Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

It does look better. Can you send me some more images--in axial and coronal planes? On Wed, Mar 30, 2016 at 4:26 PM, Ramtilak Gattu wrote: > > Thank you for recommending the expert options. I have run this on two > subjects (rows) and you can see the post analysis results on the right > (column

[Freesurfer] Longitudinal TRACULA - Error in path reconstruction

Hi Anastasia, I hope you’re enjoying your evening! I’m doing longitudinal TRACULA analysis on two subjects, each having two time points. I have already taken the steps of longitudinal recon-all and trac-all -prep & -bedp. Now I’m trying to do trac-all -path, but it gives me an error that I can

Re: [Freesurfer] DODS vs DOSS for correlation analysis

Hi Doug, I'm using version 5.3. I had read about the bug but the release notes for 5.3 didn't mention not using DOSS in Qdec, so I thought the issue must have been resolved. If not, I'll let my colleagues know as I believe some of them are still using DOSS in Qdec. Cheers, Cassie ___

Re: [Freesurfer] bbregister problems with PET data

Hi Adam, not sure robust_register robent will work on this type of stuff (never tested it). I would recommend to keep the radius small (2,or 3), but switch on --entcorrection. You can also try robust_register with normalized mutual information (NMI) or simple MI to see how that works. You

Re: [Freesurfer] longitudinal pipeline surface error

Hi Mihaela, does the cross sectional run of that time point, and the base look OK? Also check if this time point is aligned correctly to the base (e.g. open norm.mgz from the long and the base, they should be aligned). If all this is OK, then I would recommend to re-run this long run again,

[Freesurfer] Qdec

Hi Freesurfers, I compared 2 groups, while controlling for 1 covariate in qdec using freesurfer 5.1. There were no significant interactions with the covariate so I need to use DOSS. I read on several post that DOSS has some bugs related to the generation of contrasts in qdec and that mri_glmfit

[Freesurfer] bbregister problems with PET data

Hi Freesurfer team, I’m encountering a problem using bbregister on PET data: -- When I attempt to register a PET volume to T1-space the asymmetric tracer uptake of the PET throws off proper registration. (Treating the PET as a T1 because of the non-specific white matter uptake > grey matter sign

Re: [Freesurfer] whole brain is yellow

Hello doug, What threshold seems plausible? Thanks Miracle Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Monday, March 28, 2016 4:18 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole brain is yellow Try

Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Claudia, Sorry for the late response. I am aware of this bug and I'm exploring possible solutions. How often does it happen in your data (i.e., how many subjects out of how many)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaim

[Freesurfer] Increase VBOX disksize

Dear Sir/Madam I am using freesurfer to proceeding brain MRI data. I have 30 cases. However, the space for home is no enough. I am wondering how can I increase disk space to computing my data. I use Vbox unbentu system. thanks Lawrence ___ Freesurfer mai

Re: [Freesurfer] Regarding: oblique view

Hi Sampada could you include our previous corresponance in your emails so I can keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic cheers B