Dear Freesurfers,
I have a problem with labels. I select a given Talairach coordinate that
interests me, draw an approximately circular label around it in
tksurfer, and save it. When I open that same label in tkmedit, the
central Talairach coordinate is changed and the whole label is somewhat
shif
Hi Irene,
the label has to shift somewhat in tksurfer, since it will sample it onto
the surface. Unless the entire label you drew was exactly on the surface
boundary to begin with.
cheers
Bruce
On Tue, 21 Dec 2010, Irene Altarelli wrote:
> Dear Freesurfers,
>
> I have a problem with labels. I
you can
setenv FSLDIR /usr/pubsw/packages/fsl/3.3.7
then re-source the stable3 environment.
doug
jkus...@partners.org wrote:
> Hi Doug,
>
> Thanks for your messages. We have to keep using stable3 for the rest of this
> study. Does this mean we can just use a command to use the older version of
Dear Colleague,
Following is the error we get upon running the mri_annotation2label command
r...@ubuntu:~# mri_annotation2label --subject one \ --h rh --labelbase
./label/aparc-rh
ERROR: Option --h unknown
r...@ubuntu:~# mri_annotation2label --subject one \ --hemi rh --labelbase
./label/apar
that works for me:
mri_annotation2label --subject bruce --hemi rh --labelbase .
subject = bruce
annotation = aparc
hemi = rh
labelbase = .
surface = white
Reading surface
.
.
can you remove the \ in your command line?
Bruce
On Tue, 21 Dec
2010 subraman...@nbrc.ac.in wrote:
>
> Dear Collea
Hi Diederick,
the ICV is computed from the linear talairach.xfm transform (including
skull). There are all kinds of other talairach transforms produced by
recon all, so make sure you are looking at the talairach.xfm (not ...lta
or ..._with_skull.lta).
You might want to read:
http://surfer.nmr.mgh
As I said, there are several talairach transforms.
You need to look at the talairach.xfm.
The wiki says:
To check the quality of the registration file talairach.xfm file:
cd $SUBJECTS_DIR/subject/mri/transforms
tkregister2 --xfm talairach.xfm \
--targ $FREESURFER_HOME/average/RB_all_withskull
Hi,
I want to use FreeSurfer to analyze a longitudinal study. For each
subject in my study, I already used FreeSurfer 4.2 to perform the
cross-sectional analysis. However, FreeSurfer 4.2 did not have a
longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for
this purpose (in the FreeSurfe
Is there a quick way to transform the orig.mgz data back to the
'original" orientation of the orig/001.mgz data set? i.e., undo the
conform?
Greg
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That's what the rawavg.mgz is. You can use mri_convert with -rl rawavg.mgz to
realize other conformed volumes back to that space
On Dec 21, 2010, at 5:50 PM, "Harrington, Gregory S."
wrote:
> Is there a quick way to transform the orig.mgz data back to the
> 'original" orientation of the orig
Dear all
I would like to write an MRI anatomical volume and a surface in freesurfer
format.
The surface is correspondent to the white matter tessellation, while the volume
represents T1 anatomical slices, both obtained from softwares external to
FreeSurfer.
Using the two functions save_mgh.m an
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