[Freesurfer] Generating cortical correspondence vectors

External Email - Use Caution Hello FreeSurfer Developers, I'm interested in regenerating cortical correspondence vectors between pial and white surfaces as described in "Microstructural parcellation of the human brain." Is this currently the default way that freesurfer extracts

[Freesurfer] Global and lobar gyrification index

Hi all, Is there a way to calculate total hemispheric and lobar values of gyrification index? Either through a freesurfer-based command or through calculating the convex hull areas independently? We've thought about averaging local gyrification index for the hemisphere but think that direct c

Re: [Freesurfer] FLAIR registration

oes better? > On > Mon, 22 Feb 2016, K. Wagstyl wrote: > >> Hi all, >> >> We're trying to use FLAIR images in our recon-all pipeline. For half >> of >> the participants there are no problems using: >> recon-all -subjid SUBJECT -i T1.nii -all -FL

[Freesurfer] FLAIR registration

Hi all, We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial However for the other half the FLAIR registrations are either a bit off or completely flipped, inclu

Re: [Freesurfer] Partial volume correction for intensity sampling

i Konrad > > if you read Rebecca Shafee's recent paper: > > http://www.ncbi.nlm.nih.gov/pubmed/25449739 > > you can see what we do about this kind of thing. The stream is > largely > undocumented but you are welcome to try it out if you like. > > cheers >

[Freesurfer] Partial volume correction for intensity sampling

Hi, Is there a way to address or account the effects of partial voluming when sampling grey matter intensity (mri_vol2surf)? In particular, where there is cortical thinning, I'm also finding intensity changes that could either be due to changes in the amount of partial voluming or a change in