Hi NIck:
Thanks for your information.
I always use recon-all with -all option to reconstruct my data, and the
command can successfully finished, Does it mean that I have got a good tal
transform?
subjA06 also has been reconstructed with recon-all, but it did not get a
good tal transform as
In my previous mail I sent you the FSLview screenshot( the .nii one)
ALso, I am attaching the original picture which was in BV. It shows system
coordinates (which is RAS coordinates in BV). The position of the ROIs seem
to be reversed when viewing with fslview. which is the space which FSlview
dis
Raka,
Yes, it is ok to just copy those three binaries from 4.3 or 4.2 to your
4.1 installation.
Nick
On Thu, 2009-04-16 at 05:15 -0700, raka maitra wrote:
> Hello
>
> I am using Freesurfer v 4.1.0
> I would like to have the advantage of the updated qdec of v 4.2 or 4.3 for my
> data.
> Specif
Dana,
There is also a '-bigventricles' flag which you can pass to recon-all,
which affects mri_ca_register and mri_ca_label. Not sure of its
efficacy though.
Nick
On Thu, 2009-04-16 at 14:54 -0400, Bruce Fischl wrote:
> Hi Dana,
>
> the really huge ventricle subjects do sometimes fail with th
Barnali,
Does the ROIs.nii volume open and display correctly in fslview?
Nick
On Thu, 2009-04-16 at 13:36 -0700, Barnali Basu wrote:
> Hi
>
> We are trying to another method to open a BV ROI in FS. My colleague
> has sent me ROI generated in BV in Nifti format, which when I try to
> open in FS
Asaf,
See the 'FreeSurfer Course' tutorial on the slicer tutorial page:
http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training
It has a section on creating a 3d model of one or more subcortical
structures (saved in vtk file format).
Nick
On Sat, 2009-04-18 at 12:41 -0300, Pedro Paulo de Maga
Dave,
I'm not 100% certain, but I think you need to create a mask volume from
your subcortical.label file, and then use the --mask option with
mri_glmfit instead of --label (see mri_glmfit --help). That is, create
a volume with a '1' in the voxels of interest, and '0' elsewhere and
pass that to -
Zhen,
The -tal-check flag included with recon-all will perform the QA check
that Avi mentions, with the addition of creating a z-score comparing the
subject's QA score to a set of QA scores of known-good talairach
alignments. The -tal-check flag runs by default in recon-all (in -all
and -autoreco
Hi,
While going through the annotation of the clusters, we noticed that the
regions that the cluster summary prints out do not correspond to the actual
location in the brain. For example, in the summary one of the clusters is
reported to be in the isthmus of cingulate. However, when I look at the
there is a lot of overlap but they are not quite the same. I think 30-35 of
them are the same, but a few are different.
On Wed, 22 Apr 2009, Michael Harms wrote:
And just to bring this discussion full circle, how does the training set
for the subcortical segmentation relate?? Is the traini
And just to bring this discussion full circle, how does the training set
for the subcortical segmentation relate?? Is the training set (and
associated manual labeling) that is used for the subcortical
segmentation composed of the same 39 subjects used for both the current
spherical template and
Ah...Excellent! Thanks so much for clearing things up for me.
Cheers,
Jenifer
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 22, 2009 11:55 AM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] spherical tem
Hi Jennifer,
the spherical stuff has nothing to do with the CMA. And in fact the
spherical registration itself is not based on any manual labelings, just
estimates of cortical geometry from a set of training subjects. The
cortical parcellations do depend on manual labelings, but this is also
Is any information about the manually-parcellated (CMA) training set used to
create the spherical template used in fsv4.*? The information reported in
Cerebral Cortex (2004) 14(1):11-22 reports 36 MRI volumes from an ongoing study.
Does this sound about right?
Or have there been any updates to t
Hi Katie,
looks like an incorrectly fixed topological defect. You need to edit the
wm.mgz to remove the defect and rerun autorecon2-wm
cheers,
Bruce
On Wed, 22 Apr 2009,
Kathryn Devaney wrote:
Hello freesurfers,
I am running a reconstruction of a macaque in stabe4, and I am having a
probl
I'll try now. Thank you very much! Marina-freesurfer-boun...@nmr.mgh.harvard.edu escribió: -Para: "marina.lo...@crccorp.es" De: "Pedro Paulo de Magalhaes Oliveira Junior" Enviado por: freesurfer-boun...@nmr.mgh.harvard.eduFecha: 22/04/2009 11:08cc: Freesurfer Mailing List Asunto: RES: [Fre
Check the User contribution section of the FreeSurfer wiki. I've put there a
small script to do this.
Sent from my Nokia phone @E71
-Msg original-
De: marina.lo...@crccorp.es
Enviada: 22/04/2009 05:43:39
Assunto: [Freesurfer] Individual thickness data extraction from plot
Hello all,
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