Hi Anderson,
On returning to this to add my F-tests, I noticed that Flameo also
generates "zfstat" files that appear to correspond to the fstat files. So
that means maybe I don't need to manually convert the F-tests to Zstats
using ftoz myself before running cluster correction?
However, when I use these Flameo generated files with cluster vs. my own
generated fzstat files, I get totally different thresholding results. For
example, when I manually use ftoz, using the degrees of freedom, I get
rather large clusters surviving for all 4 of my f-tests. When I run cluster
with the Flameo generated zfstat files, I get virtually no clusters across
all 4 f-tests (at the same t=3.1 and p0.01 threshold).
So I am confused, because in theory they should be the same exact data, and
therefore yield the same exact clusters. Can you please provide some
insight as to (a) whether I am doing the ftoz wrong or (b) whether the
zfstat represents something else, that I shouldn't use?
Thanks! see my code below, in case helpful.
Michelle
############# STEP 1 ############
#get smoothness estimates for the whole brain using mask
#DOF for design 3 = 225 - 83 = 142
smoothest -d 142 -r res4d.nii.gz -m mask.nii.gz >>
cluster_correction/smoothness_output_wholebrain_mask.txt
########## STEP 2 convert your F stat files #########
foreach f(1 2 3 4)
# convert F test into Z test for design 1
# note sure if i need to do this... .
# number of columns in F test contrast = 24
# number of rows in contrasts = 142
ftoz -zout fzstat${f}_converted fstat${f} 24 142
#mask zstat image using ANATOMICAL brain mask
# "fzstat converted" version is the file I generated using ftoz
# "zfstat" version is the Flameo generated file
fslmaths zfstat${f}.nii.gz -mas mask.nii.gz zfstat${f}_mask.nii.gz
fslmaths fzstat${f}_converted -mas mask.nii.gz
fzstat${f}_converted_mask.nii.gz
end
############# STEP 3 ############
#####cluster-wise hypothesis testing for voxels passing threshold tcd cl
#REQUIRES GETTING INPUTS FROM SMOOTHEST FILE
#DLH 0.0444563
#VOLUME 226501
#RESELS 104.047
cd cluster_correction/
foreach f (1 2 3 4)
# for "zfstat" version Flameo generated file
cluster -i ../zfstat${f}_mask.nii.gz -t 3.1 -o
zfstat${f}_corrected_clusters_3.1_p.01 -d 0.044 --volume=226501 -p .01
--othresh=fsztat${f}_corrected_thresh_3.1_p.01.nii.gz >
cluster_info_wholebrain_3.1_fzstat${f}_corrected_p.01.txt
# for "fzstat converted" - my version generated using ftoz
cluster -i ../fzstat${f}_converted_mask.nii.gz -t 3.1 -o
fzstat${f}_converted_corrected_clusters_3.1_p.01 -d 0.044 --volume=226501
-p .01 --othresh=fzstat${f}_converted_corrected_thresh_3.1_p.01.nii.gz >
cluster_info_wholebrain_3.1_fzstat${f}_converted_corrected_p.01.txt
end
On Mon, Dec 12, 2016 at 11:13 AM, Anderson M. Winkler <
[log in to unmask]> wrote:
> Hi Michelle,
>
> One correction: the dof1 should be the dof of the numerator, so you'd swap
> the first and second values.
>
> All the best,
>
> Anderson
>
>
> On 9 December 2016 at 11:11, Anderson M. Winkler <[log in to unmask]>
> wrote:
>
>> Hi Michelle,
>>
>> Yes, the conversion is right. Re: large design, I'm not sure if there is
>> a script that would do it... sorry.
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 8 December 2016 at 18:02, Michelle VanTieghem <
>> [log in to unmask]> wrote:
>>
>>> Hi Anderson,
>>>
>>> So If I have 24 rows of my design1_contrast.con file, and then 24
>>> columns of my ftest file, then the numerator of df is 24, correct?
>>>
>>> ftoz -zout fzstat fstat1 134 24
>>>
>>> Would give me the correctly converted Z statistic for my F-tests?
>>>
>>> Also, you recommended using FEAT instead of the command line. Did you
>>> mean setting it up in the FEAT gui? I haven't been doing that because the
>>> FEAT gui freezes when I try to enter this model, because it has so many
>>> EVs. I cannot get a work around so that this doesn't happen. If you have
>>> any suggests I would greatly appreciate!
>>> Alternatively, is there a way to hand-make the .fsf file without having
>>> to open the GUI to enter my design? Can I use a .fsf file to only perform
>>> cluster thresholding on the f-test files?
>>>
>>> Thanks!
