that looks to me like it accurately segmented all the un-partial-volumed white matter in the cerebellum. Are you hoping it would segment the smaller folia as wm? I guess it could, but those voxels all look like they have gm in them too
On Mon, 4 Sep 2017, José Gómez-Feria Ferreiro wrote:
Hi Bruce,
Sure, here it is the file:
Thanks,
Jose
2017-09-04 16:47 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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 <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) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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