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

[Douglas N Greve]

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 
>
> On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] 
> > 
> 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.  -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
> > 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. -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
> >  
>  >> 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 

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

[Douglas N Greve]

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 
>
> On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] 
> > 
> 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.  -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
> > 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. -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
> >  
>  >> 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

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

[S.V.Shepherd [work]]

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.sheph...@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.  -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  > 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. -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
>> > > 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
>> > gr...@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
>> > 

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

[S.V.Shepherd [work]]

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.  -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 
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. -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
> > > 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
> > gr...@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/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
> > 

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

[Douglas N Greve]

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. -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 
> > 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
> gr...@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/
>
> ___
> Freesurfer mailing list
> 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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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[S.V.Shepherd [work]]

mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm
aboutFace.para  -nconditions 13  -TR 2.  -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 
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
> gr...@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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>
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noisereg__TCs_Milo_43.dat
Description: Binary data


selxavg3-sess-bold-a_401_Av_s_task_fmov_bgrnd_icadenoise-160504135301 - Copy.log
Description: Binary data
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Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[Douglas N Greve]

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
gr...@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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[Freesurfer] error in fast_selxavg3 (line 1248)

[S.V.Shepherd [work]]

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
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