When you use -gammafit, it automatically sets the time window to 40. If
you really want it at 80, but -timewindow before -gammafit. Do you
really expect the MION hrf to last 80 sec?

On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
>
>         External Email - Use Caution
>
> Hi!
> I am having difficulties setting the timewindow parameter in
> mkanalysis-sess in Freesurfer v5.3.
> I am trying to use 80 (data acquired with MION), but the parameter
> does not seem to affect analysis.info <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs&s=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s&e= >, where it
> is always 40.
> Is it possible to force a different timewindow?
> Below is some info from analysis.info <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs&s=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s&e= >.
> Thanks, Caspar
>
>
> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve
> Exp $
> # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd bold
> -native -timeoffset -2/2 -event-related -paradigm xxxx.para
> -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80*
> -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis xxxx -funcstem xxxx
> -runlistfile xxxx.list -nuisreg motion.dat 6 -tpef tpef.dat -acfbins
> 14 -acffwhm 0 -mask xxxx -force
>
>
> analysis xxxx
> mcstem fmc
> funcstem xxxx
> fsd bold
> runlistfile xxxx.list
> TR 2
> RegDOF 6
> PerSession 1
> RawSpace volume native
> mask xxxx
> RawFWHM 0
> RawSTC none
> UseB0DC 0
> ApplySubCortMask 1
> inorm 100
> acfbins 14
> fixacf  1
> acffwhm 0
> acfsvd  0
> designtype event-related
> tpexclude tpef.dat
> nskip 0
> polyfit 2
> HPFCutoffHz 0.0109
> HeteroGCor 0
> nconditions 4
> parname xxxx.para
> RefEventDur 0.5
> *timewindow 40.000000*
> prestim 0
> TER 0.050000
> gamma 0 8 0.3 0
> stimulusdelay -2/2
> Condition 1 Condition01
> Condition 2 Condition02
> Condition 3 Condition03
> Condition 4 Condition04
> nuisreg motion.dat 6
>
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