Thanks so much!
-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 May 6, 2010, at 8:32 AM, Matthew Webster wrote:
> Hi,
> Yes, the most recent ubuntu patch should fix this.
>
> Many Regards
>
> Matthew
>
>> Hi Matthew,
>>
>> I haven't heard anything regarding this, and I'm just curious whether you were to replicate the issue I found, and whether the recent update to flameo fixes this.
>>
>> Any update would be welcome.
>>
>> Thank you!
>>
>> -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 26, 2010, at 12:51 PM, Reynolds, Jeremy wrote:
>>
>>> 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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