No need to use --init-fsl (if using version 6). For mri_vol2surf add 
--projfrac 0.5 to sample in the middle of the ribbon  (unless you 
specifically want to sample on the gray/white border)


On 4/6/18 10:11 AM, Crawford, Anna wrote:
> Hello,
>
> I used the following commands and then opened the surface as an overlay on 
> the inflated volume, but I am not about to look at the time series. The view 
> time course is grayed out so that I can not click on it. Did I miss a step or 
> lose the actual time series somewhere?
>
> bbregister --s S2sdt/subject/ --mov 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>   --out 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>  --srcreg 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>  --hemi lh
>
>
> Thank you,
> Anna
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve 
> <dgr...@mgh.harvard.edu>
> Sent: Thursday, April 5, 2018 5:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>
> Use bbregister. Run with --help to get docs (make sure to use --projfrac
> 0.5). Once you have it on the surface, you can step through each frame
> in freeview
>
>
> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
>> Hello,
>>
>> I have a time series (.hdr/.img) that I want to overlay onto a
>> surface, specifically the inflated surface from the anatomy. I suspect
>> I have to use mri_vol2surf, which requires a source registration
>> file. How do I get this file? Then once I have this file, will I be
>> able to view step by step through the time series on the inflated volume?
>>
>> Thanks for your help,
>> Anna
>>
>>
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