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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> Freesurfer mailing list
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-- 
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
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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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> Freesurfer mailing list
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>
>
> 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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>


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
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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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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

There are a bunch of columns in the design matrix that are 0, meaning 
that it expects some kind of stimulus to be there but it was not in the 
parfile. Do you only have eccen for this or do you also have polar?
doug


On 11/08/2014 11:25 AM, Francesca Strappini wrote:
 Hi, I attached the file, thank you!

 Best
 Francesca

 2014-11-06 18:58 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu:


 Can you send me
 
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat

 On 11/06/2014 09:53 AM, Francesca Strappini wrote:
  Dear all,
 
  I'm trying to run a retinotopy analysis in several subjects but it
  crashed with an error in one subject. I ran this command line:
 
  selxavg3-sess -a rtopy.HS.rh -s SUBJ09
 
 
  and this is the last part of the output with the error message.
  Any help would be much appreciated.
 
  Best
  Francesca
 
 
   M A T L A B (R) 
Copyright 1984-2013 The MathWorks, Inc.
  R2013b (8.2.0.701) 64-bit (glnxa64)
August 13, 2013
 
   
  Your MATLAB license will expire in 56 days.
  Please contact your system administrator or
  MathWorks to renew this license.
   
 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com
 http://www.mathworks.com
  http://www.mathworks.com.
 

  sxa3pwd =
 
  /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
 
  
  sxa3cmd =
 
  /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s
 SUBJ09
 
   /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
  
 
  #@# SUBJ09 ###
  /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
  -
  $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
  /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
  /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
  /usr/local/freesurfer/matlab/MRIread.m
  -
  outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
  Extension format = nii.gz
  nruns = 4
  autostimdur =
 
 
  outanadir =
 
 
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
  Found 110059/126364 (87.1) voxels in mask
  Creating Design Matrix
   ... creation time =  0.005 sec
  DoMCFit = 1
  ntptot = 960, nX = 36, DOF = 924
  Saving X matrix to
 
 
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
  Error using svd
  Input to SVD must not contain NaN or Inf.
 
  Error in cond (line 36)
  s = svd(A);
 
  Error in fast_selxavg3 (line 279)
XCond = cond(XtX);
 
 
  --
  Francesca Strappini, Ph.D.
  Neurobiology Department
  Weizmann Institute of Science
  234 Herzl Street, Rehovot 7610001 Israel
  Tel.: +972 58 444 2584
  E-mail: francesca.strapp...@weizmann.ac.il
 mailto:francesca.strapp...@weizmann.ac.il
  mailto:francesca.strapp...@weizmann.ac.il
 mailto:francesca.strapp...@weizmann.ac.il
 
 
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 mailto:Freesurfer@nmr.mgh.harvard.edu
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@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
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 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
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 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 

Re: [Freesurfer] error with fast_selxavg3

[Francesca Strappini]

Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and 2 of
eccentricity.

Francesca

On Monday, November 10, 2014, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:


 There are a bunch of columns in the design matrix that are 0, meaning
 that it expects some kind of stimulus to be there but it was not in the
 parfile. Do you only have eccen for this or do you also have polar?
 doug


 On 11/08/2014 11:25 AM, Francesca Strappini wrote:
  Hi, I attached the file, thank you!
 
  Best
  Francesca
 
  2014-11-06 18:58 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu
 javascript:;
  mailto:gr...@nmr.mgh.harvard.edu javascript:;:
 
 
  Can you send me
 
  
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
 
  On 11/06/2014 09:53 AM, Francesca Strappini wrote:
   Dear all,
  
   I'm trying to run a retinotopy analysis in several subjects but it
   crashed with an error in one subject. I ran this command line:
  
   selxavg3-sess -a rtopy.HS.rh -s SUBJ09
  
  
   and this is the last part of the output with the error message.
   Any help would be much appreciated.
  
