Hello FreeSurfer Experts,
Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate?
Thank you
Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami
No, not currently. This is quite a hard problem even if you have a T2. The pulse sequences are usually low enough bandwidth that fat from the scalp and skull marrow shift into the CSF spaces making it impossible to properly segment that area as CSF. If you wanted an approximate value, you could create a binary mask from the aparc+aseg.mgz, dilated it by 3 or 4 voxels, then erode it by the same amount, then remove the original mask. The remaining voxels will be something like the sulcal CSF.
doug
On 10/22/2014 04:50 PM, Mohammed Goryawala wrote:
Hello FreeSurfer Experts,
Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate?
Thank you
Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug.
I was looking at a paper "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D. M., PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of cranial, brain and sulcal CSF volumes in male and female deficit and nondeficit patients with schizophrenia. Psychiatry Research: Neuroimaging, 162, 91-100.", which estimates sulcal CSF volume as 2.4.4. Sulcal CSF (sCSF)
The sCSF was derived by subtracting T otal B rain V olume and V entricular V olume from T otal C ranial V olume .
Can such a strategy be explored using FreeSurfer output ?
Thanks for your advice
Mohammed
On Thu, Oct 23, 2014 at 12:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
No, not currently. This is quite a hard problem even if you have a T2. The pulse sequences are usually low enough bandwidth that fat from the scalp and skull marrow shift into the CSF spaces making it impossible to properly segment that area as CSF. If you wanted an approximate value, you could create a binary mask from the aparc+aseg.mgz, dilated it by 3 or 4 voxels, then erode it by the same amount, then remove the original mask. The remaining voxels will be something like the sulcal CSF.
doug
On 10/22/2014 04:50 PM, Mohammed Goryawala wrote:
Hello FreeSurfer Experts,
Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate?
Thank you
Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
In theory that works, but remember the FS total cranial volume is only an estimate based on the talairach transform. It is not counting voxels that are inside the skull.
On 10/23/2014 12:30 PM, Mohammed Goryawala wrote:
Thanks Doug.
I was looking at a paper "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D. M., PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of cranial, brain and sulcal CSF volumes in male and female deficit and nondeficit patients with schizophrenia. Psychiatry Research: Neuroimaging, 162, 91-100.", which estimates sulcal CSF volume as
2.4.4. Sulcal CSF (sCSF)The sCSF was derived by subtracting T
otal B rain V olume and V entricular V olume from T otal C ranial V olume . Can such a strategy be explored using FreeSurfer output ?
Thanks for your advice Mohammed
On Thu, Oct 23, 2014 at 12:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, not currently. This is quite a hard problem even if you have a T2. The pulse sequences are usually low enough bandwidth that fat from the scalp and skull marrow shift into the CSF spaces making it impossible to properly segment that area as CSF. If you wanted an approximate value, you could create a binary mask from the aparc+aseg.mgz, dilated it by 3 or 4 voxels, then erode it by the same amount, then remove the original mask. The remaining voxels will be something like the sulcal CSF. doug On 10/22/2014 04:50 PM, Mohammed Goryawala wrote: > Hello FreeSurfer Experts, > > Is it possible to estimate the sulcal CSF volume in Freesurfer > processing? If not directly are there any indirect means that can give > me an estimate? > > Thank you > > Mohammed Goryawala, PhD > Department of Radiology > Miller School of Medicine, University of Miami > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks
On Thu, Oct 23, 2014 at 12:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
In theory that works, but remember the FS total cranial volume is only an estimate based on the talairach transform. It is not counting voxels that are inside the skull.
On 10/23/2014 12:30 PM, Mohammed Goryawala wrote:
Thanks Doug.
I was looking at a paper "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D. M., PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of cranial, brain and sulcal CSF volumes in male and female deficit and nondeficit patients with schizophrenia. Psychiatry Research: Neuroimaging, 162, 91-100.", which estimates sulcal CSF volume as
2.4.4. Sulcal CSF (sCSF)The sCSF was derived by subtracting T
otal B rain V olume and V entricular V olume from T otal C ranial V olume . Can such a strategy be explored using FreeSurfer output ?
Thanks for your advice Mohammed
On Thu, Oct 23, 2014 at 12:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, not currently. This is quite a hard problem even if you have aT2.
The pulse sequences are usually low enough bandwidth that fat fromthe
scalp and skull marrow shift into the CSF spaces making it impossible to properly segment that area as CSF. If you wanted an approximatevalue,
you could create a binary mask from the aparc+aseg.mgz, dilated it by 3 or 4 voxels, then erode it by the same amount, then remove the original mask. The remaining voxels will be something like the sulcal CSF. doug On 10/22/2014 04:50 PM, Mohammed Goryawala wrote: > Hello FreeSurfer Experts, > > Is it possible to estimate the sulcal CSF volume in Freesurfer > processing? If not directly are there any indirect means that can give > me an estimate? > > Thank you > > Mohammed Goryawala, PhD > Department of Radiology > Miller School of Medicine, University of Miami > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Mohammed Goryawala