External Email - Use Caution Yes I did. Caspar
On Fri, Sep 13, 2019 at 16:19 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Did you put -timewindow before -gammafit ? > > > On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote: > > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao&s=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg&e=> > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao&s=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg&e=>. > 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=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao&s=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg&e=> >> < >> 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=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao&s=EmEPqCEEylIHfrDEVX7i7KSiT1QrAnz4423QPVyGdJg&e=> >> < >> 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 listfreesur...@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao&s=t-A20t3KCEfTc4pagqnd_aAO3zSxSYO1iVlDBsVVz-k&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=DwICAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=4hnvhCVX4pJzRESmdot0FI0cS7sKUWI-cIDKsihmrao&s=t-A20t3KCEfTc4pagqnd_aAO3zSxSYO1iVlDBsVVz-k&e=
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