   Best
   Francesca
  
  
M A T L A B (R) 
 Copyright 1984-2013 The MathWorks, Inc.
   R2013b (8.2.0.701) 64-bit (glnxa64)
 August 13, 2013
  

   Your MATLAB license will expire in 56 days.
   Please contact your system administrator or
   MathWorks to renew this license.

  
   To get started, type one of these: helpwin, helpdesk, or demo.
   For product information, visit www.mathworks.com
  http://www.mathworks.com
   http://www.mathworks.com.
  
 
   sxa3pwd =
  
   /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
  
   
   sxa3cmd =
  
   /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s
  SUBJ09
  
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
   
  
   #@# SUBJ09 ###
   /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
   -
   $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
   /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
   /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
   /usr/local/freesurfer/matlab/MRIread.m
   -
   outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
   Extension format = nii.gz
   nruns = 4
   autostimdur =
  
  
   outanadir =
  
 
  /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
   Found 110059/126364 (87.1) voxels in mask
   Creating Design Matrix
... creation time =  0.005 sec
   DoMCFit = 1
   ntptot = 960, nX = 36, DOF = 924
   Saving X matrix to
  
 
  
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
   Error using svd
   Input to SVD must not contain NaN or Inf.
  
   Error in cond (line 36)
   s = svd(A);
  
   Error in fast_selxavg3 (line 279)
 XCond = cond(XtX);
  
  
   --
   Francesca Strappini, Ph.D.
   Neurobiology Department
   Weizmann Institute of Science
   234 Herzl Street, Rehovot 7610001 Israel
   Tel.: +972 58 444 2584
   E-mail: francesca.strapp...@weizmann.ac.il javascript:;
  mailto:francesca.strapp...@weizmann.ac.il javascript:;
   mailto:francesca.strapp...@weizmann.ac.il javascript:;
  mailto:francesca.strapp...@weizmann.ac.il javascript:;
  
  
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  mailto:Freesurfer@nmr.mgh.harvard.edu javascript:;
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu javascript:; mailto:
 gr...@nmr.mgh.harvard.edu javascript:;
  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/
 
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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

Check in the rtopy.par file for the polar and make sure it actually says 
polar (and not eccen) inside

On 11/10/2014 01:23 PM, Francesca Strappini wrote:
 Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and 
 2 of eccentricity.

 Francesca

 On Monday, November 10, 2014, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 There are a bunch of columns in the design matrix that are 0, meaning
 that it expects some kind of stimulus to be there but it was not
 in the
 parfile. Do you only have eccen for this or do you also have polar?
 doug


 On 11/08/2014 11:25 AM, Francesca Strappini wrote:
  Hi, I attached the file, thank you!
 
  Best
  Francesca
 
  2014-11-06 18:58 GMT+02:00 Douglas N Greve
 gr...@nmr.mgh.harvard.edu javascript:;
  mailto:gr...@nmr.mgh.harvard.edu javascript:;:
 
 
  Can you send me
 
  
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
 
  On 11/06/2014 09:53 AM, Francesca Strappini wrote:
   Dear all,
  
   I'm trying to run a retinotopy analysis in several
 subjects but it
   crashed with an error in one subject. I ran this command line:
  
   selxavg3-sess -a rtopy.HS.rh -s SUBJ09
  
  
   and this is the last part of the output with the error
 message.
   Any help would be much appreciated.
  
   Best
   Francesca
  
  
M A T L A B (R) 
 Copyright 1984-2013 The MathWorks, Inc.
   R2013b (8.2.0.701) 64-bit (glnxa64)
 August 13, 2013
  
   
   Your MATLAB license will expire in 56 days.
   Please contact your system administrator or
   MathWorks to renew this license.
   
