Hi all,
I want to use the --prv (per vertex regressors) option in mri_glmfit, but
there is very little information in the Wiki and I couldn't find any
relevant info in the mailing list.
I have two .mgz files, one contains the dependent variable, the other is
the source of my pvr. I tried loading
Dear FreeSurfer expertsI'm trying to study WM-lesions of my data. As I saw in previous messages to the forum and papers, it is contained in the aseg.mgz as the WM-hypointensities volume (label-ID 77), but it has only one value from the whole brain in the aseg.mgz, the left/right fields appear empty
Dear FS experts
How can I force tksurfer to truncate the positive values and not the
negative ones?
Thanks in advance
Best regards
Jürgen
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University
Hi Jurgen
I don't think you can - you'll need to do it in matlab or something
cheers
Bruce
On Wed, 12 Dec 2012, Jürgen Hänggi wrote:
Dear FS experts
How can I force tksurfer to truncate the positive values and not the
negative ones?
Thanks in advance
Best regards
Jürgen
--
Dear all,
A few questions come to me when I used LME Matlab toolbox. Then Jorge
kindly answered my questions and he also asked me to post our discussion to
Freesurfer list so everyone knows what's going on here :)
Cheers, Ting
---
*S
Dear All,
Excuse the basic nature of these quetions. I coregistered 2 analyze volumes
in SPM (pre and post resection MR scans for same patient) with cost
function masking. I imported the preresection scan in Freesurfer, and
processed it with recon -all.
1) What transform matrices should I multiply
Dear FS-experts,
I'm trying to follow the instructions on
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to get
volumetric stats etc on a functional ROI derived from marsbar.
The tutorial looks all clear to me, however, I have already problems at the
first step.
If I want
Hi Ting
Just use the default procedure. We
limited the number of iterations for the estimation procedure to 20
for the mass-univariate analysis. If the model for the covariance is
correct, that is to say, you have correctly specified the set of
random effects that is supported by your data then t
Under View->Configure->Overlay select both "Truncate" and "Inverse"
under display options.
doug
On 12/12/12 8:19 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> How can I force tksurfer to truncate the positive values and not the
> negative ones?
>
> Thanks in advance
> Best regards
> Jürgen
>
>
Hi Jon
if you upload this subject we'll take a look
Bruce
On Wed, 12 Dec 2012, Jonathan Holt wrote:
> I've had this happen a handful of times and I'm wondering what I can do about
> it. For reference using Freesurfer 5.0.0.
>
> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_
OK will do... I'll upload both versions, before and after recon-all ran. I am
beginning to think it's an issue with the script that I am running... I'm
looking at another brain and there are areas I did not touch at all where white
matter voxels are being added or removed...
On Dec 12, 2012, a
Dear Freesurfers,I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 & 79 do not appear in the aseg.mgz, and I'm a bit lost with it.Can any one help me?Best Regards,Gabriel.
Hi Gabriel
we don't lateralize them by default, so look for WM_hypointensities (77)
instead. It would be pretty easy to lateralize them based on neighboring
labels.
cheers
Bruce
On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:
>
> Dear Freesurfers,
>
> I'm looking for a way to comput
Hello,
thank you for your help with the first steps of running Tracula.
I was trying to run trac-all step 3 (paths), but was getting an error
with the mergedph1samples file. I saw on the mailbase that you have
suggested to run bedpost directly to fix this
I have 3 questions about this:
1) do I
Yes I did loo at the total WH-hypointensities(77), and substract them without a problem.What do you mean with lateralize them based on neighboring labels? How can I perform such thing on FS?Actually I'm interested in knowing to wich specific label o region they are.Bests,GabrielEl 12/12/12, Bruce F
1) Can't hurt to delete.
2) Yes.
3) Yes.
On Wed, 12 Dec 2012, s0675204 wrote:
Hello,
thank you for your help with the first steps of running Tracula.
I was trying to run trac-all step 3 (paths), but was getting an error
with the mergedph1samples file. I saw on the mailbase that you have
sug
Hi Lars, the way it works is that each pvr that you spec on the cmd line
indicates another column in the design matrix. If you want multiple
columns then add multiple --pvr options (thus pvr1, pvr2, etc). If you
do not spec an X matrix or fsgd file, then it will assume that you want
a column of
Thanks bruce, for your answer,Does it exist a tool on FS or matlab to do such asignment of voxels from the WM-hypointensities (77) to the neighbouring labels?If so, does it can use whoever the aseg.mgz,the aparc+aseg or the wmparc.mgz to do this asignment?Thanks,GabrielEl 12/12/12, Bruce Fischl e
then I would either use TRACULA (if you have DWI) or the wmparc to generate
ROIs. I meant that you could count whether there are more lh or rh wm
labels neighboring each one to figure out which hemi they are in
cheers
Bruce
On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:
Yes I did lo
wmparc should do it I think, although we don't have any tools for doing
so it wouldn't be very hard in matlab
On Wed, 12 Dec 2012, Gabriel Gonzalez
Escamilla wrote:
Thanks bruce, for your answer,
Does it exist a tool on FS or matlab to do such asignment of voxels from the
WM-hypointensitie
Dear FreeSurfer experts,
I apologize in advance if my questions seem naive or too simple:
I am completely new to FreeSurfer and I am still attempting to understand
how to make good use of its potential.
I believe I want to use it in an unusual way. I have been given two
cortical surfaces, both i
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