Hi Matthew,
Sorry for the delay. Here's the requested information.
FSL 4.1.4
Kubuntu 9.04 x86_64
Thanks!
-Jeremy
Jeremy Reynolds, Ph.D.
Assistant Professor
Department of Psychology,
University of Denver
2155 S. Race St
Denver, CO 80208
Phone: 303.871.4622
Fax: 303.871.4747
[log in to unmask]
On Apr 23, 2010, at 6:24 AM, Matthew Webster wrote:
> Hi,
> Many Thanks - can you confirm which version and architecture of FSL you are using?
>
> Many Regards
>
> Matthew
>
>> Hi Matthew,
>>
>> Done. The reference number is 429010.
>>
>> Thanks again!
>>
>> -Jeremy
>>
>> Jeremy Reynolds, Ph.D.
>> Assistant Professor
>> Department of Psychology,
>> University of Denver
>> 2155 S. Race St
>> Denver, CO 80208
>> Phone: 303.871.4622
>> Fax: 303.871.4747
>> [log in to unmask]
>>
>> On Apr 22, 2010, at 2:17 AM, Matthew Webster wrote:
>>
>>> Hello,
>>> Thank you for the files - could you also upload the associated FEAT directory ( it would help enormously if we had access to the filtered_func data etc )
>>>
>>> Many Regards
>>>
>>> Matthew
>>>
>>>>
>>>>> From: "Reynolds, Jeremy" <[log in to unmask]>
>>>>> Date: 19 April 2010 18:22:15 BST
>>>>> To: "[log in to unmask]" <[log in to unmask]>
>>>>> Subject: Re: [FSL] zfstat, fstat, zflame1lowerfstat
>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>
>>>>> Thanks so much for the help tracking this down. The file is uploaded, and the reference number is 355348.
>>>>>
>>>>> Please let me know if you need anything else -- logfiles, etc.
>>>>>
>>>>> Thanks again!
>>>>>
>>>>> -Jeremy
>>>>>
>>>>> Jeremy Reynolds, Ph.D.
>>>>> Assistant Professor
>>>>> Department of Psychology,
>>>>> University of Denver
>>>>> 2155 S. Race St
>>>>> Denver, CO 80208
>>>>> Phone: 303.871.4622
>>>>> Fax: 303.871.4747
>>>>> [log in to unmask]
>>>>>
>>>>> On Apr 19, 2010, at 4:21 AM, Mark Woolrich wrote:
>>>>>
>>>>>> Hi Jeremy,
>>>>>>
>>>>>> OK. Will need to take a look at this. Please could you upload the
>>>>>> stats directory in question
>>>>>>
>>>>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>>>>>
>>>>>> and then email me the upload ID.
>>>>>>
>>>>>> Cheers, Mark.
>>>>>>
>>>>>> On 10 Apr 2010, at 19:58, Reynolds, Jeremy wrote:
>>>>>>
>>>>>>> Hi Mark,
>>>>>>>
>>>>>>> Thanks for the response. I am just using flame1, so that is helpful.
>>>>>>>
>>>>>>> As for image size -- I am attaching a larger version below, but I'm
>>>>>>> not sure if I can go any larger due to the limits of the mailing
>>>>>>> list. Let me know if this is still not large enough.
>>>>>>>
>>>>>>> Thanks again.
>>>>>>>
>>>>>>> -J
>>>>>>>
>>>>>>> <Screen shot 2010-04-06 at 10.36.31 AM.gif><ATT00001..txt>
>>>>
>>>>> Hello all,
>>>>>
>>>>> I am having some difficulty understanding the relationship between
>>>>> the fstatX and zfstatX (and zflame1lowerfstatX) files produced by
>>>>> flameo (running flame1), and I was wondering if someone could help
>>>>> me out.
>>>>>
>>>>> After looking at the source of flameo and gsmanager.cc, I can see
>>>>> that zfstatX is the same as zflame1lowerfstatX, which is consistent
>>>>> with my results. What confuses me, though, is that these 2 files are
>>>>> not the same as if I performed:
>>>>>
>>>>> ftoz -zout zfstatX_f2zredo fstatX fdof1_fX fdof2_fX
>>>>>
>>>>> despite the fact that my look at the source code seemed to indicate
>>>>> that the z statistic should be created with very similar internal
>>>>> calls across ftoz and flameo (in Gsmanager::f_ols_contrast within
>>>>> flameo). Because the z-converted files are not the same, I'm not
>>>>> sure which file I should trust to use for inference. The fstat file
>>>>> (and the zfstat file produced by an explicit call to ftoz) looks
>>>>> like what I would expect, in that the image histogram looks
>>>>> continuous, and the spatial distribution of those statistics across
>>>>> the brain looks exactly like I would expect. The zfstat file
>>>>> produced directly by flameo looks like a thresholded image in which
>>>>> the absolute value of all voxels is greater than approximately 5.75.
>>>>> I have attached a picture of the three image histograms, with the
>>>>> fstat image on the left, the zfstat image produced by flameo in the
>>>>> middle, and the zfstat file produced by a call at the command line
>>>>> to ftoz.
>>>>>
>>>>> To help with interpretation, here is some more information regarding
>>>>> my design. In the first-level analysis, I am attempting to use FIR
>>>>> basis functions to estimate a timecourse in response to various
>>>>> stimulus conditions. I am using a set of 10 delta functions that
>>>>> span the 20 s following stimulus onset. I am then using a second-
>>>>> level model on the copes reflecting each of the delta functions,
>>>>> such that I have 10 copes for each of the 18 subjects (180 input
>>>>> files total). In the second-level model, I am using an intercept (1
>>>>> regressor) and dummy coded factors for subject (17 regressors, each
>>>>> corresponding to the presence of a different subject) and timepoint
>>>>> (9 regressors, each corresponding to the presence of a different
>>>>> time point). The f statistic of interest is the main effect of
>>>>> timepoint, which should have a first degree of freedom of 9, and a
>>>>> second degree of freedom of 153 (the fdof1_fX and fdof2_fX files do
>>>>> reflect this).
>>>>>
>>>>> Any help would be much appreciated. Thanks in advance.
>>>>
>>>
>>
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