hmmm, not much gray/white contrast in the cerebellum. Can you send me the
aseg.presurf.mgz also?
On Mon, 4 Sep 2017, José Gómez-Feria Ferreiro wrote:
Hello Bruce,
Thank you for your email. I understand the issue about distinguishing between
grey and white matter.
However, I can get a nice segmentation of cerebellum using SPM, but
unfortunately I can't get the
.msh file that I use in SIMNIBS when I run FSL + Freesurfer.
Do you have an example of how to use the -canorm-usecps flag. I'm attaching the
norm.mgz file here,
is that the file you need?
All the best,
José Gómez-Feria Ferreiro
MD/PhD candidate
Grupo de Trastornos del Movimiento. Lab 104
Programa de Investigación de Neurociencias
Instituto de Biomedicina de Sevilla (IBiS) Hosp.Univ. Virgen del
Rocío/CSIC/Univ. de Sevilla
Avda. Manuel Siurot s/n.
41013 - Sevilla (España)
2017-09-01 16:28 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
HI José
the cerebellum scan quality can be hugely variable due to its intrinsic
structure (tiny,
almost fractal folia) and distance from isocenter. If you upload the
subject we will
take a look, or send a snapshot. Sometimes if the cerebellum is too dark
in the norm.mgz
you can add a control point and recreate the using the -canorm-usecps flag
cheers
Bruce
On Fri, 1 Sep 2017, José Gómez-Feria Ferreiro wrote:
Dear Freesurfer,
I have been doing some MRI segmentations using the "mri2mesh"
command (which
does "recon all").
However, I noticed the cerebellum segmentation is not correctly
done. It
considers the cerebellum as
white matter but it also has grey matter. Is there a way to make a
more
precise segmentation of the
cerebellum?
Best regards,
José Gómez-Feria Ferreiro
MD/PhD candidate
Grupo de Trastornos del Movimiento. Lab 104
Programa de Investigación de Neurociencias
Instituto de Biomedicina de Sevilla (IBiS) Hosp.Univ. Virgen del
Rocío/CSIC/Univ. de Sevilla
Avda. Manuel Siurot s/n.
41013 - Sevilla (España)
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