Dear Lucas,
No. ptoz is an FSL-command. Its syntax is (for a p=0.05)
ptoz 0.05 -g <number of resels>
Number of resels can be calculated based on the 'smoothest' command or
(even better) based on the information you can find in the
"*.feat/stats/smoothness" file:
number of resels = VOLUME / RESELS
Then, the 'ptoz' command will give you the z-threshold for p = 0.05 (or
any) corrected for FWE
In the next step, you just have to threshold your zstat with the given
z-value:
After you have stored the VOLUME and RESEL information in the respective
variable: e.g.:
VOLUME=47487
RESEL=2.34
NRES=`echo "scale=4; $VOLUME / $RESEL" | bc`; # you need 'bc', because
this is a floating point operation
Z=`ptoz 0.05 -g $NRES`;
fslmaths zstat1 -thr $Z $thresholded_zstat1
I hope it helps,
Auer, Tibor M.D. Ph.D.
Biomedizinische NMR Forschungs GmbH
am Max-Planck Institut für Biophysikalische Chemie
Am Fassberg 11
37077 Göttingen
Germany
Phone/Work: +49-(0)551-201-1725
Phone/Home: +49-(0)551-387-0076
Mobile: +49-(0)176-8012-7921
Mail: [log in to unmask]
2010.09.14. 13:36 keltezéssel, Lucas Eggert írta:
> Dear Tibor,
>> Dear Lucas,
>>
>> AFAIK, you cannot convert a z-map to FWE-p-map; but if your goal is
>> to threshold your z-map with FWE, then you can calculate the z(p=0.05
>> FWE) threshold with ptoz command with using the -g switch.
> That is exactly what I want to do: Determine the Z-value that
> represents a p-value of e.g. 0.05 (FWE-corrected).
>
> However, I do not understand what you mean with '-g switch'. Do you
> mean something like
>
> fslmaths zstat1.nii.gz -g -ptoz output.nii.gz?
>
> Thank you very much!
> -Lucas
>
>>
>> Bests,
>>
>> Auer, Tibor M.D. Ph.D.
>> Biomedizinische NMR Forschungs GmbH
>> am Max-Planck Institut für Biophysikalische Chemie
>> Am Fassberg 11
>> 37077 Göttingen
>> Germany
>> Phone/Work: +49-(0)551-201-1725
>> Phone/Home: +49-(0)551-387-0076
>> Mobile: +49-(0)176-8012-7921
>> Mail: [log in to unmask]
>>
>>
>>
>> 2010.09.14. 12:32 keltezéssel, Lucas Eggert írta:
>>> Dear Experts!
>>>
>>> How can I determine the FWE-corrected p-Value for a given Z-value?
>>>
>>> I tried
>>>
>>> fslmaths zstat1.nii.gz -cpval fwe-corrected.nii.gz
>>>
>>> ... but that results in an image with only values of 1 in every voxel.
>>>
>>> Best wishes,
>>> -Lucas
>>>
>>
>>
>
>
|