  
   To get started, type one of these: helpwin, helpdesk, or demo.
   For product information, visit www.mathworks.com
 http://www.mathworks.com
  http://www.mathworks.com
   http://www.mathworks.com.
  
 
   sxa3pwd =
  
   /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
  
   
   sxa3cmd =
  
   /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a
 rtopy.HS.rh -s
  SUBJ09
  
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
   
  
   #@# SUBJ09 ###
   /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
   -
   $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve
 Exp $
   /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
   /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
   /usr/local/freesurfer/matlab/MRIread.m
   -
   outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
   Extension format = nii.gz
   nruns = 4
   autostimdur =
  
  
   outanadir =
  
 
  
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
   Found 110059/126364 (87.1) voxels in mask
   Creating Design Matrix
... creation time =  0.005 sec
   DoMCFit = 1
   ntptot = 960, nX = 36, DOF = 924
   Saving X matrix to
  
 
  
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
   Error using svd
   Input to SVD must not contain NaN or Inf.
  
   Error in cond (line 36)
   s = svd(A);
  
   Error in fast_selxavg3 (line 279)
 XCond = cond(XtX);
  
  
   --
   Francesca Strappini, Ph.D.
   Neurobiology Department
   Weizmann Institute of Science
   234 Herzl Street, Rehovot 7610001 Israel
   Tel.: +972 58 444 2584
   E-mail: francesca.strapp...@weizmann.ac.il javascript:;
  mailto:francesca.strapp...@weizmann.ac.il javascript:;
   mailto:francesca.strapp...@weizmann.ac.il javascript:;
  mailto:francesca.strapp...@weizmann.ac.il javascript:;
  
  
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  mailto:Freesurfer@nmr.mgh.harvard.edu javascript:;
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR 

[Freesurfer] error with fast_selxavg3

[Francesca Strappini]

Dear all,

I'm trying to run a retinotopy analysis in several subjects but it crashed
with an error in one subject. I ran this command line:

selxavg3-sess -a rtopy.HS.rh -s SUBJ09

and this is the last part of the output with the error message.
Any help would be much appreciated.

Best
Francesca


 M A T L A B (R) 
  Copyright 1984-2013 The MathWorks, Inc.
R2013b (8.2.0.701) 64-bit (glnxa64)
  August 13, 2013


Your MATLAB license will expire in 56 days.
Please contact your system administrator or
MathWorks to renew this license.


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

  
sxa3pwd =

/usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed


sxa3cmd =

/usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s SUBJ09

 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m


#@# SUBJ09 ###
/usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
-
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/matlab/MRIread.m
-
outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
Extension format = nii.gz
nruns = 4
autostimdur =


outanadir =
/usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
Found 110059/126364 (87.1) voxels in mask
Creating Design Matrix
 ... creation time =  0.005 sec
DoMCFit = 1
ntptot = 960, nX = 36, DOF = 924
Saving X matrix to
/usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 36)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

Can you send me
/usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat

On 11/06/2014 09:53 AM, Francesca Strappini wrote:
 Dear all,

 I'm trying to run a retinotopy analysis in several subjects but it 
 crashed with an error in one subject. I ran this command line:

 selxavg3-sess -a rtopy.HS.rh -s SUBJ09


 and this is the last part of the output with the error message.
 Any help would be much appreciated.

 Best
 Francesca


  M A T L A B (R) 
   Copyright 1984-2013 The MathWorks, Inc.
 R2013b (8.2.0.701) 64-bit (glnxa64)
   August 13, 2013

 
 Your MATLAB license will expire in 56 days.
 Please contact your system administrator or
 MathWorks to renew this license.
 

 To get started, type one of these: helpwin, helpdesk, or demo.
 For product information, visit www.mathworks.com 
 http://www.mathworks.com.

   
 sxa3pwd =

 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed

 
 sxa3cmd =

 /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s SUBJ09

  /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
 

 #@# SUBJ09 ###
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
 -
 $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /usr/local/freesurfer/matlab/MRIread.m
 -
 outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
 Extension format = nii.gz
 nruns = 4
 autostimdur =


 outanadir = 
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
 Found 110059/126364 (87.1) voxels in mask
 Creating Design Matrix
  ... creation time =  0.005 sec
 DoMCFit = 1
 ntptot = 960, nX = 36, DOF = 924
 Saving X matrix to 
 /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
 Error using svd
 Input to SVD must not contain NaN or Inf.

