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)
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)
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
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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
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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 itsintrinsic 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. Virgendel 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
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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.
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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