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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