I won't comment on the feat-specific aspect of this, but just as
a sanity check I simulated Z's and checked the two approaches as
follows...
fslmaths
$FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -randn z -odt float
fslmaths
$FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -add 1 var -odt float
ttologp
-logpout logp var z 200
fslmaths
logp -exp logp2p -odt float
fslmaths
z -ztop z2p -odt float
fslmaths
p -div ztop p-div-ztop
fslmaths
p -sub ztop p-ztop
Here, I find that logp2p and z2p are virtually identical except
for the the largest z-values, and the differences there are explained
by the difference between the exact 'Z' p-value and totologp
incorrectly regarding my Z's as a T with 200 DF.
As far as I can tell all of your files should be at
float precision, but can you double check that all of your intermediary
files are float (with fslinfo, and the first 'data_type' line)?
-Tom
On Thu, Jun 17, 2010 at 12:09 PM, wolf zinke
<[log in to unmask]>
wrote:
Hi Stephen,
Since in fslmaths it is not stated that there is the choice between
one-sided and two-sided I did assume that it is for one-sided tests.
I was creating a p-value image as described on the fdr-webpage:
ttologp -logpout logp1 varcope1 cope1 `cat dof`
fslmaths logp1 -exp p1
and also one with the fslmaths method:
fslmaths zstat1.nii.gz -ztop fm_p
just to asses the difference of both resulting images I subtracted them
from each other:
fslmaths fm_p -sub p1 pdiff
and additional the ratio of both images:
fslmaths fm_p -div p1 prat
The histogram of the ratio image shows a peak at 0.5, so maybe it is a
tailing-issue, but it is not a clear factor 2 difference between both
images, so maybe there is an additional differenced caused by
roundings. Is the fslmaths -ztop option for a two-tailed conversion?
Thanks for the help
wolf
Stephen Smith wrote:
Hi - how different are they? Is it just a
factor of two -
i.e. in one case you're assuming two-tailed testing and in the other
one-tailed?
Cheers.
On 8 Jun 2010, at 15:48, wolf zinke wrote:
Hi,
I hope this is not an obvious stupid question ;-) . I want to prepare
data for an FDR correction, which requires an image of p values as
input. The FDR website describes how to obtain a p-value image by using
ttologp with the varcope and cope files as input and feeding the
resulting file into fslmaths with the -exp option. I was now wondering
if I could not just transform the available z-value image to a p-value
image just by using one fslmaths call with the -ztop option. However,
the p-value images of both methods are not identical. What is the
difference between both methods? Is it possible to transform just the
zstats to prepare the data for an FDR correction?
Thanks for any comments,
wolf
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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)
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http://www.fmrib.ox.ac.uk/~steve
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____________________________________________
Thomas Nichols, PhD
Principal Research Fellow, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick
Coventry CV4 7AL
United Kingdom
Email:
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