[Freesurfer] freesurfer-Linux-rh9-dev20050627.tar.gz
Hi everybody I have seen this new dev release on freesurfer site. Do you think it is good for me to update my old version ( feb 2004) ? The old version works properly but I don't know if there are new functions in this new release that are important for freesurfer. Thank you very much for your help Max _ Personalizza MSN Messenger con sfondi e fotografie! http://www.ilovemessenger.msn.it/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] command line problems with tkmedit/tksurfer
Does it still work with csurf? Do you have libglut installed? If so, find libglut.so and make sure that there's a link from libglut.so.3 to it. On Tue, 2 Aug 2005, David Soscia wrote: Guys, I am having trouble getting volumes/surfaces to show when I use the command line to try to bring them up. Prior, I was just using the csurf interface to bring up all my volumes, but now that I've make my first final surface I'm trying to get the pial surface using the command line. I type in... tksurfer /up/to/the/directory/before/mri, surf, tmp, scripts, etc lh pial (or others, they all dont work) and i get this error every time... tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory it does the same thing when i try to open something with tkmedit...any ideas on what the problem is? Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scripts in TkSurfer
I have a question about creating scripts for TkSurfer. I really know next to
nothing about scripts in general so these are rather basic questions. There
seems to be a lot of scripting commands for TkMedit but not for TkSurfer. Is
there a general list of the basic commands?
First of all, the scripting langugage for tkmedit and tksurfer is Tcl, so
you should get an introduction to Tcl on the web or from a book. The
syntax is pretty simple.
You will start up tksurfer from the command line normally, so you can load
your subject and surface from there. Then, you pass the script you want to
run with the -tcl option. For example:
tksurfer bert lh inflated -tcl my_script.tcl
my_script.tcl would be a text file with your script commands.
Display the color bar
in a for loop
Overlay a .w file Redraw the image
Save as a .rgb image
end loop
To turn on the color bar:
set colscalebarflag 1
To read a .w file, use the commands:
set val filename
sclv_read_binary_values field
Where filename is the .w file name and field is 0-9, signifying which
overlay layer you want to load this into. If you load an overlay into a
layer that is already filled, it will replace what's there.
You will need to force a redraw of the screen after loading an overlay, so
use this command:
redraw
To save an rgb image:
set rgb filename
save_rgb
Where filename is the name of the RGB file you want to create.
There are different kinds of loops available, but if you want to loop over
a series of elements in a list, such as file names to load, you can use:
foreach varname list {
}
This will iterate over all the elements in list, setting varname to
each. For example:
set colscalebarflag 1
foreach file_name { overlay1.w overlay2.w overlay3.w } {
set val $file_name
sclv_read_binary_values 0
redraw
set rgb ${file_name}-capture.rgb
save_rgb
}
This will load overlay1.w and create overlay1.w-capture.rgb, then
overlay2.w and create overlay2.w-capture.rgb, and so on.
You may need to use full file names if you don't want to load everything
from the current directory and save all the RGBs there. Tcl has a nice set
of functions in the file command to do stuff like join paths, extract
file names, and chop off extensions, e.g.:
set path [file join path to my data]
- path becomes /path/to/my/data
set file_name [file tail /path/to/my/data/overlay1.w]
- file_name becomes overlay1.w
set simple_file_name [file name overlay1.w]
- simple_file_name becomes overlay1
So:
set base_directory [file join path to my data]
set file_name overlay1.w
set val [file join $base_directory $file_name]
...
set rgb_directory [file join path to my rgbs]
set rgb [file join $rgb_directory [file tail [file name
$val]]].rgb
This will set val to /path/to/my/data/overlay1.w, and rgb to
/path/to/my/rgbs/overlay1.rgb
There's a lot here, so I would suggest starting out with an introduction
to Tcl, then creating a simple script to load and display an overlay file,
then gradually add to it.
--
Kevin Teich
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Re: [Freesurfer] talairach transform issues
Hi Tracy, I don't know what the problem could be, but you can always by-pass the automatic talairaching with manual with tkregister2. When you run recon-all just make sure to include -notalairach as the last option. doug Tracy Wang wrote: Hi All, It seems that my talairach transforms are still suspect, FOF values falling between the 13-.17 range. I've tried Xiao Han's suggestion to skull strip first, but it the final objective function value is still high. Once the transform is applied on the image in native space, it does look a little blurry and jagged, like the resolution has changed. Any ideas or insight of what the problem may be? Thanks! Tracy Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] unload segmentation?
Hi when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? Thanks, Kristine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unload segmentation?
toggle it on and off with Ctrl-G On Tue, 2 Aug 2005 [EMAIL PROTECTED] wrote: Hi when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? Thanks, Kristine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unload segmentation?
when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? Sorry, there's no way to unload a segementation volume. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unload segmentation?
To clarify, this will turn off the display of the volume, not free up the memory. Not sure which you were initially asking. On Tue, 2 Aug 2005, Brian T. Quinn wrote: toggle it on and off with Ctrl-G On Tue, 2 Aug 2005 [EMAIL PROTECTED] wrote: when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