>>>
>>> On Thu, Dec 8, 2016 at 5:33 AM, Anderson M. Winkler <
>>> [log in to unmask]> wrote:
>>>
>>>> Hi Michelle,
>>>>
>>>> F-tests have the same DOF as the t-test (for the denominator). For the
>>>> numerator, the t test has always df=1 (usually omitted) and the F-test has
>>>> DOF that is the same as the number of lines in the contrast (e.g., for a
>>>> simple 3 group comparison with or without nuisance variables, it's 2).
>>>>
>>>> All the best,
>>>>
>>>> Anderson
>>>>
>>>>
>>>> On 7 December 2016 at 18:31, Michelle VanTieghem <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> Hi Anderson,
>>>>>
>>>>> Also, how do I determine the DOF for my F-tests?
>>>>> For the z-tests I was using # rows in the design - # of columns (207 -
>>>>> 77 = 134)
>>>>> However, I'm having trouble thinking about what it should be for
>>>>> Ftests since this is a mixed effects design...
>>>>> thanks,
>>>>> Michelle
>>>>>
>>>>> On Wed, Dec 7, 2016 at 8:39 AM, Michelle VanTieghem <
>>>>> [log in to unmask]> wrote:
>>>>>
>>>>>> Hi Anderson,
>>>>>>
>>>>>> Do you mean setting it up in the FEAT gui? I haven't been doing that
>>>>>> because the FEAT gui freezes when I try to enter this model, because it
>>>>>> has so many EVs. Is there a way to use an .fsf file without having to open
>>>>>> the GUI to enter my design? Can I use a .fsf file to only perform cluster
>>>>>> thresholding on the f-test files?
>>>>>>
>>>>>> Thanks!
>>>>>> M
>>>>>>
>>>>>> On Wed, Dec 7, 2016 at 2:55 AM, Anderson M. Winkler <
>>>>>> [log in to unmask]> wrote:
>>>>>>
>>>>>>> Hi Michelle,
>>>>>>>
>>>>>>> You'd use ftoz to convert to a z-score map. That said, if you'll use
>>>>>>> the random field theory for inference, it might be much simpler and less
>>>>>>> error-prone to simply use FEAT. It does everything for you and you don't
>>>>>>> have to worry about these commands.
>>>>>>>
>>>>>>> All the best,
>>>>>>>
>>>>>>> Anderson
>>>>>>>
>>>>>>>
>>>>>>> On 6 December 2016 at 21:33, Michelle VanTieghem <
>>>>>>> [log in to unmask]> wrote:
>>>>>>>
>>>>>>>> Hi Anderson,
>>>>>>>>
>>>>>>>> Ok great thanks. I have run the f-tests. Now I would like to use
>>>>>>>> smoothest and cluster in order to identify significant clusters of
>>>>>>>> activation for F4, the Group x Emotion interaction. However, cluster, as
>>>>>>>> far as I can tell from the information on FSL wiki, is used with zstat
>>>>>>>> files.
>>>>>>>> Can I do the same exact thing, but replace zstat files (of a
>>>>>>>> specific contrast) with the fstat files (to test the omnibus interaction)?
>>>>>>>> When testing F-tests in cluster, does make sense to use a t-
>>>>>>>> threshold (e.g. 3.1)?
>>>>>>>> I would think there should be F threshold, but that doesn't appear
>>>>>>>> to be an option in cluster....
>>>>>>>> Here is an example of what I would like to do:
>>>>>>>>
>>>>>>>> smoothest -d 134 -r res4d.nii.gz -m mask.nii.gz >>
>>>>>>>> cluster_correction/smoothness_output_wholebrain_mask.txt
>>>>>>>>
>>>>>>>> fslmaths fstat4.nii.gz -mas mask.nii.gz
>>>>>>>> cluster_correction/fstat4_mask.nii.gz
>>>>>>>>
>>>>>>>> cluster -i fstat4_mask.nii.gz -t 3.1 -o fstat4_clusters_3.1 -d
>>>>>>>> 0.043 --volume=234781 -p .05 --othresh=fstat4_thresh_3.1.nii.gz >
>>>>>>>> cluster_info_wholebrain_3.1_fstat4.txt
>>>>>>>>
>>>>>>>> I appreciate any input!
>>>>>>>> Thank you,
>>>>>>>> Michelle
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Michelle VanTieghem
>>>>>> PhD student in Psychology
>>>>>> Developmental Affective Neuroscience Lab
>>>>>> Columbia University
>>>>>> [log in to unmask]
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Michelle VanTieghem
>>>>> PhD student in Psychology
>>>>> Developmental Affective Neuroscience Lab
>>>>> Columbia University
>>>>> [log in to unmask]
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Michelle VanTieghem
>>> PhD student in Psychology
>>> Developmental Affective Neuroscience Lab
>>> Columbia University
>>> [log in to unmask]
>>>
>>
>>
>
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
[log in to unmask]
