External Email - Use Caution
Hi Freesurfer team,
I have gotten this error message on a successful run before:
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly
Hi Abeoseh
You need to take a look at the output and see what is causing the large defect.
It is usually something like a big piece of skull left around.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Flemister, Abeoseh B.
Sent: Thursday, January 25, 2024 10:33 AM
To:
External Email - Use Caution
Dear Freesurfer Team,
I registered a Macromolecular Proton Fraction (MPF) map on T1 image using
multimodal registration in FSL and used freesurfer for the parcellation as
instructed by one of your colleagues. I want to really confirm that whether
the
Hi Ernest
Take a look at mri_segstats. I think it should do what you want (and it has an
extensive help with examples, thanks to Doug)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Thursday, January 25, 2024 11:31 AM
To: Freesurfer support list
Sub
External Email - Use Caution
Hi,
I have T1 relaxation maps over 4 time points. In terms of longitudinal
analysis, could these maps be fed into Freesurfer longitudinal pipeline to
control for intersubject variability of signal intensity? Any other method
you would recommend?
Many
Hello FreeSurfer team,
I have been using FreeSurfer for some time without difficulty, but I recently
encountered a problem that I cannot overcome. When I run recon-all using a
command like this:
recon-all -s b047test -i
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_J
Your recon-all command doesn't have the directive to tell it what to run - add
option '-all' to your command.
See this wiki page for detail
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Weisholtz, Daniel S.,MD
Sent
