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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, where it is always 40. Is it possible to force a different timewindow? Below is some info from analysis.info. 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
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 http://analysis.info, where it is always 40. Is it possible to force a different timewindow? Below is some info from analysis.info http://analysis.info. 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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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. < DGREVE@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 CautionHi! 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=DwIG...
, 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=DwIG...
. 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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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. 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <http://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 <http://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 <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=
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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. < DGREVE@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 CautionHi 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_...
Caspar
On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@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=DwIG...
<https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwIG...
>, 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=DwIG...
<https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwIG...
>. > 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.ed...
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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.infohttp://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.infohttp://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. <DGREVE@mgh.harvard.edumailto:DGREVE@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 CautionHi 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_...
Caspar
On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@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<http://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<http://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> <mailto: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> <mailto: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=
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Yes I did. Caspar
On Fri, Sep 13, 2019 at 16:19 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Did you put -timewindow before -gammafit ?
On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote:
External Email - Use CautionHi 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. < DGREVE@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 CautionHi Doug, Thanks for the advice. I think the Leite et al. 2002 NeuroImage paper can be interpreted that way. See Figure 1 and 2.
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Caspar
On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@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.infohttps://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=DwIG...
<https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwIG...
>, where it > is always 40. > Is it possible to force a different timewindow? > Below is some info from analysis.infohttps://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=DwIG...
<https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info&d=DwIG...
>. > 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.ed...
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Caspar M. Schwiedrzik -
Greve, Douglas N.,Ph.D.