Hi Claire
there is no output in the terminal window when you type the tksurfer
command? Does it just return to the prompt?
Bruce
On Thu, 16 Oct 2014, Claire
Morley wrote:
Hi Bruce,
Thanks so much for your response. It`s just when I try to type the test
commands from this link:
Hi Ting
can you send us the commands that you used to establish correspondence and
to map the vertices?
cheers
Bruce
On Thu,
16 Oct 2014, Ting Li wrote:
Hi, experts,
I am trying to use the template fsaverage_sym and tried to map the same set
of vertices onto the left and right pial
Claire,
Can you provide me with the following information about the Mac you are
using:
1) What version of OSX are you using? (Apple - About this Mac)
2) What version of XQuartz are you using (Applications - Utilities -
XQuartz then click X11 - About)
-Zeke
On 10/16/2014 08:46 AM, Bruce
Dear all,
I am trying to convert the curv surface into a volume by using the following
command:
mri_surf2vol –surf curv –hemi lh –template $subj/mri/T1.mgz –surfval
$subj/surf/lh.curv –projfrac 0 –volregidentity $subj –o CurvatureVolume.nii
I get the following error: the lh.curv has many more
Hi,
When I used preproc-sess processing my data, the registration output is off a
great of deal. The functional data was collected using 7T, and the surface was
reconstructed successfully from 3T data and was checked visually multiple
times. I am using fs5.3 installed on a linux system.
Dear Freesurfer users,
I had a question regarding how to combine multiple register.dat files
into one file. Essentially, I have a T1 image which I created masks for in
native space. I then import the T1 image into freesurfer and run through
the recon-all pipeline. Subsequently, I use
the curv file is not a surface. A surface has a list of vertices, the
xyz at each vertex, and the neighboring vertices. lh.white and rh.pial
are example surface files. The curv file just has a curv value at each
vertex with no info about xyz etc. If you do not specify a --surf, then
it will
Dear all,
I'd like to ask which steps are essential to check if I'm interested
only in the volume based (aseg) results.
I think Skull strip and Talairach transformation are essential.
Any other steps I need to check?
Thanks,
Gabor
___
Freesurfer
The problem is probabably that the fsl flirt registration failed and
that caused bbr to fail. If you have spm and matlab installed, running
it with
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
bbregister --s field --init-spm --6 --bold --mov bold/template.nii --reg
Hi Doug,
Thanks for the promptly response. I do have spm8 and spm12b installed. Which
version should I use? Also, how to change the spm as the inital registration
method in the preproc-sess?
Xiaomin
Date: Thu, 16 Oct 2014 12:00:04 -0400
From: gr...@nmr.mgh.harvard.edu
To:
I have not tested it with spm12, so use spm8. There is not currently a
way to run the spm init from preproc-sess, so you'll have to run it from
register-sess.
On 10/16/2014 12:04 PM, Xiaomin Yue wrote:
Hi Doug,
Thanks for the promptly response. I do have spm8 and spm12b
installed.
Is it right that the prep roc-sess includes the following steps: 1)
mktemplate-sess; 2) mkbrainmask-sess; 3)register-sess; 4) mc-sess; 5)
rawfunc2surf-sess. So, I need to rerun step3, 4, and 5 manually, is that
right?
Thanks,Xiaomin
Date: Thu, 16 Oct 2014 12:12:23 -0400
From:
It does include those steps, but you won't need to re-run them manually.
Just run register-sess, then run preproc-sess as you normally would. It
should see that the most recent files are the registration files and
then perform all the steps afterwards. You should double check that it
does not
Dear FreeSurfer users,
I'm interested in using FreeSurfer on my Thinkpad X230 (Ivy Bridge)
laptop with 8GB of RAM. My laptop does not have a dedicated graphics
card, but rather an Intel HD Graphics 4000. Do you think I would
still be able to run FreeSurfer, or should I really opt for a
This is currently a topic of many questions on the list etc. I also
have plans (once I get my hands on some hardware, to do some
systematic tests, but these will not be happening soon). With well
updated intel linux (I assume you are talking about running linux
natively on your laptop) drivers,
Most modern video graphics card will perform fine, but be aware that
graphics cards that use CPU memory as video memory (as I believe is the
case with your card) the will have a noticeably slow redraw rate. But
bottom line, you will be able to run freesurfer.
-Zeke
On 10/16/2014 02:06 PM,
Hi Gabor
I would start with the aseg and work backwards from there. If it looks ok
you are all set
Bruce
On Thu, 16 Oct 2014, Gabor Perlaki wrote:
Dear all,
I'd like to ask which steps are essential to check if I'm interested
only in the volume based (aseg) results.
I think Skull strip
you should be able to run recon-all, but how fast it will be on a laptop
cpu is another question. Have you tried running
tksurfer/freeview/tkmedit? I suspect it will work, but some graphics
cards have given us trouble
cheers
Bruce
On Thu, 16 Oct 2014, velo...@physics.utexas.edu
wrote:
Dear
Dear Freesurfer experts,
As I run mkcontrast-sess, I receive no octave error:
fsl@fslvm6 MT_Localizer]$ mkcontrast-sess -analysis MT.lh -contrast MS -a 1
-c 2
INFO: Found 2 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 1. -1.
mkcontrast
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