On 05/04/2016 04:08 PM, S.V.Shepherd [work] wrote: > I can /also /confirm that it ran fine when the big matrix was changed > from taskreg to nuisreg, so we can probably consider the issue > resolved. I suspect the problem is with multi-column taskregs. If I > want to have the regressors tracked equivalently across runs, I'd need > to add them as taskregs, one column per file. Can you send me the Xtmp.mat file from a run that fails? > > Just to confirm: There's no way to visualize the nuisreg > loadings/maps, right? right > > stephen > > _stephen v. shepherd phd_ > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 > USA // 212.327.7699 <tel:212.327.7699> > > On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] > <[email protected] <mailto:[email protected]>> > wrote: > > I can confirm that having taskregs with a paradigm works. For > example, I've run successfully analyzed the following: > > mkanalysis-sess -native -event-related -refeventdur 10 > -paradigm aboutFace.para -nconditions 13 -TR 2.0000 -rlf > rlf_aboutFace_subjvid -funcstem fm2tas1 -mask brain -analysis > a_401_Av_s_task_fmov_bgrnd_icadenoise -taskreg > taskreg_face__zmove.dat 1 -taskreg taskreg_face__bgrnd.dat 1 > -fsd bold -gammafit 0 8 -gammaexp 0.3 -polyfit 2 -acfbins 1 > -nuisreg motion.dat 3 -force > > The only thing that's changed is the addition of the IC-derived > taskreg matrix. > > stephen > > _stephen v. shepherd phd_ > The Rockefeller University / 1230 York Avenue / New York > NY 10065-6307 USA // 212.327.7699 <tel:212.327.7699> > > On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve > <[email protected] <mailto:[email protected]>> wrote: > > I don't think it is going to work to have both a -taskreg and a > paradigm. You should be able to model it as a nuisance > regressor. The > fact that it may be the same across runs won't make much of a > difference. > doug > > On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote: > > mkanalysis-sess -native -event-related -refeventdur 10 > -paradigm > > aboutFace.para -nconditions 13 -TR 2.0000 -rlf > > rlf_aboutFace_subjvid -funcstem fm2tas1 -mask brain -analysis > > a_401_Av_s_task_fmov_bgrnd_icadenoise -taskreg > > taskreg_face__zmove.dat 1 -taskreg taskreg_face__bgrnd.dat 1 > > -taskreg noisereg__TCs_Milo_43.dat 43 -fsd bold -gammafit 0 8 > > -gammaexp 0.3 -polyfit 2 -acfbins 1 -nuisreg motion.dat 3 > -force > > > > I've attached example noisereg__TCs_Milo_43.dat and a log > which I > > think includes relevant terminal outputs up to the error. > Please let > > me know if I should provide more information. > > > > s > > > > > > > > _stephen v. shepherd phd_ > > The Rockefeller University / 1230 York Avenue / New York NY > 10065-6307 > > USA // 212.327.7699 <tel:212.327.7699> > > > > On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve > > <[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> wrote: > > > > Can you send your mkanalysis-sess command? Can you also > send one > > of the > > regressor files? And can you send the full selxavg3 > terminal output? > > > > On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote: > > > I've modified an analysis to include a vector of noise > time courses > > > estimated using ICA. Since IC effects should be > consistent across > > > runs, I'm using taskregs instead of nuisregs. I can > define the > > > analysis and set up contrasts fine; however, when I > run the analysis > > > (selxavg3-sess), I get the following error: > > > > > > [...] > > > Saving h.dat to > > > > > > > /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat > > > Error using zeros > > > Size inputs must be integers. > > > > > > Error in fast_selxavg3 (line 1248) > > > hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % > Add zero > > for cond 0 > > > > > > >> ------------------------------------------ > > > ERROR: fast_selxavg3() failed\n > > > a_401_Av_s_task_fmov_bgrnd_icadenoise failed > > > [...] > > > > > > ============================ > > > > > > Looking at h.dat, I notice "Nh" is set 3.625000e+00 > rather than > > "1" as > > > usual. > > > > > > Any tips on how to debug further? > > > > > > _stephen v. shepherd phd_ > > > The Rockefeller University / 1230 York Avenue / New > York NY 10065-6307 > > > USA // 212.327.7699 <tel:212.327.7699> > <tel:212.327.7699 <tel:212.327.7699>> > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > [email protected] <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was > sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > <mailto:[email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > [email protected] > <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
