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Are the fsaverage versions coming from the following (as reported in
recon-all.log within the fsaverage directory) significantly different ?
freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20101225
freesurfer-x86_64-redhat-linux-gnu-dev4-20090216
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Hello everyone, and happy new year.
I know it's never a good idea to mix versions within a study, but that's
what has happened in a large study here, so I am trying to get a sense of
what changes there have been.
I was wondering if there is a way to
Is it possible to set the smooth overlay option (i.e. no of iterations)
from command line instead of freeview? I am taking some screenshots that
would look nicer with a smoothed overlay.
Dorian
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if file with a medial view, and
> zip through them all with nmovie
>
> cheers
> Bruce
> On Thu, 9 Mar 2017, Dorian P. wrote:
>
> > Thank you Bruce, Douglas.
> > Yes, I think thicknesses were obtained with v 5.3.0. There might be
> errors
> > as Bruce pointed out, I
9, 2017 at 11:23 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
>
> On 03/08/2017 09:27 PM, Dorian P. wrote:
> > Hi Freesurfers,
> >
> > I am using R to perform thickness analyses. All subjects are
> > transformed in fsaverage space and all values
Hi Freesurfers,
Thank you for the help you provide through this list.
Is there a way to get, for each vertex, the identify (or thickness values)
of the surrounding vertices in a 10mm radius? The command mris_convert has
the '-v' option, but that produces only 5-6 vertices and there is no option
sian kernel instead of the
> box kernel that you describe. Set the fwhm to the radius you want
> (mris_fwhm with --smoothonly option)
>
>
> On 01/31/2017 04:48 PM, Dorian P. wrote:
> > Hi Freesurfers,
> >
> > Thank you for the help you provide through this list.
> >
ransform should be by looking up the spherical coordinates on the
> sphere.reg for that vertex index and using that to find the corresponding
> fsaverage sphere.reg vertex.
>
> cheers
> Bruce
> On Wed, 25 Jan 2017, Dorian P. wrote:
>
> > Hi, I am trying to find the corresp
Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial
in fsaverage space. I manage to transform lh.pial in fsaverage space but
this does not give corresponding points or a way to do point by point
transformation.
I want to do the same with some vertices from
Hi Freesurfer list,
A hopefully quick inquiry:
What are the default parameters for segmentation in Freesurfer? If priors
are used, what weight is given to the priors? Is there any other default
worth considering when estimating thickness?
Thank you.
Dorian
Hi folks,
I am using the parcellation of Freesurfer for some other analyses. I see
that the parcellation if obtained rather late in the pipeline:
http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
However, asking does not hurt: is there any short route to get the Desikan
parcellation without
Hi all,
A while ago I asked how can I calculate the average thickness of the three
lateral temporal gyri, and Bruce kindly suggested to draw the label on
fsaverage and use transforms to calculate it for each subject. I may try to
do that, but given my time constrains and my level of knowledge of
Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Dorian
yes, that would work.
cheers
Bruce
On Wed, 23 Jul 2014,
Dorian P. wrote:
Hi all,
A while ago I asked how can I calculate the average thickness of the
three
lateral temporal gyri, and Bruce kindly suggested to draw the label
Dear Freesurfer followers/developers,
I am doing a study involving temporal lobes and the parcellations from
Desikan and Destrieux atlases have very different results. I like the full
gyrus parcellation of Desikan but the temporal pole is very small and
limited, while in Destriux the temporal
?
Not by default, bu you can create one easily enough with
cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz
doug
On 06/23/2014 01:03 PM, Dorian P. wrote:
Dear Freesurfer
Dear Freesurfers,
Is there a way to bring the colormaps of Freesurfer to MRIcron. Right now
when I bring parcellations in MRIcron there is no good way to distinguish
parcels, because the parcels are numerated 1000+ for left hemisphere, 2000+
for right, 3000+ for white matter left, etc. This makes
Hi list,
Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D
studio max? I would be curious on the procedure to follow, more
specifically on which file to export/import/convert.
Thank you.
Dorian
TJU
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by 1000 to give you tenths of
percents
doug
On 10/24/2013 12:58 PM, Dorian P. wrote:
Thank you Douglas.
The eTIV has values like 1543825. Dividing ROIs by this value would
create very small values.
Is there a standard TIV (i.e. from the talairach brain) to use as
denominator
Dear all,
Excuse if these are simple questions but I am a bit confused on the
significance of the volume measures.
1. Are the volumes of ROIs calculated after normalization?
2. If volumes are calculated post-normalization, why is correction for eTIV
needed?
3. What is the quickest way to
) to correct/normalize roi volumes?
Dorian
2013/10/24 Douglas N Greve gr...@nmr.mgh.harvard.edu
On 10/24/2013 10:37 AM, Dorian P. wrote:
Dear all,
Excuse if these are simple questions but I am a bit confused on the
significance of the volume measures.
1. Are the volumes of ROIs calculated
Anupa,
If you want to run several subjects at the same time just open different
command windows. On each you can run a recon all. You can also run a list
of recon on each window. Just put the commands in a text file, name it
something like i.e. group1.sh and run the command sh group1.sh. Each
Dear list,
We are buying a computer dedicated mostly to Freesurfer. Initially we
thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good
choice. However, I noticed that Freesurfer seem better tuned to use CUDA.
Many of the messages I read are from 2010 so I am not sure whether this
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