Dear FS experts
We have done a group analysis with FS, but we are not absolutely sure which
is the most adequate design matrix to describe our data. We compared two
groups and used one covariate of no interest (mean thickness, total area,
etc.). Because there are two different options to create th
Hi,
I recently installed freesurfer, AFNI etc but am having problems with mc-sess.
The script runs and gets to the stage in each run where it calls up matlab,
enters the MRIwrite command but then gives the message below. It then hangs.
>> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pc
John Herrington wrote:
I'm new to optseq and to rapid E-R designs generally. I have a two
questions about it. If it helps, here's my (tentative) design - I'm
creating a task with 5 conditions (including rest) with a TR of 2320 ms
and trial SOA of 4640 ms (my stimuli are on screen for 1 sec o
Freesurfites,
If you are encountering the problem where the 'qdec' app exits stating a
'BadMatch' error, then a work-around is, prior to starting qdec, to
type, if using tcsh:
setenv XLIB_SKIP_ARGB_VISUALS 1
or if using bash:
export XLIB_SKIP_ARGB_VISUALS=1
Graphics will run much slower, as
You mean you want to display your group volume-based results on the
average surface? That's unusual, but it can be done. You need to create
a registration file between your group average and the standard space
templage, eg, something like:
fslregister --mov $FSLDIR/etc/standard/avg152T1.nii.
RMS is root-mean-square of the difference between the intensities of
target volume and the indexed volume. The 10th is the vector motion of
the center of rotation with respect to the target image (ie, before
correction).
Brittany Cassidy wrote:
Hi all,
I'm analyzing some motion data and I
Hi all,
I'm analyzing some motion data and I had a two quick questions about the
last two columns of the fmc.mcdat file. According to the wiki, the 9th
column is RMS error after correction. Could someone shed some light on
what RMS stands for and how it's useful? Also, the 10th column is th
and the papers describing the subcortical segmentation scheme are found
at the bottom of the main wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki
in the section 'subcortical segmentation'.
On Tue, 2007-11-13 at 15:17 -0500, Doug Greve wrote:
> Look in $FREESURFER_HOME/FreeSurferColorLUT.tx
Look in $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
joel bruss wrote:
This is the last question that I have...sorry to keep bothering you
all. Is there a page on the FS wiki or is there a man page that
details the value of each sub-cortical parcel? I see that each masked
are has a value (1,
This is the last question that I have...sorry to keep bothering you
all. Is there a page on the FS wiki or is there a man page that
details the value of each sub-cortical parcel? I see that each masked
are has a value (1, 2, 3, etc.) but before I make assumptions about
which values correspond wit
I'm new to optseq and to rapid E-R designs generally. I have a two
questions about it. If it helps, here's my (tentative) design - I'm
creating a task with 5 conditions (including rest) with a TR of 2320 ms
and trial SOA of 4640 ms (my stimuli are on screen for 1 sec of this time).
1) I've been
Yes, it is quite confusing, and like most confusing things it is
historical in nature. When tkregister was originally written by
Anders/Marty, they set it up to map from the targ RAS to the mov RAS.
From an internal standpoint, it makes sense, but it is backards when
you think about "moveable"
Hi Joel,
both the .m3z (nonlinear) and the .lta (linear) are transforms from the
subject to the atlas coordinate system, but all the labeling is done in
the subject space, so you should be set.
cheers,
Bruce
On Tue, 13 Nov 2007, joel bruss
wrote:
Hello-
I'm running FreeSurfer v4.01on SUS
Postdoctoral and Research Assistant Positions Available in structural and
functional neuroimaging.
Massachusetts General Hospital-Athinoula A. Martinos Center for Biomedical
Imaging, Charlestown MA
PLEASE POST FOR ALL INTERESTED PARTIES.
START DATE: Immediately
Full-time postdoctoral and
btw, you can have mri_vol2vol convert directly to analyze by using a
.img extension. But why use analyze?
joel bruss wrote:
Nick-
Doug wrote:
Try this:
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz
--regheader --interp nearest
doug
Sure
Nick-
Doug wrote:
>Try this:
>mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz
>--regheader --interp nearest
>doug
Sure enough, this worked. What I mean by "norm" is the file
/mri/norm.mgz which gets created in the CA Normalize section of
recon-all. Mike was kind enough to
Joel,
All freesurfer volume files, including aseg.mgz, are in native MRI
space. The various talairach transforms are used to align to the
atlases used in freesurfer. I'm not sure what you mean by 'norm' space.
The --apply_transform flag of mri_convert can be used to convert a
volume to talairach
Try this:
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz
--regheader --interp nearest
doug
joel bruss wrote:
Hello-
I'm running FreeSurfer v4.01on SUSE Linux
I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but
in the native MRI space. I see that t
Hello,
I've become confused about the direction of the transformation specified
in the talairach.xfm file.
It seems that if you "manually" specify the --targ and --mov volumes in
conjunction with the --xfm option, that the "target" must be the
talairach average to get proper alignment:
e.g.,
tkr
Hello-
I'm running FreeSurfer v4.01on SUSE Linux
I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but
in the native MRI space. I see that the output of "CA Label" produces
a file that is fit to the "CA Normalize" step but I can't figure out
the transform that was used. Specifi
we haven't distributed it yet, but it would just take the form of label
maps with associated probabilities in fsaverage space. You would need to
do our surface-based averaging for it to apply. We haven't gotten the
auditory cortex data yet, but probably could if you were interested.
On Tue, 1
Bruce,
it's auditory cortex I am interested in. If there is a tutorial or explanation
somewhere, could you please point me to it. Is this already available in FS?
Thanks
Martin
On Tuesday 13 November 2007 14:38:52 you wrote:
> what areas specifically? We have analyzed their data and have a pape
what areas specifically? We have analyzed their data and have a paper
accepted at Cerebral Cortex on the surface-based equivalent atlas, which
is quite a bit more accurate than the linear or nonlinear volumetric
ones, and are getting ready to release it for general use.
cheers,
Bruce
On Tue, 1
Thanks for reply, Bruce
On Tuesday 13 November 2007 13:43:03 you wrote:
> Hi Martin,
> I'll leave a) for Doug (and yes it is doable). For b) we'll need more
> info. What kind of atlas? Is it in some common space?
It is a Julich probabilistic histological atlas, which is a part of the latest
FSL.
Hi Martin,
I'll leave a) for Doug (and yes it is doable). For b) we'll need more
info. What kind of atlas? Is it in some common space?
cheers,
Bruce
On Tue, 13 Nov 2007,
Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis
(FLAME1+2) from differen
Hi Linda,
we haven't found any problems in that age range. Down to 3 years old is
probably fine, although if you were scanning that young there might be
some things we would advise. 1l years old is no problem though.
cheers,
Bruce
On Tue, 13 Nov 2007, Linda.E Campbell wrote:
Hi,
I am about
Hi,
I can not find my way to map the results of the FSL fMRI group analysis
(FLAME1+2) from different subjects on their average surface. Here is in more
details what I have done:
1. fMRI analysis of each subject in FSL
2. group analysis (FLAME1+2) in FSL
3. cortical reconstruction of each subje
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