 Error in cond (line 36)
 s = svd(A);

 Error in fast_selxavg3 (line 279)
   XCond = cond(XtX);


 -- 
 Francesca Strappini, Ph.D.
 Neurobiology Department
 Weizmann Institute of Science
 234 Herzl Street, Rehovot 7610001 Israel
 Tel.: +972 58 444 2584
 E-mail: francesca.strapp...@weizmann.ac.il 
 mailto:francesca.strapp...@weizmann.ac.il


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-- 
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
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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

Hi Leila, yes, the problem is probably in that fsfast sets the TER=.05. 
I never expected the TR or the event duration to be less than this 
(silly me). The -refeventdur does not really effect much, it just 
controls some scaling. Setting it to 16ms is fine.
doug


On 07/23/2013 08:23 AM, Leila Reddy wrote:
 Hi Doug,

 Thanks for your reply. Yes, it does work with a longer -refeventdur. In
 fact, I had tried that yesterday before posting my original message but
 I'd forgotten to make the corresponding changes to the 3rd column of the
 paradigm file and so kept getting the error message.

 The shortest I can bring -refeventdur down to is 0.05. Anything smaller
 causes the same error as before. In the end it's not a huge problem for
 us if we have to set an event duration of 50ms instead of 16.6 ms but
 I'd like to understand what is going on.

 So, I wondered if the error had anything to do with the fact that when I
 run mkcontrast-sess the script automatically sets -TER to 0.05. I re-ran
 the analysis and set -TER and -refeventdur to 0.016 in mkanalysis-sess.
 The analysis runs with no
   error for selxavg-sess and visually (with
 tksurfer) the results look the same as with -TER and -refeventdur set to
 0.05.

 Since the help for mkanalysis-sess -TER says  It is best to know what
 you are doing if you are going to change this.,  I'd like to know if it
 makes sense to change the TER like I have. What does the TER achieve (if
 that's not too complicated a question)?

 Thanks again,
 Leila


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 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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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
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Re: [Freesurfer] error with fast_selxavg3

[Leila Reddy]

Hi Doug,

Thanks for your reply. Yes, it does work with a longer -refeventdur. In 
fact, I had tried that yesterday before posting my original message but 
I'd forgotten to make the corresponding changes to the 3rd column of the 
paradigm file and so kept getting the error message.

The shortest I can bring -refeventdur down to is 0.05. Anything smaller 
causes the same error as before. In the end it's not a huge problem for 
us if we have to set an event duration of 50ms instead of 16.6 ms but 
I'd like to understand what is going on.

So, I wondered if the error had anything to do with the fact that when I 
run mkcontrast-sess the script automatically sets -TER to 0.05. I re-ran 
the analysis and set -TER and -refeventdur to 0.016 in mkanalysis-sess. 
The analysis runs with no error for selxavg-sess and visually (with 
tksurfer) the results look the same as with -TER and -refeventdur set to 
0.05.

Since the help for mkanalysis-sess -TER says  It is best to know what 
you are doing if you are going to change this.,  I'd like to know if it 
makes sense to change the TER like I have. What does the TER achieve (if 
that's not too complicated a question)?

Thanks again,
Leila
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[Freesurfer] error with fast_selxavg3

[Leila Reddy]

Hi,

I am running into an error with fast_selxavg3 (NaN values in XtX). Other have 
people reported similar problems on the mailing list and I've tried 
implementing some of the suggestions (namely, using -nowhiten and checking that 
all events exist in my paradigm file), but I can't get rid of the error.


I have an event-related design with very short events (duration of 1 screen 
refresh = 16.6ms) presented at random intervals. The error only occurs for the 
-gammafit and -spmhrf analyses and not for -fir. When I check the Xtmp.mat 
there are indeed NaNs in the first 2 columns of the X matrix. The commands I 
issue and the output of bugr are below.I attach the paradigm file from one run 
of the experiment (there are 5 runs in all but I started focusing on just one 
in order to troubleshoot). TR=2 and numTRs=172.


