Sorry!
Uncorrected is easy: there is a `ztop` command:
ztop 3.5 --> 0.000233: this is an uncorrected p.
For corrected however...
I would simply try a "manual iterative" approach. :-) Of course, you can
script it.
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. 16:15 keltezéssel, Lucas Eggert írta:
> No, I mean the other way around:
>
> Let's assume, I have use Z=3.5 to threshold my statistical map, and
> now I would like to know what the corresponding p-Level of this
> threshold is (corrected and uncorrected).
>> 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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