Re: [Freesurfer] convert 4d volume time series to GIFTI surface time series

a concern? Thanks, Kathleen On 9/16/10 2:37 PM, "Hansen, Kathleen (NIH/NIMH) [F]" wrote: Thanks so much, Nick. I used your suggestion for the call to mris_convert and it seems to be working fine. Thanks also for the pointer to mri_info to check dimensions. This gave more he

Re: [Freesurfer] convert 4d volume time series to GIFTI surface time series

imensions). n. On Thu, 2010-09-16 at 12:49 -0400, Hansen, Kathleen (NIH/NIMH) [F] wrote: > Dear all, > Any help that you could give on this pretty basic question would be much > appreciated. I've been trying to use the excellent fmri-to-anatomical > registration produced by Free

[Freesurfer] convert 4d volume time series to GIFTI surface time series

Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using m

Re: [Freesurfer] initial G-W contrast is negative

the header). doug Hansen, Kathleen (NIH/NIMH) [F] wrote: > Thanks. The tkregister2 check gives some new information. The initial > registration is not very bad when checked in tkregister2. Also, the final > registration is perfectly acceptable when checked in tkregister2, so my

Re: [Freesurfer] initial G-W contrast is negative

pm. Second, you can tweak the initial registration by hand to get it "close" (ie, within 5mm and 5deg), then use --init-reg doug Hansen, Kathleen (NIH/NIMH) [F] wrote: > Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it > was not acquired at the same time a

Re: [Freesurfer] initial G-W contrast is negative

PM, "Douglas Greve" wrote: It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view? doug On 8/19/10 1:50 PM, Hansen, Kathleen (NI

[Freesurfer] initial G-W contrast is negative

Hello, The following command has produced a very wrong registration and a warning: bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a

[Freesurfer] User-defined colormaps

Hello, If we are visualizing fmri surface data with tksurfer, how can we load our own user-defined colormaps? If this is not possible in tksurfer, is it possible using some other Freesurfer function? Thank you, Kathleen ___ Freesurfer mailing list Fre

[Freesurfer] writing out a transformed fmri volume

Hi, We have had several naive questions about registration recently, and thank you all very much for your patience. Here is another one. We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate th

Re: [Freesurfer] Registration of talairach and original space?

We have another question that is very related, so I will ask that at the same time: We have a region of interest defined on an individual subject's surface. How can Freesurfer translate that ROI into the coordinates of the original fmri data? It's clear to us how to get from fmri to the surfa