I did get FLOBS working in FSL ver 3.3, which we also had running on our
analysis machine. I had two conceptual questions about the mechanics of
using a set of custom basis functions that I could not gleam from the cited
paper.
First, based on the range of m1, m2, etc. one specifies in FLOBS, are
different HRF shapes (delays, widths, etc.) fit to different voxels in the
GLM analysis? If so, is there a way to generate a map of which shape was
best fit to each voxel?
Second, is using only one basis function with a range of timing (m1, m2,
etc.) values a valid HRF? If not, what is the best way to combine, in a
higher-level analysis, the individual contrast activation maps generated for
each basis function when several are used? When using a custom basis set,
the design matrix seems to appear automatically with only one contrast per
basis function and no way to specify a different design matrix, such as
creating a contrast that averages the basis functions. Could all the COPE
images for the different basis functions for all subjects be averaged
together in a single group analysis, or is that statistically inappropriate
for some reason?
Some insight on these issues would be greatly appreciated.
Thank you,
~Keith
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Steve Smith
Sent: Thursday, October 30, 2008 5:28 AM
To: [log in to unmask]
Subject: Re: Error loading FLOBS directory in GLM
Hi - yes, this is a bug that was reported last week - we'll announce
the fix as soon as it's sorted.
Cheers.
On 29 Oct 2008, at 15:07, Keith Vogt wrote:
> Hello,
>
> I am attempting to create a set of optimal basis functions using
> FLOBS. The
> flobs report seems to be created OK and a directory with 10 files is
> made.
> However, when I try to load this directory for convolution as
> an "Optimal/custom basis function" in the GLM window, I get an error:
> wrong # args: should be "feat5:checkbfcustom w i"
> More details are copied in the attached log file. If I ignore this
> error and try to
> proceed, there is an error in processing the model: "F-test 1 isn't
> valid...",
> even though I haven't explicitly set an F-test. This error seems to
> consistently occur regardless of the number of basis functions used
> in FLOBS,
> the number of EVs set up, or the basic shape specified. This is my
> first time
> using the FLOBS utility, so any help is greatly appreciated.
>
> I'm running FLS version 4.0.3, with FEAT version 5.92 on a Linux
> platform. I
> also tried this on a Windows PC with VMware running the same version
> of FSL
> and the same result occurred.
>
>
> Thanks,
> ~Keith
> <FLOBS_in_GLM.log>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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