Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

Not sure it's helpful. The simplest way I can think of is to directly edit WM.mgz. You can load wm.mgz into matlab, it's basically a 3D matrix. You can directly set values for wm matrix, for instance wm(wm(:)>200)=110; Then you save the new wm matrix into wm.mgz. On 9/5/16 10:54 AM,

Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

Hi Ben sorry, but I don't know how to fix it automatically. You have voxels that look just like wm in the gm - that's going to be tough to avoid. You could try messing with some of the mris_make_surfaces options, but I don't have much confidence that it will help. Any idea why you are

Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

Hi Bruce and Clara, Many thanks for your comments. Indeed the bright points are segmented as WM in wm.mgz, however these errors do not occur only in a few places but in many slices throughout the brain so manual edits will be very extensive, which is why we wanted to double check that there is no

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

If the T2 is already high-res, and having already the T1, I don’t think that the FLAIR would help much. Cheers, /E Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 5 Sep 2016, at 16:22,

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

Sorry, but a 3-channel segmentation is not part of the future FS6. Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 5 Sep 2016, at 15:54, Jovicich, Jorge

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

Dear Jorge, In my case I am using either T1+T2 or T1+FLAIR. I had no intention of using all three at once, but now I am also wondering if this would be an improvement. Cheers, Renata On Mon, Sep 5, 2016 at 4:54 PM, Jovicich, Jorge wrote: > Hi Eugenio, > > just to

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

Hi Eugenio, just to confirm I understand the currently available options. There are two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D FLAIR). It would be great to see if the combo option improves things even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR).

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

The same one; just change the input file and the analysis ID - T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz T2 - FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz FLAIR Cheers, /Eugenio Juan Eugenio Iglesias Senior Research Fellow

[Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

Dear FS experts, I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0. For controls on which I had already run recon-all -all, I added the T2 sequence with the following command: recon-all -s \