At the beginning I thought the same thing but a colleague built an another
specific template with n = 40 like fsaverage. The results seems to be
equivalent. Actually it is weird because when you look at the shape of the
inflated fsaverage, it is smoother than mine but when you look at the
curvature
Dear Anastasia and all,
how can I understand which are the region of the brain in which the brain base
been parecellated that each tract generated by TRACULA connect?
For example if I look at the left uncinate fascicles how can I know which are
the ROIs of the statistical output from the corti
Hi,
I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
export
Hi Lucia - You can look at the tracula output over the cortical
parcellation and subcortical segmentation in the individual's diffusion
space like this:
freeview dmri/dtifit_FA.nii.gz
dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv
dpath/merged_avg33_mni_bbr.mgz
Hope this hel
Do you mean that the inflated surface has more curves in it than the
fsaverage one? What version are you using? I think that newer versions
of make_average_surface (run by make_average_subject) run the inflation
out further. Try this
cd $SUBJECTS_DIR/averagesubject/surf
mris_inflate -dist .01
Hi all,
When running a functional analysis and comparing two experimental
conditions, we observed that there are some voxels/vertices where both
condition A and condition B have a positive % signal change from baseline,
and condition A has greater activity than condition B.
In other regions, both
Thanks Anastasia, this is useful for visualization. But to construct a table
with for each tracts the parcellation regions that it connects do I need to
look at the image?
Lucia
On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote:
>
> Hi Lucia - You can look at the tracula output over the c
I think it is just what bruce said: with 80 subjects instead of 40 you
will have a lot more smearing.
On 10/18/2013 11:27 AM, Sophie Maingault wrote:
> Yes that what I mean and the command mris_inflate fixed this problem,
> thanks a lot ! However the curvature profile between fsaverage and my
>
Hi Lucia - You can probably do that with mri_segstats. Try something like:
mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i
dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz
And similarly for any other pathway. S
Not always, but yes, in some instances the aseg crosses.
> - Original Message -
> From: Bruce Fischl
> Sent: 10/18/13 01:22 PM
> To: silve...@gmx.com
> Subject: Re: [Freesurfer] medial wall crossing the surface
>
> Does the aseg cross as well?
>
>
>
> On Oct 17, 2013, at 10:07 PM, "sil
I have about 100 subjects that have been run on 5.0 and I'd like to update them
to 5.3. Is there a flag for recon-all that just runs the steps that would be
affected by the version change? I seem to recall seeing a flag on the wiki but
can't find it now. Maybe it was just for small patches?
no, sorry, but if you rerun recon-all on the existing subject dirs it
will preserve the existing manual edits
cheers
Bruce
On Fri, 18 Oct 2013, Ruth Carper
wrote:
I have about 100 subjects that have been run on 5.0 and I'd like to update
them to 5.3. Is there a flag for recon-all that just
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