hi dahlia!
the 'mkanalysis' script in the retinotopy analysis stream has an optional
'nskip' argument that allows you to ignore N TRs from the beginning of
each run. so you can just append '-nskip 2' to your 'mkanalysis' command.
-jon
On Thu, 18 May 2006, Dahlia Sharon wrote:
> Hi,
>
> I'
Hi,
I'm analyzing a retinotopy data-set in which each scan started with 2 TRs
of a blank screen, and then proceeded to 8 cycles as usual. Is there any
possibility to tell a retinotopy analysis to ignore these 2 TRs?
Thanks!
Dahlia.
PS - I can't answer as to why these 2 blank TRs were put the
Anthony,
See the references section at the bottom of the main wiki page, where
most of the papers themselves can be downloaded:
https://surfer.nmr.mgh.harvard.edu/fswiki
On Thu, 2006-05-18 at 17:02 -0400, Doug Greve wrote:
>
> btw, most of these are also listed at the end of:
>
> recon-all -
Jeremie,
The AFNI package must be installed and setup independently from
Freesurfer. Since you have it installed, it sounds like you just need
to add the AFNI bin path to the search path. Something like this:
setenv PATH "$PATH":"$AFNI_BIN"
rehash
Then test if it finds to3d by running it.
btw, most of these are also listed at the end of:
recon-all -help
Bruce Fischl wrote:
Be careful what you ask for :)
--
if you use surface recons
Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical
Be careful what you ask for :)
--
if you use surface recons
Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical
activity by combining EEG and MEG with MRI cortical surface reconstruction:
A linear approach. Journal of C
Surfers,Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data...maybe there are some papers that talk about this?? Anthony
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Still working thru these steps with a 0.5 mm monkey volume...I've run mri_nu_correct with no problem, set my control points, and then I run mri_normalize as follows:mri_normalize –monkey –f control.dat -g 1 nu.mgz T1.mgzbut I end up with a 1mm resampled volume with a poor normalization.anything I c
Are you sure the volume is conformed?
On Thu, May 18, 2006 at 12:14:30PM -0400, Mark Pinsk wrote:
> I just installed the latest release on my mac ox 10.4
>
> Trying to set control points on a monkey volume, and something wierd
> keeps happening... I will middle-click to set the control point, a
is your volume "conformed"? That is, did you run mri_convert --conform
on it? tkmedit doesn't like other types of volumes, so it needs to be
isotropic and 256^3.
On Thu, 18 May 2006, Mark Pinsk wrote:
I just installed the latest release on my mac ox 10.4
Trying to set control points on a
I just installed the latest release on my mac ox 10.4
Trying to set control points on a monkey volume, and something wierd
keeps happening... I will middle-click to set the control point, and
the green cross will appear, but when I move to another location to
set another control point, the
Hi Jeremie,
could you include the information detailed in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
thanks,
Bruce
On Thu, 18 May 2006,
Dreyfuss
Jeremie wrote:
Hello everyone,
I'm new here to the freesurfer community, and i've install the latest package
on my Linux.64 version
Hello everyone,
I'm new here to the freesurfer community, and i've install the latest package
on my Linux.64 version. I've completed the installation stages described on MGH
site
and it all seemed to work quite well until I've tried to run the mc-sess
routine.
The error message I got was that AF
Hi Anthony,
a couple of things. First, we do have a metric preservation term in
the inflation, so that not too much metric distortion is incurred during
the deformation. But the real answer to your question is that there is
correspondene between the inflated and other (e.g. white) surfaces, s
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