t of disk space? Is the file
> aseg.auto_noCCseg.label_intensities.txt writeable in the subject's dir?
> On
> Wed, 18 Nov 2009, Narly A Golestani wrote:
>
> >
> >
> > Dear all,
> >
> > I am encountering a problem with 'recon-all -all' with one subject using
> > freesurf
Dear all,
I am encountering a problem with 'recon-all -all' with one subject using
freesurfer version 4.5 which I did not encounter when using version 4.4.
With the older version, the stream ran without error, whereas the
processing produces the following error with version 4.5:
##
7;, which only appear in the cortparc2
> stage. i havent tried this, so i dont know if the atlas will work
> though.
>
> Nick
>
>
> On Tue, 2009-10-20 at 18:03 +0100, Narly A Golestani wrote:
> > Hello all,
> >
> > Thanks Chistophe for your answers.
> >
&
Hello all,
I would like to know whether the T1 parameters such as TR, TE, TI, and
flip angle can systematically influence mean curvature values obtained by
recon-all -all.
I have processed 2 data sets with the following T1 parameters, and am
noticing that the mean curvature values systematically
Hello all,
Thanks Chistophe for your answers.
I have not heard back regading some of the other points.
I would like to know:
1) The fs release in which ?h.aparc.a2005s.annot replaced
?h.aparc.a2002s.annot. I assume it was before 2007 (I used version 3.0.5
in 2007).
2a) *** If it is possible
terior segment of the lateral sulcus, runs
> >>>>> anterior and lateral and joins the lateral aspect of the temporal
> >>>>> lobe.
> >>>>>
> >>>>> * The transverse temporal gyrus (or Heschl's gyrus) is just ant
in Freesurfer, the
> >>> posterior ones being included in the planum temporale since they
> >>> where shown not to correspond to primary, but to secondary
> >>> auditory cortex
> >>>
> >>> I hope that it helped
> >
to Christophe Destrieux, cc'd, who I think can
> > > answer your question about how that region is labelled.
> > >
> > > It is not possible to do translucent viewing in tksurfer. However, it
> > > is possible in qdec. Just use the load surface and load a
on-all on your average.
>
> doug
>
> Narly A Golestani wrote:
> > Dear all,
> >
> > I have some 3-D volumes (labelled regions of interest) generated manually
> > on *normalised* structural images.
> >
> > I would like to use freesurfer to run the anatomica
Dear all,
I have some 3-D volumes (labelled regions of interest) generated manually
on *normalised* structural images.
I would like to use freesurfer to run the anatomical_stats command on
these volumes. Is this possible? These labels (volumes) were not
generated using freesurfer. Can I trans
Hello,
I would like to know more about the automatic labelling of the transverse
temporal gyrus is done. I looked at the below article but don't see any
details about this structure.
https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf
I would for example like to know how
Hello everyone,
I would like to know if there are left-right orientation issues when
converting images from nifti format to the mgz format. I suspect not as
nifti, unlike analyze, contains the left-right information in the file
itself. But I would like to make sure that there are not issues suc
Hi there,
I have a question regarding the longitudinal processing stream in the new
release. I've already analyzed my data at different time points using the
cross-sectional processing stream using the previous version of
freesurfer, and would like to know if this is the same as doing so with
th
Dear all,
I installed freesurfer_Linux_centos4_x86_64-stable-pub-v4.2.0-full on
SuSE Enterprise (SLED 10.2), and ran recon-all. The process ran until
near the end, and then terminated with the following error:
*
.
Reporting on 49 segmentations
#
Dear users,
Applications are invited for a 3-year PostDoc position at the Department
of Fundamental Neuroscience at the University of Geneva in Switzerland,
under the supervision of Dr. Narly Golestani. Projects will include
using fMRI and EEG to better understand brain functional plasticity
ari
Dear all,
I see from previous posts to the list that it is possible to use servers
to run freesurfer. I'm in the process of selecting a machine, and would
appreciate any input anyone might have on which machine is optimal.
In particular I'm concerned about eventual problems described on the
mail
Hi there,
I see on the freesurfer installation for mac page that it says:
'Look here for the 'tiger' download, saving
freesurfer-Darwin-tiger--full.dmg to your local machine.'
Should I take the tiger download even if I have the 10.5 intel version of
mac (and not 10.4)? and regardless, should I
ess', and you can
> select up to four regressors: two discrete (say, gender and diagnosis),
> and two continuous (say, age and left-hippo volume).
>
> I think I answered your question, but Doug is the stats wizard, so he
> may chime-in, or you can restate your question.
>
>
Dear all,
Am I correct in thinking that the measures of cortical volume, area, and
thickness, as well as subcortical volumes obtained after running the
reconall pipeline (and found in the 'aparc' and 'aseg' files,
respectively) are native ones? Or are they based on normalised brains,
thus 'contr
Dear all,
Does qdec allow analyses of covariance, and if so, how? is it possible
for example to test the effect of a regressor while controlling for the
effect of a particular measure?
thanks,
best,
Narly.
___
Freesurfer mailing list
Freesurfer@nmr.mg
Dear all,
I have 2 questions regarding doing analyses using QDEC:
1) can I use QDEC to analyse results on data for which I ran recon-all
using the last (ie: older, not most recent) version of Freesurfer, or
should I rerun recon-all on all the data using the new version of
Freesurfer? (I hope no
s stringent as if you want to do a thickness study.
>
>
> cheers,
> Bruce
>
> On Mon, 9 Jul 2007, Narly
> A Golestani wrote:
>
> >
> > Dear all,
> > I am a new FreeSurfer user, and have a quick question before beginning to
> > process T1 data: on the beginner
Dear all,
I am a new FreeSurfer user, and have a quick question before beginning to
process T1 data: on the beginners guide (entitled 'Cortical Reconstruction
with FreeSurfer'), it says that the input ought to be from MPRAGE or from
SPGR sequences. 1) Are these the only sequences that FreeSurfer
ly be the best choice. Once
> installed, be sure to try tkmedit and tksurfer, as shown here:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
>
> Nick
>
> On Thu, 2007-06-07 at 15:59 +0100, Narly A Golestani wrote:
> > Hello,
> > I would like to install F
Hello,
I would like to install FreeSurfer on Mandrake 10.2 (Mandriva), and would
like to know which version I should download. The available versions
appear to be for: CentOS 4, CentOS 4 x86_64, or Red Hat 9. Also, posts
to the archive seem to suggest that Mandrake may not be an optimal
platfor
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