External Email - Use Caution Hi Doug, Thanks for the advice. I think the Leite et al. 2002 NeuroImage paper can be interpreted that way. See Figure 1 and 2. http://pop.cerco.ups-tlse.fr/pdf0609/leite_fp_02_283.pdf
Caspar On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > 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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs&s=XDAGWnQ0EfzafF02Dt9oANY0hss4c_WbhPUxaZKWHI4&e= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs&s=XDAGWnQ0EfzafF02Dt9oANY0hss4c_WbhPUxaZKWHI4&e=
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