Its hard to tell without seeing the pixel intensities under the segmentation,
but at first glance, it looks fine to me
Sent from my phone, please excuse brevity and typos
From: Ramesh Babu
Sent: Monday, May 1, 06:58
Subject: Re: [Freesurfer] Hippo-subfiled Need Help
To: Freesurfer support list
Dear list and especially Martin,
we have used Freesurfers crosssectional as well as the longitudinal stream
and are inspecting the outcomes at the moment.
We have as quality assurance been inspecting regions where the
difference between initial CROSS results and the corresponding LONG
results
I can't seem to replicate your results locally, even with the recon-all
you used. The one thing I'm missing is the expert options file. Can you
send that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with
Neuroscience of Language Postdoctoral Position at the University of California,
San Francisco (UCSF) in California, USA
The Hoeft Neuroscience Lab (http://brainLENS.org PI: Fumiko Hoeft MD PhD) at
the UCSF Dept of Psychiatry and Weill Institute for Neurosciences is looking
for a full-time post
Thanks Bruce!
That’s really good to know. So therefore, no need to have a “compromise” set of
echo images for dura correction if I’m not feeding both inputs to recon-all?
Would it make sense to run both days separately and just average thickness
values between ROIs to reach a single value for e
Hi Jared
again it depends on data quality. If it is good enough you are probably
better off just picking the best scan and reconning it.
cheers
Bruce
On Mon, 1 May 2017, Jared Saletin wrote:
Thanks Bruce!
That’s really good to know. So therefore, no need to have a “compromise” set
of echo
Dear list and Eugenio,
I have run for each subject
mri_label2vol --label SUBJ/label/rh.perirhinal_exvivo.thresh.label --regheader
SUBJ/mri/norm.mgz --fill-ribbon --subject SUBJ --hemi rh --o
SUBJ/mri/rh.perirhinal.nii.gz
next, to use FS-FAST on perihrinal.nii.gz, I have run
fcseed-config -seg
Dear Doug,
that is strange. What precisely you cannot replicate? The results with v5.3 or
with v6.0? What subject from the group I uploaded you have tried?
I could try to run the comparison again but I have seen the results already in
many subjects and the difference between -cubic and no cubic
It is subject #1, trying to replicate in our version of 5.3 using the
scripts/recon-all.local-copy
./recon-all.local-copy -all -FLAIRpial -s 1.dng.v53.local-cubic -cubic
The results were close, but they were not exact
On 5/1/17 4:13 PM, Antonin Skoch wrote:
Dear Doug,
that is strange. What
thanks guys!
On Fri, Apr 28, 2017 at 4:16 PM, Douglas N Greve
wrote:
> No, you can do it with
>
> mri_binarize --i aparc+aseg.mgz --match ID --o roi.ID.nii.gz
>
> where ID is the parc id from the FreeSurferColorLUT.txt
>
>
> On 04/28/2017 06:58 PM, VA Research wrote:
> > Does freesurfer output i
Doug,
did you process from scratch or did you retain edits to brainmask.mgz and
wm.mgz?
The -cubic should not be necessary, since recon-all (which I primarily obtained
from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ has
UseCubic=1 ).
I could try to replicate v5.3 agai
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