There was a discussion on the freesurfer email list where BET was used
successfully for monkey segmentation.  You might check the freesurfer archives
and follow up with the authors...

Cheers, Darren

----- Original Message -----
From: "Mark Jenkinson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Wednesday, August 21, 2002 11:06 AM
Subject: [FSL] FSL and primates


> Hi,
>
> This is a forward of a series of emails that I have been dealing
> with about using FSL with non-human brains.  I thought this would
> be of interest to people reading this list.
>
> The last issue is also unresolved and any suggestions would be good
> (I've some suspicions but would like to have them confirmed).
>
> Here are the emails (last one at the end)...
>
> Cheers,
>         Mark
>
>
>
>
> -----Original Message-----
> From: Mark Jenkinson [mailto:[log in to unmask]]
> Sent: Saturday, August 03, 2002 12:13 AM
> To: Gaby Pell
> Subject: Re: FSK
>
>
>  > A colleague of mine is using FSL for some fMRI analysis.
>  > He has been having problems with errors which he says have only been
>  > occurring when running primate analysis - not human experiments.
>
>  > Is FSL somehow anti-vivisectionist or something?!
>
> Actually, yes!
> A lot of FSL routines are tuned to work with human sized brains.
> Hence the defaults for natural voxel sizes, FOVs etc only work properly with
human images.
>
> The ones that are particularly sensitive are:
> BET - I suspect it never works properly on non-human images
> FLIRT and MCFLIRT - forces 8,4,2,1mm scales which are not appropriate for
small
> images/brains.
>
> Both FAST (after the non-brain structures are removed) and the stats for FEAT
(if appropriate
> values for smoothing etc are chosen) should be fine.
>
> One solution is often to change the voxel size to make the brain more
human-sized.
> This often fixes the problems - although manual brain extraction might still
be necessary.
>
> Cheers,
> Mark
>
>
> ------------------------------------------------------------------------------
---------
>
> -----Original Message-----
> From: Mark Jenkinson [mailto:]
> Sent: Monday, August 05, 2002 12:44 PM
> To: Lipton, Michael
> Subject: Re: FSK
>
> Hi,
>
>  > So there is some logic to this issue. The feat error file (enclosed)
>  > seems to complain at the autocorrelation step. Would changing the
>  > voxel size defaults
>  >
>  > (if that's possible) be possible in McFlirt?
>  >
> The error could easily be a knock-on from failure in motion
> correction or something.
> It sounds like a blank image is getting generated at some point, and
> without examining the data step by step there isn't much I can do.
>
> To change the voxel size is pretty easy though, and should be
> tried. This just needs a new header file to be made with the
> appropriate info. Use avwcreatehd with most parameters copied
> from the previous header (find them using avwhd)
> but with the voxel size changed by globally scaling it up so that the
> new voxel size makes the brain size in mm about right for a human.
> Hopefully this will fix the problems with mcflirt.
>
> As for bet - just turn it off within FEAT - that's the
> easiest and best option.
>
> Cheers,
> Mark
>
>
> ------------------------------------------------------------------------------
----------
>
> -----Original Message-----
> From: Lipton, Michael
> Sent: Monday, August 05, 2002 12:44 PM
> To: Mark Jenkinson
> Subject: Re: FSK
>
> Thanks for the feedback.
>
> I scaled the data up by a factor of three and turned off both BET and MCFLIRT
(there is essentially 0 motion in the data
> anyway). The analysis goes further but still dies in an error before
completing. From my uninitiated look at the output
> it seems that the autocorrelation worked, but something later on in the
analysis (?rendering?) goes bad.
>
> If you don't mind having a look at the attached file, I would be very grateful
for any suggestion.
>
> Best,
>
> Michael
>
>
>
> Started FEAT at Thu Aug 15 10:38:56 EDT 2002 on chiana
> Total original volumes = 180
> /usr/local/fsl/bin/avwroi /data/lipton/monkey/scaled
/data/lipton/monkey/scaled.feat/example_func 90 1
>
> /usr/local/fsl/bin/ip /data/lipton/monkey/scaled
/data/lipton/monkey/scaled.feat/filtered_func_data 10 -s 1.27388535032
> -m /data/lipton/monkey/scaled.feat/mask -I 10000 -t 15.0 -1
> rm -rf /data/lipton/monkey/scaled.feat/prefiltered_func_data*
>
> /usr/local/fsl/bin/film_gls -rn /data/lipton/monkey/scaled.feat/stats -sa -ms
5 -sp /usr/local/fsl/bin/susan_smooth
> /data/lipton/monkey/scaled.feat/filtered_func_data
/data/lipton/monkey/scaled.feat/design.mat 23.205000
> Log directory is: /data/lipton/monkey/scaled.feat/stats
> Loading image... Completed
> Applying threshold to Series... Completed
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 254
> sig = 0
> Spatially smoothing auto corr estimates
> /usr/local/fsl/bin/susan_smooth
/data/lipton/monkey/scaled.feat/stats/preSmoothVol 1
> /data/lipton/monkey/scaled.feat/stats/postSmoothVol 5 3D 0 1
/data/lipton/monkey/scaled.feat/stats/epivolume 0
> /data/lipton/monkey/scaled.feat/stats/usanSize
> ......................................
> rm -rf /data/lipton/monkey/scaled.feat/stats/postSmoothVol*
/data/lipton/monkey/scaled.feat/stats/preSmoothVol*
> /data/lipton/monkey/scaled.feat/stats/usanSize* Completed
> Tukey M = 13
> Tukey estimates... Completed
> Completed
> Prewhitening and Computing PEs...
> 0.63075,Completed
> Saving results...
> Unthresholding Series... Completed
> Saving image... Completed
> Thresholding Series... Completed
> Unthresholding Series... Completed
> Saving image... Completed
> Unthresholding Series... Completed
> Saving image... Completed
> Completed
> /usr/local/fsl/bin/smoothest -d 1.780000e+02 -m
/data/lipton/monkey/scaled.feat/mask -r
> /data/lipton/monkey/scaled.feat/stats/res4d >
/data/lipton/monkey/scaled.feat/stats/smoothness
>
> rm -f /data/lipton/monkey/scaled.feat/stats/res4d*
>
> /usr/local/fsl/bin/contrast_mgr  /data/lipton/monkey/scaled.feat/stats
/data/lipton/monkey/scaled.feat/design.con
> Loading image... Completed
> Thresholding Series... Completed
> /usr/local/fsl/bin/avwmaths /data/lipton/monkey/scaled.feat/stats/zstat1 -mul
/data/lipton/monkey/scaled.feat/mask
> /data/lipton/monkey/scaled.feat/thresh_zstat1domain error: argument not in
valid range
>      while executing
> "expr int ( $VOLUME / $RESELS ) "
>      (procedure "feat4:poststats" line 57)
>      invoked from within
> "feat4:poststats 0"
>      (procedure "feat4:proc" line 328)
>      invoked from within
> "feat4:proc [ file rootname [ lindex $argv 0 ] ]"
>      (file "/usr/local/fsl/bin/feat" line 17)
>
> MaximumZ(1)=0.000000
>