Re: [Freesurfer] fs-fast sfa-sess retinotopy error

In /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional/bold/005, is there a file called f.nii? doug Jason Connolly wrote: > Dear freesurfer experts: > > I am new to fs-fast and I am currently running sfa-sess on some retinotopy > data and I think the main error is "cannot determ

Re: [Freesurfer] Retinotopic mapping of only polar data

If the activation is showing up in the wrong places, then that probably means that the registration is off. Have you checked the registration. doug f.le...@donders.ru.nl wrote: > Probably my e-mail just slipped through, so just a short notice that I still > have the problem with the overlay men

Re: [Freesurfer] mri_glmfit-sim and longitudinal analysis

No, you can't do this with our simulator. You can analyze the time points for each subject separately, then combine those results in a higher level analysis, then perform the permutation test. doug Thomas, Adam (NIH/NIMH) [E] wrote: > > I have a small group of subjects where each subject has be

[Freesurfer] fs-fast sfa-sess retinotopy error

Dear freesurfer experts: I am new to fs-fast and I am currently running sfa-sess on some retinotopy data and I think the main error is "cannot determine format of 005/f" I read in a previous post related to retinotopy that you need to add the full path to the .nii files and then it will work.

[Freesurfer] recon-all now taking too long

Hi, I have noticed that recently recon-all is taking a lot longer than usual to finish. It used to take around 30 to 48 hours, but the last couple that I have done are taking a whole week. It seems to get stuck in a repetitive step and it numbers each iteration like this: not handling expand

Re: [Freesurfer] error in autorecon1

Hi Cindy, try running it with -no-gcut and see if it helps. cheers, Bruce On Mon, 18 Jan 2010, Cindy Eckart wrote: Dear Freesurfers, when I try to run the recon-all flow, it exits at the skull stripping stage in some subjects, giving out error messages like this: register_mri: find_optim

[Freesurfer] error in autorecon1

Dear Freesurfers, when I try to run the recon-all flow, it exits at the skull stripping stage in some subjects, giving out error messages like this: register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm pe