[VoxBo] many questions

[Charan Ranganath, Ph.D.]

Thanks Dan. I definitely don't want to hold up the new voxbo release (we 
desperately could use a version of VBview with visualization of time 
courses on par with the old idl-based voxel surfer).

That said, it would seem to be logical to incorporate FDR-corrected 
thresholds in vbthreshcalc (that would also allow you to calculate FDR 
corrections on t-maps, rather than on glms that were performed in 
voxbo), and to add the masking capability to vbthresh.

Regarding AFNI, we're mainly using the .brik format as an intermediary 
to get voxbo data readable by the multivoxel pattern analysis toolbox 
(which is currently set up to only read AFNI-formatted data). Right now, 
we go from .img format-->.brik, which is not so bad. So I guess afni 
conversion is a low priority.

In the words of bartles and james, "thank you for your support." CR

Daniel Y Kimberg wrote:
> Charan Ranganath wrote:
>> (1) Is there a way for vbthreshcalc (or some other program) to read info
>> from a glm directory in order to calculate corrected thresholds? Also,
>> can it read mask files to incorporate that information?
> 
> No, right now you pretty much have to give the threshold calculator
> all the info it needs manually.  I've had on my list for a long time
> to get it integrated into vbview, at which point it would get the info
> automatically, but I haven't yet.  I should bump that up on my list.
> 
>> (2) Is there a way to get FDR-corrected thresholds in VoxBo?
> 
> Yes -- in vbstatmap, if you specify a contrast that results in a p
> value (tp or fp) and give it the -q argument for the requested FDR, it
> will print the threshold to your terminal.
> 
>> (3) Is there any support for conversion to/from AFNI .brik/.head files?
> 
> Not at the moment.  I was working on code for this, but abandoned it
> when AFNI started moving to NIfTI.  Does AFNI provide tools to convert
> briks to nifti?
> 
>> (4) Is there any command-line program that will apply a mask to a .cub
>> or .tes file and remove anything outside of the mask? [this would be a
>> logical feature for vbthresh, but I don't think it does it]
> 
> vbmaskmunge will do this.  The syntax is a little obscure, but for the
> simplest case you can do this:
> 
> vbaskmunge mask.cub -a statmap.cub -o masked_statmap.cub
> 
>> I realize that there is a new release imminent, but if it's not yet
>> ready, these are some features that would be very useful.
> 
> Some gruesome but necessary changes to vbview and vbsingle are holding
> up the release, but I may be able to get vbthreshcalc plugged into
> vbview as well.
> 
> dan
>