External Email - Use Caution Hi Doug, apart from the question whether or not to set the timewindow parameter to 80 for MION responses, I noticed that there is a discrepancy between analysis.info and h.dat with regard to this parameter in v5.3. If I set timewindow to 80 in mkanalysis-sess, it correctly prints this parameter into analysis.info. However, in h.dat for the same analysis, timewindow is 40. I don't know if that is relevant, but it seems weird. Maybe it was already addressed in version 6.
Caspar Am Di., 13. Aug. 2019 um 22:51 Uhr schrieb Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>: > That is in response to a 60 sec stimulus. The time window is the time > needed to account for a very brief stimulus (ie, the impulse response). > fsfast will automatically take into account the duration of the stimulus > as listed in the paradigm file. > > On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote: > > > > 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. > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__pop.cerco.ups-2Dtlse.fr_pdf0609_leite-5Ffp-5F02-5F283.pdf&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs&s=_NKVTMtmRmOeLrYx6styS12TMjsFNuVd2jKFxUKr85Y&e= > > > > Caspar > > > > On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto: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=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs&s=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA&e= > > > > < > 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=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs&s=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA&e= > > > > < > 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 > > <mailto: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 <mailto: > 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=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs&s=i_FJSmFIcapkW_xJ--l5OIaUFPa5sRkfUKIJVjbQpRs&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=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs&s=i_FJSmFIcapkW_xJ--l5OIaUFPa5sRkfUKIJVjbQpRs&e=
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
