310^3? This is on our to-do list.
Bruce
On Thu, 13 Jul
2006, Abdel Douiri wrote:
Hi all,
I want to try Freesurfer in object with a physical sizes are (310.00 mm,
310.00 mm, 310.00 mm) but I ha
Can you say exactly what you're doing so we can try to reproduce it?
On Wed, Jul 12, 2006 at 10:46:34PM -0700, Chacko Cherian wrote:
> when i want to print-out the outputs using "Save TIFF
> as" it isn't giving me any results.Is there something
> else that I need to do to save the outputs as TIFF
Hi Darren,
I just found out that when you save a label in tksurfer, it saves it
using the orig surface coords, which explains the discrepancy. Try
running label2label with --trgsurf orig. Alternatively, you can save
your label in the white surface if you start up tksurfer with -orig
white
do
Hmmm, I just tried this and did not have a problem. There's something
funny going on here. The indices for both labels are the same, only the
cooridnates are different. This means that the source label and the new
label are using different surfaces. Are you sure you created the source
label fr
Hi Doug,
I'm using the matlab routine 'read_surf' from the 3.0.3 distribution to read
a surface generated by mri_tessellate.
The magic number for the surface is: 16777213, which does not match either
the QUAD or the TRI magic numbers listed in read_surf and hence does not
read it.
Is there an up
Hi Satra,
I think the magic # should still be 16777215. Did your surface get
corrupted somehow?
Bruce
On Thu, 13 Jul 2006, Satrajit Ghosh wrote:
Hi Doug,
I'm using the matlab routine 'read_surf' from the 3.0.3 distribution to read
a surface generated by mri_tessellate.
The magic number for
I don't know. I did not write that. Maybe Bruce knows?
Satrajit Ghosh wrote:
Hi Doug,
I'm using the matlab routine 'read_surf' from the 3.0.3 distribution to read
a surface generated by mri_tessellate.
The magic number for the surface is: 16777213, which does not match either
the QUAD or the
Hi Bruce,
tksurfer can read the surface but matlab cannot. I'm therefore not sure if
it is corrupted. I'm running on a 64 bit opteron, if that makes a
difference.
Satra
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thursday, July 13, 2006 1:56 PM
To: Satrajit
Hello all,
The cortical thickness table which is located in the
stats folder..i am currently opening it with my vi
editor.Is there any way to open it directly as a
spreadsheet to print it out??
THanks
Chacko.
__
Do You Yahoo!?
Tired of spam? Yahoo
Use the asegstats2table or aparcstats2table utilities, which are new to
v3.0.3 of freesurfer. For help:
asegstats2table --help
and
aparcstats2table --help
On Thu, 2006-07-13 at 12:27 -0700, Chacko Cherian wrote:
> Hello all,
> The cortical thickness table which is located in the
> stats f
Have you tried opening it in excel? Alternatively, you can run
aparcstats2table. This program was intended to be run on multiple
subjects in order to produce a spreadsheet, but you can run it on one
subject just as well. This is a fairly recent addition (within the last
8 weeks), so you might
Nick, Doug or anyone with thoughts on the matter,
This is a return to a similar question I raised in June-2nd thread "Some FS
input questions", but a little less awkward.
We'd like to present to FS already brain-extracted volumes that are already
"conformed", ie: 256^3, and 1 mm isotropic
Thi
I defined the label on the inflated surface, I don't know what the
coordinates are mapped into when they are saved from tksurfer. I guess
the vertex numbers go through a lookup into the orig surface to get
those coordinates.
When I ran the label2label mapping a second time, using the results of
Hi Graham,
the EM Registration with Skull is for generating ICV measures, which of
course you won't be able to get with the skull gone.
Bruce
On Thu, 13 Jul 2006,
Graham Wideman wrote:
Nick, Doug or anyone with thoughts on the matter,
This is a return to a similar question I raised in Jun
Graham,
Thanks for pointing these out. We've corrected the page (but it still
needs quite a bit more work to make it a true 'file spec').
Nick
On Wed, 2006-07-12 at 20:05 -0700, Graham Wideman wrote:
> Folks: (Probably Nick S?)
>
> Comments on the MghFormat wiki doc page:
>
> https://surfer.
Graham,
In general, you should be careful when selecting the '-nosomething'
options, as recon-all does not perform much checking for these flags
(only the -autorecon1,2,3 flags contain the validity checks).
An option when experimenting with the flags is to use the -dontrun flag,
which just print
OK Nick thanks, that's good insight into the intent behind the noxxx options
etc.
Graham
At 7/13/2006 06:38 PM, Nick Schmansky wrote:
>Graham,
>
>In general, you should be careful [...]
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https:
19 matches
Mail list logo
