Just use the 'ptoz' command without the -g switch:
Z=`ptoz 0.05`; # gives you the uncorrected z-threshold for p=0.05
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. 16:05 keltezéssel, Lucas Eggert írta:
> Perfect!
>
> Thank you very much!
>
> Last question regarding these kinds of conversions:
>
> How do I determine the corrected and the uncorrected p-value for a
> given Z-value?
>
> Thank you again!
>
> All the best,
> -Lucas
>> 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
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
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