Re: [Freesurfer] error in fast_selxavg3 (line 1248)

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer