Re: [Freesurfer] recon-all on newborn

Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate. Autorecon Processing Stages: Motion Correction and Conform NU (Non-Uniform intensity normalization)

Re: [Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0

Hi Torben, Would it be possible to send us the volume and the surface file? Best, Ruopeng > On Jul 4, 2017, at 3:32 AM, Torben Lund wrote: > > Hello FreeSurfer Developers > > I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the > Freeview

[Freesurfer] petsurfer stats for multiple segmentations

Dear freesurfer support, I am using the PetSurfer to process our PET data. But by default, it would only generate stats for the segmentation with the aparc atlas. However, I want to obtain the stats for different freesurfer atlases, like in the freesurfer outputs (aseg,stats,

Re: [Freesurfer] recon-all on newborn

Hi S Das, We are trying to release the infant pipeline by the end of the summer. Lilla On Tue, 4 Jul 2017, Das S. wrote: > Dear Freesurfer expert, > I want to perform recon-all pipeline on neonates data.Can I do so? > I was going through some mail archives and there it is said that on T1

Re: [Freesurfer] lopsided hemisphere

Hello Bruce, Thank you for your advice! I really appreciate it! Happy 4th July. Kind regards, Michael From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 04 July

Re: [Freesurfer] lopsided hemisphere

Hi Michael I don't think there is really a problem here - it is just that either the brain is oriented strangely or it indeed asymmetric. In any case the segmentations and surfaces look accurate cheers Bruce On Tue, 4 Jul 2017, Michael Davies wrote: Hello, I have encountered a lopsided

[Freesurfer] lopsided hemisphere

Hello, I have encountered a lopsided hemisphere when analysing the data. What procedure do i need to employ to fix the problem? Any advice would be greatly appreciated! Kind regards, Michael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Pial surface editing

Hi Michelle yes, you can try putting already stripped data through, or I think if you convert the afni skull stripped volume to $subject/mri/brainmask.mgz recon-all should recognize that it is different from the auto stripping and use it instead cheers Bruce On Tue, 4 Jul 2017, Michelle

Re: [Freesurfer] Fwd: wm topological defects

Hi Manuel it's impossible to tell from a single slice. cheers Bruce On Tue, 4 Jul 2017, Manuel Delgado wrote: > To illustrate the previous case here there is an image in which there is a > discrepancy between the wm surface and the smoothwm.nofix. Is it necessary > to fix it or not? > Thanks

Re: [Freesurfer] wm topological defects

Hi Manuel you should examine the ?h.white and ?h.pial for accuracy, and only use the .nofix surfaces if you are trying to figure out why the white/pial are not as accurate as you would like Bruce On Tue, 4 Jul 2017, Manuel Delgado wrote: > Dear all: > Regarding wm edits, it is shown in the

Re: [Freesurfer] Medial Surface Problem

sure. Can you upload the data again to our ftp site? Don't use the filedrop - use ftp and make sure you include the cross and the long of all the timepoints for this subject, and also the coordinates of the location you are seeing the problem cheers Bruce On Tue, 4 Jul 2017, Bronwyn Overs

[Freesurfer] MNI Coordinates

Hi All, I am trying to visualise nodes of a brain network reconstructed using FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain Net Viewer and Network Based Statistics software. In order to do so, I need to upload a .txt file listing Freesurfer labels coordinates

Re: [Freesurfer] Pial surface editing

Hello, I am just following up on this question. Thanks! Michelle On Tue, Jun 27, 2017 at 4:46 PM, Michelle VanTieghem < michelle.vantieg...@gmail.com> wrote: > Hi Bruce, > > The -gcut does not appear to make any difference on our skull stripping. I > also saw that you can change flags for

[Freesurfer] remove skull from gtmseg.mgz

Hello Freesurfer, After running the first step of PETsurfer ( https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). I viewed the image it created using freeview. When I change, the color map to Lookup Table, the image also included the skull. How can I remove the skull from gtmseg.mgz/prevent it

[Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 - with links to files

Hello FreeSurfer Developers I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the Freeview program. For version 1.0 superimposing a gifti surface on top of a nifti volume works beautifully (see results here: https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0

[Freesurfer] recon-all on newborn

Dear Freesurfer expert, I want to perform recon-all pipeline on neonates data.Can I do so? I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all. But again there is another paper where it says Freesurfer can perform segmentation

[Freesurfer] Fwd: wm topological defects

To illustrate the previous case here there is an image in which there is a discrepancy between the wm surface and the smoothwm.nofix. Is it necessary to fix it or not? Thanks -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n*

[Freesurfer] wm topological defects

Dear all: Regarding wm edits, it is shown in the tutorial how to proceed with "holes" that appear in the smoothwm.nofix. However, those holes do not necessarily affect the wm matter surface. So is it recommendable to check if holes in the smoothwm.nofix surface affect the real wm surface before