Hi Mark,
thanks for the explanation. This makes sense now. I actually noticed,
that my analysis ran faster than usual.
Just one more idea - in future updates in might be useful to avoid
changes which could interfere with other command-line tools without
notice. An error message (something like "This FEAT option has been
deprecated in design.fsf...") would help me to figure out what's wrong
earlier. Another way would be to leave the option and reroute the
pipeline so that the scripts could produce same/similar output, even
though doing an extra analysis step...
Thank a lot!
Cheers
On 6 August 2014 10:31, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> This option is gone for good and for strong reasons.
> We found that the amount of RAM and disk space used to create and store the necessary covariance matrices to allow for completely general and separate post-stats was becoming huge for many common designs and prevented certain designs from being run at all. However, most of this was unnecessary computation and storage as only a handful of contrasts would be wanted, even when there were quite a lot of EVs. Consequently we took the decision to reduce the computational burden and memory/disk overhead by coupling stats and post-stats together, so that only the stats for the requested contrasts were calculated. This has had huge benefits (in our lab and in others) and is something that we are definitely going to stick with.
>
> If you are just going to re-threshold then I suggest that you either use the individual command-line tools to do the re-thresholding or run Stats and Post-stats together again. The stats part should be noticeably faster now in many cases too, so this might not be so problematic.
>
> All the best,
> Mark
>
> P.S. we will answer the question about overwrite_yn in a separate email.
>
>
>
>
> On 5 Aug 2014, at 16:25, Pavel Hok <[log in to unmask]> wrote:
>
>> Dear FSL experts,
>>
>> after an upgrade an option to run post-stats only is missing in the
>> Feat GUI, the same in design.fsf generated by Feat. Is that option
>> gone for good? What is the rationale behind this? I was using this in
>> my scripts to speed up some re-thresholding tasks. Does that mean,
>> that I have to re-run Stats every time now? Thanks!
>>
>> Cheers
>>
>> Pavel
>>
>> --
>> -------------------------------------------------------------------------------
>> -- MUDr. Pavel Hok
>> -------------------------------------------------------------------------------
>> -- Laboratoř funkční magnetické rezonance
>> -- Neurologická klinika
>> -- Lékařská fakulta
>> -- Univerzita Palackého v Olomouci
>> -- Fakultní nemocnice Olomouc
>> -------------------------------------------------------------------------------
>> -- Laboratory of functional magnetic resonance imaging
>> -- Department of Neurology
>> -- Faculty of Medicine and Dentistry
>> -- Palacky University Olomouc
>> -- University Hospital Olomouc
>> -- Czech Republic
>> -------------------------------------------------------------------------------
>> -- I.P. Pavlova 6, 775 20 Olomouc
>> -- web: fmri.upol.cz
>> -- tel.: +420 588 443 418
>> -- e-mail: [log in to unmask]
>> -------------------------------------------------------------------------------
>
--
-------------------------------------------------------------------------------
-- MUDr. Pavel Hok
-------------------------------------------------------------------------------
-- Laboratoř funkční magnetické rezonance
-- Neurologická klinika
-- Lékařská fakulta
-- Univerzita Palackého v Olomouci
-- Fakultní nemocnice Olomouc
-------------------------------------------------------------------------------
-- Laboratory of functional magnetic resonance imaging
-- Department of Neurology
-- Faculty of Medicine and Dentistry
-- Palacky University Olomouc
-- University Hospital Olomouc
-- Czech Republic
-------------------------------------------------------------------------------
-- I.P. Pavlova 6, 775 20 Olomouc
-- web: fmri.upol.cz
-- tel.: +420 588 443 418
-- e-mail: [log in to unmask]
-------------------------------------------------------------------------------
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