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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve greve@nmr.mgh.harvard.edu 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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
On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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.
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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
On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve greve@nmr.mgh.harvard.edu 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
On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 theanalysis
> (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 NY10065-6307
> USA // 212.327.7699 <tel:212.327.7699> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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/
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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.
Just to confirm: There's no way to visualize the nuisreg loadings/maps, right?
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699
On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] < stephen.v.shepherd@gmail.com> 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
On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
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
On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 timecourses
> 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 theanalysis
> (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 NY10065-6307
> USA // 212.327.7699 <tel:212.327.7699> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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/
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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] <stephen.v.shepherd@gmail.com mailto:stephen.v.shepherd@gmail.com> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > 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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > 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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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On Wed, May 4, 2016 at 4:26 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send me the Xtmp.mat file from a run that fails?
I think I have a fix for this if you want to edit your version of fast_selxavg3.m
Change this line:
if(~isempty(analysis) & DoGLMFit & strcmp(flac.designtype,'event-related'))
To:
% Check to make sure that each task ev as the same number % of regressors before saving the h.dat file evtaskind = flac_evtaskind(flac0); % number of regressors in each ev nregperev = zeros(length(evtaskind),1); for n = 1:length(evtaskind) nregperev(n) = flac0.ev(evtaskind(n)).nreg; end nregperevunique = length(unique(nregperev));
if(~isempty(analysis) & DoGLMFit & nregperevunique==1 & strcmp(flac.designtype,'event-related'))
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.
Just to confirm: There's no way to visualize the nuisreg loadings/maps, 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] <stephen.v.shepherd@gmail.com mailto:stephen.v.shepherd@gmail.com> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > 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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > 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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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S.V.Shepherd [work]