On Thu, 22 Jan 2009 08:30:36 +0000, Steve Smith <[log in to unmask]> wrote:
Hi FSL users,
I had a question in regards to family-wise error vs FDR correction.
Which of these would show more results when doing a two group comparison?
Is one more stringent than the other? I tried to use FDR after running
randomise but I received statistical significance in several areas across
the brain as opposed to the corrp_tstat1 file(familywise error). I am not
sure if my FDR is correct or which of the two results is more valid?
Below are the fdr commands I used.
randomise -i GM_mod_merg_s2 -m GM_mask -o GM_mod_merg_s2 -d design.mat -t
design.con -T -n 5000 -V
>>output file is GM_mod_merg_s2_tfce_p_tstat1
fslmaths GM_mod_merg_s2_tfce_p_tstat1 -mul -1 -add 1
1_minus_GM_mod_merg_s2_tfce_p_tstat1
fdr -i 1_minus_GM_mod_merg_s2_tfce_p_tstat1 -m GM_mask -q 0.05
>>after this step it said the threshold is 0 even though I entered 0.05, so
not sure why?
fslmaths GM_mod_merg_s2_tfce_p_tstat1 -thr .95
thresh_GM_mod_merg_s2_tfce_p_tstat1
fslview $FSLDIR/data/standard/MNI152_T1_2mm thresh_fslvbm_tfce_p_tstat1 -l
Red-Yellow -b 0.95,1
Thanks,
Ajay Kurani
>Hi - yes I'm pretty sure this would be fine. FDR won't give the same
>results as the (family-wise-error rate) corrected p-values, but it is
>valid.
>
>Cheers, Steve.
>
>
>
>On 22 Jan 2009, at 08:10, Eric Kan wrote:
>
>> Hi Steve,
>> thanks for your reply. So unfortunately I do need corrected p values
>> as you have guessed. And I also need to get around resource issues
>> with my particular dataset+ randomise...
>>
>> would it be ok to take the uncorrected p values (tfce_p_tstatX
>> files) that are generated and run them through a fdr to handle the
>> multiple comparison correction?
>>
>> So something like this:
>> 1) Chop up image, run randomise tfce
>> 2) Recombine uncorrected pvalue volume back to single volume
>> 3) Perform fdr correction on volume and threshold accordingly to
>> output
>>
>> Would that work? I notice on the website they using the voxel-based
>> thresholding in the example. Would fdr work for tfce as well or is
>> it specific to vox analysis? (sorry my statistics is very shaky so
>> hopefully this isn't too silly a question)
>>
>> Thanks!
>> Eric
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of Steve Smith [[log in to unmask]]
>> Sent: Wednesday, January 21, 2009 11:41 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Randomise mask
>>
>> Hi - if you are just wanting uncorrected voxelwise p-values then
>> that's ok. However you are most likely needing p-values that are
>> corrected for multiple comparisons across all voxels, in which case
>> I'm afraid that chopping up the images like this is not allowed,
>> sorry!
>>
>> Steve.
>>
>>
>> On 22 Jan 2009, at 01:58, Eric Kan wrote:
>>
>>> Hello,
>>>
>>> I have some TBM data that I have been trying to pass through FSL's
>>> randomise
>>> program to do the statistics. My progress is in the original thread
>>> was
>>> titled "Radomise_parallel with data generated outside FSL"
>>>
>>> Specifically the issue was that randomise_parallel was not running
>>> through
>>> to completion due to lack of adequate resources on our computer
>>> nodes (each
>>> TBM volume is ~20MB in size, 31 volumes total).
>>>
>>> As a workaround, I tried to chop up the volume into 11 separate rois
>>> (via
>>> -mask) to compute statistics individually, and then recombining each
>>> piece
>>> via fslmaths -add to get my whole volume again. This seemed to work
>>> well
>>> from the standpoint of getting the data to run through to completion
>>> on the
>>> compute nodes.
>>>
>>> I'm concerned however, that by arbitrarily chopping up the volume,
>>> I'm
>>> changing the statistical outcome when compared to analyzing the
>>> volume as a
>>> whole.
>>>
>>> Does anyone know if doing what I did changes the statistical outcome
>>> of my
>>> data?
>>>
>>> Thanks for any input you can give...
>>>
>>> I ran a threshold free analysis:
>>> randomise_parallel -i <input 4D data> -o OUT -d design.mat -t
>>> design.con -m
>>> mask_(1-11) -n 1000 -D -T
>>>
>>> Eric
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>>
>
>
>---------------------------------------------------------------------------
>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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