Any help would be much appreciated.

Thanks in advance,
Leila


mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related 
-paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur 
0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf 
runlist -force -nowhiten

mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1

selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh

Error message:
-
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m
/APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/APPLICATIONS/freesurfer/matlab/MRIread.m
-
outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF
Extension format = nii.gz
 1 VR.mat
nruns = 1
autostimdur = 


outanadir = 
/Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh
Found 149786/163842 (91.4) voxels in mask
Creating Design Matrix
 ... creation time =  0.005 sec
DoMCFit = 1
ntptot = 172, nX = 7, DOF = 165
Saving X matrix to 
/Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 36)
    s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);
 
 --
ERROR: fast_selxavg3() failed\n


Output of bugr:
-

FREESURFER_HOME: /APPLICATIONS/freesurfer

Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0

Kernel info: Darwin 12.0.0 x86_64

-


VRpara.para
Description: Binary data
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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

Hi Leila, does it work if you change the -refeventdur to something 
larger (eg, 2)?
doug

On 07/22/2013 06:11 AM, Leila Reddy wrote:
 Hi,

 I am running into an error with fast_selxavg3 (NaN values in XtX). Other have 
 people reported similar problems on the mailing list and I've tried 
 implementing some of the suggestions (namely, using -nowhiten and checking 
 that all events exist in my paradigm file), but I can't get rid of the error.


 I have an event-related design with very short events (duration of 1 screen 
 refresh = 16.6ms) presented at random intervals. The error only occurs for 
 the -gammafit and -spmhrf analyses and not for -fir. When I check the 
 Xtmp.mat there are indeed NaNs in the first 2 columns of the X matrix. The 
 commands I issue and the output of bugr are below.I attach the paradigm file 
 from one run of the experiment (there are 5 runs in all but I started 
 focusing on just one in order to troubleshoot). TR=2 and numTRs=172.


 Any help would be much appreciated.

 Thanks in advance,
 Leila


 mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related 
 -paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur 
 0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf 
 runlist -force -nowhiten

 mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1

 selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh

 Error message:
 -
 $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
 /APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /APPLICATIONS/freesurfer/matlab/MRIread.m
 -
 outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF
 Extension format = nii.gz
   1 VR.mat
 nruns = 1
 autostimdur =


 outanadir = 
 /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh
 Found 149786/163842 (91.4) voxels in mask
 Creating Design Matrix
   ... creation time =  0.005 sec
 DoMCFit = 1
 ntptot = 172, nX = 7, DOF = 165
 Saving X matrix to 
 /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/Xtmp.mat
 Error using svd
 Input to SVD must not contain NaN or Inf.

 Error in cond (line 36)
  s = svd(A);

 Error in fast_selxavg3 (line 279)
XCond = cond(XtX);
   
 --
 ERROR: fast_selxavg3() failed\n


 Output of bugr:
 -

 FREESURFER_HOME: /APPLICATIONS/freesurfer

 Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0

 Kernel info: Darwin 12.0.0 x86_64

 -


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-- 
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
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Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);

[Douglas N Greve]

Do you not have any eccen runs?
doug

On 03/27/2012 06:55 AM, Kiley Seymour wrote:
 Dear Doug,

 I am aware I am becoming a regular pain. But I now encounter the 
 following problem when running selxavg3-sess -a rtopy.self.lh -s 
 CMRU1711. I have also attached my analysis.info and Xtmp.mat files

 Thanks for all of your suggestions.

