Hi, My goal is to use the best possible skull-stripped version of the input MRI. Is brainmask.mgz the one? or I was wondering if anyone has tried improving the brainmask.mgz further by masking it out using the aseg.mgz. Will that help with regards to getting rid of the dura in the brainmask.mgz. My intuition is because the generation of aseg.mgz includes a surface-based algorithm, the smoothing constraints of the surface evolution should minimize the "leakage" of the GM surface into the dura, hence the aseg might have some dura but not as much as the brainmask. Will be thankful for any suggestions/comments. Karteek
You can use the aseg.mgz (in v6) or aparc+aseg.mgz in any version.
On 05/18/2017 10:42 AM, Karteek Popuri wrote:
Hi, My goal is to use the best possible skull-stripped version of the input MRI. Is brainmask.mgz the one? or I was wondering if anyone has tried improving the brainmask.mgz further by masking it out using the aseg.mgz. Will that help with regards to getting rid of the dura in the brainmask.mgz. My intuition is because the generation of aseg.mgz includes a surface-based algorithm, the smoothing constraints of the surface evolution should minimize the "leakage" of the GM surface into the dura, hence the aseg might have some dura but not as much as the brainmask. Will be thankful for any suggestions/comments. Karteek _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Karteek
the aseg isn't surface based, sorry, but the watershed that we use to do the skull stripping is and does use smoothness constraints. If it is leaving dura around try using mri_gcut.
cheers Bruce
On Thu, 18 May 2017, Karteek Popuri wrote:
Hi, My goal is to use the best possible skull-stripped version of the input MRI. Is brainmask.mgz the one? or I was wondering if anyone has tried improving the brainmask.mgz further by masking it out using the aseg.mgz. Will that help with regards to getting rid of the dura in the brainmask.mgz. My intuition is because the generation of aseg.mgz includes a surface-based algorithm, the smoothing constraints of the surface evolution should minimize the "leakage" of the GM surface into the dura, hence the aseg might have some dura but not as much as the brainmask. Will be thankful for any suggestions/comments. Karteek _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Karteek,
as for higher resolution (>0.7mm) the brainmask often includes lots of residual, I changed my pre-processing slightly.
Currently I do bias field correct my 7T data with SPM and create a mask of the WM, GM and CSF segmentation you get along with it. Then I recon-all -autorecon1 the bias field corrected volume and mask the T1.mgz with the SPM mask and additionally run mri_gcut. This does seem to work fine on my data. Afterwards I continue with -autorecon2 and -autorecon3.
Best, Falk
________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Karteek Popuri [kpopuri@sfu.ca] Gesendet: Donnerstag, 18. Mai 2017 16:42 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura
Hi, My goal is to use the best possible skull-stripped version of the input MRI. Is brainmask.mgz the one? or I was wondering if anyone has tried improving the brainmask.mgz further by masking it out using the aseg.mgz. Will that help with regards to getting rid of the dura in the brainmask.mgz. My intuition is because the generation of aseg.mgz includes a surface-based algorithm, the smoothing constraints of the surface evolution should minimize the "leakage" of the GM surface into the dura, hence the aseg might have some dura but not as much as the brainmask. Will be thankful for any suggestions/comments. Karteek _______________________________________________ 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.
Hi,
sorry to dig up this old email (just came across it).
We have stopped with the gcut, because in some cases it cropped brain. Also passing a T2 via the -T2 flag (which is supposed to remove dura) sometimes crops cortex.
It should be made clear that at the stage of the brainmask this should be absolutely avoided. The brainmask can be larger than the brain and even include some dura or skull here and there, as surfaces often do not "grab" those regions.
If you just want a nice skull strip, maybe you should find a way to do that post surface creation (e.g. dilate the surfaces and remove anything outside (and outside the aseg labels, to include cerebellum, ventricle etc).
Best, Martin
On 05/19/2017 01:03 PM, Falk Lüsebrink wrote:
Hi Karteek,
as for higher resolution (>0.7mm) the brainmask often includes lots of residual, I changed my pre-processing slightly.
Currently I do bias field correct my 7T data with SPM and create a mask of the WM, GM and CSF segmentation you get along with it. Then I recon-all -autorecon1 the bias field corrected volume and mask the T1.mgz with the SPM mask and additionally run mri_gcut. This does seem to work fine on my data. Afterwards I continue with -autorecon2 and -autorecon3.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Karteek Popuri [kpopuri@sfu.ca] Gesendet: Donnerstag, 18. Mai 2017 16:42 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura
Hi, My goal is to use the best possible skull-stripped version of the input MRI. Is brainmask.mgz the one? or I was wondering if anyone has tried improving the brainmask.mgz further by masking it out using the aseg.mgz. Will that help with regards to getting rid of the dura in the brainmask.mgz. My intuition is because the generation of aseg.mgz includes a surface-based algorithm, the smoothing constraints of the surface evolution should minimize the "leakage" of the GM surface into the dura, hence the aseg might have some dura but not as much as the brainmask. Will be thankful for any suggestions/comments. Karteek _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Douglas N Greve -
Falk Lüsebrink -
Karteek Popuri -
Martin Reuter