p.s. remember if/when you check it that it is supposed to align skull,
not necessarily brain.
On Tue, 19 Feb 2008, Michael Harms wrote:
Hello,
In your experience, is the "talairach_with_skull.lta" transform always
reasonable, or does it sometimes fail (and if the latter, is the failure
rate d
Hi Anil,
I think mri_mask will do this.
Bruce
On Tue, 19 Feb 2008, Anil Roy wrote:
Hello All,
I used mri_binarize to create stg masks (inclusive of gray and white
matter).
I'm trying to take this a step forward to see if I can extract the actual
brain region encompassed by the mask - in oth
Hello All,
I used mri_binarize to create stg masks (inclusive of gray and white
matter).
I'm trying to take this a step forward to see if I can extract the actual
brain region encompassed by the mask - in other words, is there a way to cut
out the portion of the brain that the mask encloses. So i
You can try something like this:
mri_convert $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca gca.mgh
--frame 0
tkregister2 --targ gca.mgh --mov T1.mgz \
--lta transforms/talairach_with_skull.lta --reg tmp.reg
doug
On Tue, 19 Feb 2008, Bruce Fischl wrote:
no, it's our own (.gca) t
There's a slightly convoluted way to do this:
1. Run mri_surfcluster with --thmin y. Save the output cluster number
overlay with --ocn. This is a surface overlay where the value is the
cluster number.
2. Since the clusters are ordered based on descending peak vertex
value, you can create a ma
I don't have a way to easily test an external regressor. There are a
couple of ways to do this type of analysis though. You can use a 4
column paraidgm file and code the weight (4th col) as the reaction
time. This will weight the HRF for each presentation by its
RT. Alternatively, you can recode
Yes, you can convert almost any registration file to a register.dat
with tkregister2. See the --help.
mri_label2vol does not interpolate, per se. You can run into the
situation where more than one label maps to a single output voxel. In
that case, it uses the label that most frequently falls int
Try it without the --sval (it will get the sval from the xyz in the
surface).
doug
On Sun, 17 Feb 2008, Daniel Wakeman wrote:
Hi Doug,
Thanks.
I tried this and got the following:
[EMAIL PROTECTED] test2bem]$ mri_surf2surf --srcsubject $SUBJECT --sval-xyz
smhead.surf --sval /imaging/dw01
You can give mri_convert input direction cosines for the cols, rows,
and slices (-iid, -ijd, -ikd), then load the volume into tkmedit to
see if you got it right. Note: this is a difficult and frustrating
process.
doug
On Sat, 16 Feb 2008, Joerg Magerkurth wrote:
Hi,
I have siemens mrs data
Hi Mike,
sorry, forgot to respond to this one. Not sure about tkregister2 - I'll
leave that for Doug. I think you should be able to use mri_convert with
the .gca file to extra the mean image frame (frame 0), then check the
aligment to that.
cheers,
Bruce
On Tue, 19 Feb 2008, Michael Harms
no, it's our own (.gca) template. It's the same type of linear
registration that is used in the aseg, just this time to a template that
has a skull in it
On Tue, 19 Feb 2008, Doug Greve wrote:
Those are good questions. Bruce, does this use the mni305 template or
a different one?
On Tue, 19
Hi Cate,
hmmm, not sure about removing cluster. If you can draw around the ones you
want to retain, the significances will be saved in the .label file
Bruce
On Tue, 19 Feb 2008, Catherine Hartley wrote:
Sorry for the delayed follow-up.
Doug, I don't think mri_surfcluster allows me to imple
Those are good questions. Bruce, does this use the mni305 template or
a different one?
On Tue, 19 Feb 2008, Michael Harms wrote:
Hello,
In your experience, is the "talairach_with_skull.lta" transform always
reasonable, or does it sometimes fail (and if the latter, is the failure
rate depen
Hello,
In your experience, is the "talairach_with_skull.lta" transform always
reasonable, or does it sometimes fail (and if the latter, is the failure
rate dependent on the FS version, as is the case for talairach.xfm ?)
I ask because the ICV ("eTIV") value is derived from the determinant of
"ta
Sorry for the delayed follow-up.
Doug, I don't think mri_surfcluster allows me to implement the
criteria I want (only include clusters containing a peak vertex above
threshold x, but vertices within those clusters can be included if
they exceed threshold y (where y < x).
Bruce, I am happ
Sorry to say but, just like for Juergen, the same error pops up for
make_average_volume when run by itself or within the new
make_average_subject scripts.
-
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
James N. Porter wrote:
D
The installation was successful!
I have created the file in 'pico', as Nick Schmansky told me to do,
and fortunately the file '.license' was successfully created.
Thank you all for your kind attention,
Regards,
Henrique Fernandes
___
Freesurfer m
Henrique
You should call the file ".license". Then it will work. The file will be
invisible to your in unix unless you search for it with "ls -a".
Avram
Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall
Does glxgears work? That is an app that comes with Linux that exercises
the GLX (OpenGL X extension) code.
On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote:
> Dear FS experts,
>
> I install CentOS 5.1 and latest version of ATI driver and FS4.0.2,
> when I start tkmedit, it looks fine.
Try using pico to create the file, like this:
pico $FREESURFER_HOME/.license
(paste three lines of license file and press Ctrl-X to save).
On Tue, 2008-02-19 at 14:52 +, Henrique Fernandes wrote:
> Thanks for the suggestions,
>
>
> I'm now having another problem. I created a .license fi
Thanks for the suggestions,
I'm now having another problem. I created a .license file with the
information about my license. Although, to keep the file stored I must
have a name for it other else the system won't allow me to create that
file. So, after giving a random name to the file, dur
Dear FS experts,
I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I
start tkmedit, it looks fine. In tksurfer, it just appear a sliver of
surface without error message. In console, it stock on reading vertex.
Is there anyway to correct it ?
Thanks replay
Kl chen
Henrique.
Are you sure that freesurfer is at /Applications/freesurfer?
Execute ls -l /Applications/freesurfer
Regards
PPJ
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Henrique
Fernandes
Sent: terça-feira, 19 de fevereiro de 2008 08:52
To: freesurfer
Dear collegues,
I had a problem during the installation of Freesurfer on my computer.
I have a Mac Intel, and since the shell I'm using is the bash, I've
entered those two lines written in the installation instructions:
export FREESURFER_HOME=/Applications/freesurfer
source $
Dear FS and fsfast expert:
We want to know the effect of some external regressors such as the reaction
time of every trial. We found that external regressor can be integrated into
the GLM model with mkanalysis-sess's 'extreg' option, but we did not find
the way to do comparison of these external r
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