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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Karteek > Popuri [kpop...@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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer