Dear Alle,
> After that it goes on with error messages about division by zero.
> Not sure if those lines are useful, but here goes:
>
>> divide by zero
>> while executing
>> "expr $normmean / $median_intensity "
>> (procedure "feat5:proc_prestats" line 406)
this looks like it might be it. This is in ~line 5300 (!) of
featlib.tcl. It appears that median_intensity has the value zero. It
is set a few lines earlier by a call to fslstats.
A guess is that for some reason your volume has significant number of
voxels that are exactly zero, resulting in either of the calls
fslstats $funcdata_unmasked -k mask -p 50
or
fslstats $funcdata -p 90
returning zero.
However, I am afraid that my tcl knowledge is very limited, so I'll
leave it to Steve to figure out exactly what is going on here.
Good Luck Jesper
>> invoked from within
>> "feat5:proc_prestats $session "
>> ("-prestats" arm line 2)
>> invoked from within
>> "switch -- [ lindex $argv $argindex ] {
>> -I {
>> incr argindex 1
>> set session [ lindex $argv $argindex ]
>> }
>> -D {
>> incr argindex 1
>> set..."
>> ("for" body line 2)
>> invoked from within
>> "for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>> switch -- [ lindex $argv $argindex ] {
>> -I {
>> incr argindex 1
>> set ses..."
>> (file "/usr/local/fsl-4.1.1-x86_64/fsl/bin/feat" line 137)
>
> (I don't know if this comes from the fslmaths command or the one
> after that)
>
> So bottom line, masking is done in FEAT both with BET and without
> BET. It would be nice to be able to switch it off.
>
> bw
> Alle Meije
>
>> Dear Alle,
>>> Is it possible in some way to switch off masking in the FEAT
>>> analysis? I have some test data which looks normal, but the
>>> masking at the end of preprocessing removes almost the whole
>>> image. The stats are now only done on an uninteresting part of
>>> the image.
>> this is rather surprising. The masking is based on running BET on
>> the first image of the time series. Might it be that there is a
>> problem with that particular volume?
>> If not, you can just turn off "Bet brain extraction" in the Pre-
>> stats.
>> Good luck Jesper
>
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