Nice!
On 11 Dec 2011, at 18:09, James Porter wrote:
> Hey Folks-
>
> I've made a script to generate large feat setup files. You can find it here:
>
> https://netfiles.umn.edu/xythoswfs/webui/_xy-20594449_1-t_BJWDfhGf
>
> The script is set up to require some text files that list your inputs, X matrix, contrast vectors, and F-test designations. It also requires a basic .fsf file as a template that has all the other info about your analysis set to go. You could skip the input names part by using the Feat GUI to set up everything but the Stats model and then save that as 'template.fsf.' As noted in the script, I wrote this for use with Darwin for Mac OS X, so most users will need to switch out the parts that use 'jot' in favor of 'seq' or some other numerical list generator.
>
> -Jim
>
> ___
> Jim Porter, M.A.
> Ph.D. Candidate
> Clinical Science and Psychopathology Research
> University of Minnesota
>
>
>
>
>
>
>
>
> Print
>
> Hi Michael,
>
> Ah right, my tip only helps you with the .mat file. The other files, though, are much less of a hassle to construct, but I agree, would be nice if it could be scripted up.
>
> -Tom
>
> On Fri, Dec 9, 2011 at 4:48 PM, Michael Harms <[log in to unmask]> wrote:
> Hi Tom,
> So once you have appropriate .mat, .con, .grp, and .fts files (including
> their header information), you would have to run flameo with appropriate
> inputs from the command line, right? That is, there is no capability to
> use a manually created design matrix in conjunction with the FEAT GUI,
> is there?
>
> thanks,
> -MH
>
> On Fri, 2011-12-09 at 15:56 +0000, Thomas Nichols wrote:
>> If you are comfortable with R, try building your model there and then
>> asking for the model.matrix, i.e.
>>
>>
>> mod=lm(Y~FacA+FacB+Cov+Cov*FacA) # whatever
>> X=model.matrix(mod);
>> write.table(X,'X.dat')
>>
>>
>> Note that R uses "treatment contrasts" to create the dummy variables
>> for categorical (factor) effects; this means that the first level of
>> the factor is the reference and coded with all zeros, which means the
>> intercept will then be interpreted as the fit of that first factor
>> level. Alternatively, you can get 'sum to zero' contrasts (where the
>> first factor level is coded with -1's) by running this before you call
>> lm
>>
>>
>> options(contrasts=c("contr.sum", "contr.helmert"))
>>
>>
>> And if you have a simple model and can afford to have K regressors for
>> a K-level factor variable, you can use simple 1/0 dummy variables.
>> Ask lm to do this by dropping the intercept with this the -1 syntax:
>>
>>
>> mod=lm(Y~-1+FacA)
>>
>>
>> This only works for the first factor variable in the model, though.
>>
>>
>> -Tom
>>
>> On Fri, Dec 9, 2011 at 2:39 PM, Stephen Smith <[log in to unmask]>
>> wrote:
>> Indeed - though it could be scripted without the GUI.
>> Cheers.
>>
>>
>>
>> On 9 Dec 2011, at 14:35, Michael Harms wrote:
>>
>>> Not to my knowledge, unfortunately.
>>>
>>> -MH
>>>
>>> On Fri, 2011-12-09 at 13:48 +0100, Diederick Stoffers wrote:
>>>> Hi,
>>>>
>>>>
>>>> Is there any easy way around using the FEAT GUI for
>>>> setting up huge
>>>> design matrices? It would be great if you could specify
>>>> text files as
>>>> an input in stead of copy/paste into Glm.
>>>>
>>>>
>>>> Cheers,
>>>>
>>>>
>>>> Diederick
>>>>
>>>> Begin forwarded message:
>>>>
>>>>> From: Michael Harms <[log in to unmask]>
>>>>>
>>>>> Subject: Re: [FSL] large quantity glm setup
>>>>>
>>>>> Date: 7 juli 2011 15:40:03 GMT+02:00
>>>>>
>>>>> To: [log in to unmask]
>>>>>
>>>>> Reply-To: FSL - FMRIB's Software Library
>>>>> <[log in to unmask]>
>>>>>
>>>>>
>>>>> The FEAT GUI can be quite challenging to work with when
>>>>> specifying
>>>>> large
>>>>> designs, as it becomes very slow in responding and
>>>>> updating. How
>>>>> big of
>>>>> a design are you trying to specify? Are you having an
>>>>> issue pasting
>>>>> in
>>>>> the values themselves, or is it "freezing" after you
>>>>> Click OK within
>>>>> the
>>>>> Paste Window?
>>>>>
>>>>> That said, with patience we've always been able to use
>>>>> the Paste
>>>>> feature
>>>>> to accomplish what we need.
>>>>>
>>>>> cheers,
>>>>> -MH
>>>>>
>>>>> On Wed, 2011-07-06 at 15:13 -0700, Amy Zhong Sheng Zheng
>>>>> wrote:
>>>>>> Thank you for the response. Do I just copy the numbers
>>>>>> from excel
>>>>>> (or
>>>>>> whichever) and paste them after opening up the paste
>>>>>> button?
>>>>>> Because I
>>>>>> just tried that and every time I tried to paste the
>>>>>> numbers in the
>>>>>> paste window, feat would freeze on me. Have any ideas
>>>>>> why that
>>>>>> might
>>>>>> be the case?
>>>>>>
>>>>>> On Wed, Jul 6, 2011 at 1:59 PM, Michael Harms
>>>>>> <[log in to unmask]>
>>>>>> wrote:
>>>>>> Sure, create it in Excel, Matlab, text editor,
>>>>>> or whatever
>>>>>> is
>>>>>> most
>>>>>> convenient and just use the "Paste" button under
>>>>>> "Full
>>>>>> model
>>>>>> setup".
>>>>>>
>>>>>> cheers,
>>>>>> -MH
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, 2011-07-06 at 20:55 +0100, Amy wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I'm doing an anova with multiple factors and levels
>>>>>>> with
>>>>>> many inputs, so setting up the 1's and -1's on
>>>>>> the glm has
>>>>>> been very tedious. I was wondering if anyone
>>>>>> knows a
>>>>>> faster/efficient way to fill in the values? Is
>>>>>> there a way
>>>>>> to
>>>>>> export from excel and fill that in the
>>>>>> design.fsf?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Amy
>>>>>>
>>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> __________________________________________________________
>> Thomas Nichols, PhD
>> Principal Research Fellow, Head of Neuroimaging Statistics
>> Department of Statistics & Warwick Manufacturing Group
>> University of Warwick, Coventry CV4 7AL, United Kingdom
>>
>>
>> Web: http://go.warwick.ac.uk/tenichols
>> Email: [log in to unmask]
>> Phone, Stats: +44 24761 51086, WMG: +44 24761 50752
>> Fax: +44 24 7652 4532
>>
>>
>>
>>
>>
>
>
>
> --
> __________________________________________________________
> Thomas Nichols, PhD
> Principal Research Fellow, Head of Neuroimaging Statistics
> Department of Statistics & Warwick Manufacturing Group
> University of Warwick, Coventry CV4 7AL, United Kingdom
>
> Web: http://go.warwick.ac.uk/tenichols
> Email: [log in to unmask]
> Phone, Stats: +44 24761 51086, WMG: +44 24761 50752
> Fax: +44 24 7652 4532
>
---------------------------------------------------------------------------
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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