Dear Experts,
I have a question concerning the evaluation of the time series in the FS-Fast
stream. There is one time series for each vertex of a brain. Can single time
points or series of time points be excluded from the analysis in the following
way: Remove time point 10 from the time series
Hello,
I have computed the lh.sphere.myreg3 and rh.sphere.myreg3 files for all of my
subjects as outlined on the web page on this topic (chapter: Creating a
registration template from scratch). Now I would like to know which points in
those registered files correspond to each other. How do I ha
Dear Experts,
I am currently working with the non-linear FreeSurfer normalization.
We have a small group of subjects N = 12 and in each brain we
identified a single position with a fMRI localizer. The task is a
group comparison of the individual results for this position.
Therefore, the coordi
Dear Experts,
if functional volume data are mapped to cortical surfaces, using mri_vol2surf
and FsAverage as the target surface, a surface registration is carried out. As
far as I can see the program surfreg does the surface registration. In this
registration the cortical maps of the individual
Hello Doug,
just a very last question. Where ist the origin of the coordinate system if the
motion parameters are calculated using mc-afni2 and where is it if BBR is used?
I mean the origin in the coordinate system of the input and output volume.
Yours pfannmoe
On Mon, 13 Apr 2015 10:36:02 -0
Just to make that point: Is it valid to apply "mcparams2extreg -mcfile
fmc.mcdat -extreg mcextreg" after substitution of the numbers in
"register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion
regressors valid?
On Mon, 13 Apr 2015 10:15:08 -0400
Douglas Greve wrote:
>
> Tho
Hello Doug,
is there a possibility to extract the "motion parameter" from a BBR
registration? Possibly, the first six numbers of the
register.dof6.dat.param
file are the same parameters as found in column 2 - 7 in the file:
fmcpr.mcdat
created by mc-afni2 during the FS-Fast preprocessing.
Hello Doug,
can we finish the topic this week?
Yours pfannmoe
On Thu, 9 Apr 2015 09:41:17 -0400 (EDT)
Bruce Fischl wrote:
> Bruce
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Sorry, I ment the first six numbers in "register.dof6.dat.param".
On Thu, 9 Apr 2015 12:33:49 +0200
pfannmo...@uni-greifswald.de wrote:
> Dear Experts,
>
> is there a possibility to extract the "motion parameter" from a BBR
> registration? Possibly the first three numbers of the
>
> regist
Dear Experts,
is there a possibility to extract the "motion parameter" from a BBR
registration? Possibly the first three numbers of the
register.dof6.dat.param
file are the same parameter as found in column 2 - 7 in:
fmcpr.mcdat.
If I have a series of "register.dof6.dat.param" can I use "mc
Hi FSexperts,
I would like to compute a symmetrical template out of the anatomical images in
a group of subjects. I followed the description in:
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
Afterwards I recognized that no surfaces were generated. Since the computation
takes quiet a while
Dear Bruce,
if I take BA1, BA2, BA3a and BA3b and sum the probabilities at each vertex
there are 17 % of the vertices which show probabilities > 1. The largest
probability is 1.7778. There is a histogramm of the values attached to this
mail. Is there a possibility to correct those values?
Resp
It is in fsaverage.
On Tue, 9 Dec 2014 14:37:43 +0100
pfannmo...@uni-greifswald.de wrote:
> Dear FreeSurfer Experts,
>
> I am puzzeled about the probabilities in the Brodmann area labels. If I take
> the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain
> vertex a probab
Dear FreeSurfer Experts,
I am puzzeled about the probabilities in the Brodmann area labels. If I take
the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain
vertex a probability sum < 1 should arise. This is due to the fact that 10
brains where analyzed in order to compute
Please remove this mail. This problem was already solved.
On Tue, 7 Oct 2014 16:55:16 +0200
pfannmo...@uni-greifswald.de wrote:
> Dear FreeSurfer experts,
>
> I computed distances on the cortex surface of fsaverage using mris_pmake. The
> exact syntax of the distance computation was:
>
> mris
Dear FreeSurfer experts,
I computed distances on the cortex surface of fsaverage using mris_pmake. The
exact syntax of the distance computation was:
mris_pmake --subject fsaverage --hemi lh/rh --surface0 smoothwm --curv0 sulc
--curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs
sta
Dear Experts,
I have calculated distances with mris_pmake on the individual brain of a
subject. I would like to compute the distance between the corresponding points
on the mni brain (fsaverage). Is there a simple way to transform the distances?
Best pfannmoe
___
It would be very helpful for me.
On Fri, 18 Jul 2014 09:18:15 -0400 (EDT)
Bruce Fischl wrote:
> Hi pfannmoe
>
> this is a bug in mri_label2label that we fixed a while ago. Zeke: can
> post a new version and let people on the list know where it is?
>
> thanks
> Bruce
>
> On Fri, 18 Jul 2014,
Thank you for your Help. I figured out that it was a problem with the data
which caused this error.
On Wed, 04 Jun 2014 12:00:08 -0400
Douglas N Greve wrote:
>
> This is a strange error that I cannot figure out from the terminal
> output. What version of FS are you using? Here's something
Dear Experts,
during an fsfast analysis an error occured after selxavg3-sess was executed.
The corresponding commands were:
mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm
sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2
-analysis analy
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