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 <fischl@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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