 K

 #@# CMRU1711 ###
 /media/sf_DATA1/RETINOTOPY/CMRU1711
 -
 $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
 /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /home/virtualuser/freesurfer/matlab/MRIread.m
 -
 outtop = /media/sf_DATA1/RETINOTOPY
 Extension format = nii.gz
 nruns = 3
 autostimdur =


 outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh
 Found 138599/149490 (92.7) voxels in mask
 Creating Design Matrix
  ... creation time =  0.008 sec
 DoMCFit = 1
 ntptot = 369, nX = 33, DOF = 336
 Saving X matrix to 
 /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat
 Error using svd
 Input to SVD must not contain NaN or Inf.

 Error in cond (line 39)
s = svd(A);

 Error in fast_selxavg3 (line 254)
   XCond = cond(XtX);






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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);

[Douglas N Greve]

FSFAST assumes that you do. A silly way around this is to just replicate 
your polar runs and call them eccen runs.
doug

On 03/27/2012 12:35 PM, Kiley Seymour wrote:
 no I don't.

 On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu  wrote:
 Do you not have any eccen runs?
 doug

 On 03/27/2012 06:55 AM, Kiley Seymour wrote:
 Dear Doug,

 I am aware I am becoming a regular pain. But I now encounter the
 following problem when running selxavg3-sess -a rtopy.self.lh -s
 CMRU1711. I have also attached my analysis.info and Xtmp.mat files

 Thanks for all of your suggestions.

 K

 #@# CMRU1711 ###
 /media/sf_DATA1/RETINOTOPY/CMRU1711
 -
 $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
 /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /home/virtualuser/freesurfer/matlab/MRIread.m
 -
 outtop = /media/sf_DATA1/RETINOTOPY
 Extension format = nii.gz
 nruns = 3
 autostimdur =


 outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh
 Found 138599/149490 (92.7) voxels in mask
 Creating Design Matrix
   ... creation time =  0.008 sec
 DoMCFit = 1
 ntptot = 369, nX = 33, DOF = 336
 Saving X matrix to
 /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat
 Error using svd
 Input to SVD must not contain NaN or Inf.

 Error in cond (line 39)
 s = svd(A);

 Error in fast_selxavg3 (line 254)
XCond = cond(XtX);






 ___
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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 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.



-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);

[Douglas N Greve]

You will have to mri_convert all the .nii files so that they have the 
proper TR.

On 03/27/2012 12:51 PM, Kiley Seymour wrote:
 Hi Doug. I just made a dummy folder with an eccen run. It got around
 the error  XCond = cond(XtX) but took me back to the original error :
 TR mismatch error despite me re-doing the preprocessing and re-
 mri_concat-enating my SPM nii files into a 4D file for each run.

 Do you think using mri_concat with --regheader could be the problem?
 Or perhaps the fact that dicoms were converted to nii files in a
 program that was not freesufer?

 K


 On Tue, Mar 27, 2012 at 6:35 PM, Kiley Seymour
 kileyseym...@googlemail.com  wrote:
 no I don't.

 On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu  wrote:
 Do you not have any eccen runs?
 doug

 On 03/27/2012 06:55 AM, Kiley Seymour wrote:
 Dear Doug,

 I am aware I am becoming a regular pain. But I now encounter the
 following problem when running selxavg3-sess -a rtopy.self.lh -s
 CMRU1711. I have also attached my analysis.info and Xtmp.mat files

 Thanks for all of your suggestions.

 K

 #@# CMRU1711 ###
 /media/sf_DATA1/RETINOTOPY/CMRU1711
 -
 $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
 /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /home/virtualuser/freesurfer/matlab/MRIread.m
 -
 outtop = /media/sf_DATA1/RETINOTOPY
 Extension format = nii.gz
 nruns = 3
 autostimdur =


 outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh
 Found 138599/149490 (92.7) voxels in mask
 Creating Design Matrix
   ... creation time =  0.008 sec
 DoMCFit = 1
 ntptot = 369, nX = 33, DOF = 336
 Saving X matrix to
 /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat
 Error using svd
 Input to SVD must not contain NaN or Inf.

 Error in cond (line 39)
 s = svd(A);

 Error in fast_selxavg3 (line 254)
XCond = cond(XtX);






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 --
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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