rmAverageTime.m error on pRF tutorial

[brunodireito]

I am getting an error, on rmAverageTime.m (line 30) when using the tutorial dataset. On the rmMakeStimulus.m function, the script used to store a copy of the images not getting convolved (line 120 - 135) calls rmAverageTime without rotating the params.stim(n).images_org matrix.

This is actually done before the first average during the HRF conv step.

Can I just transpose the data?

[JWinawer]

I see that Matlab2017B introduced a built-in niftiread and niftiwrite. I wonder if it's too soon to switch over to these and eliminate our mex functions? It would make life simpler to rely on Mathworks functions and solve a lot of headaches with environment, compiling, etc.

https://www.mathworks.com/help/images/ref/niftiread.html https://www.mathworks.com/help/images/ref/niftiwrite.html

-Jon

On Tue, Jun 19, 2018 at 11:02 AM, Bruno Miguel notifications@github.com wrote:

Size arguments must be real integers.

I have a 4D single complex array in Matlab. When I try to use writeFileNifti.m and writeFileNifti.mexa64 to write the NIfTI file, the result NIfTI file is not correct. It seems the matrix is messed up.

Ps. I am using Matlab 2018a with CentOS 6.9. writeFileNifti.m and writeFileNifti.mexa64 were downloaded on 6/12/2018 from here.

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[JWinawer]

It seems that my response about niftiwrite was directed to an earlier comment, which was deleted and replaced with a comment about pRFs.

Regarding the pRF questions: can you tell us what tutorial dataset you are running?

I would recommend testing with the tutorial in the vistasoft code: t_pRF.m

[arokem]

Out of curiosity: has anyone had a chance to try out these functions? Do they produce the same output as the Shen's toolbox?

I guess it's possible that they took the toolbox and integrated it into their code-base (it's released under a permissive license).

On Mon, Jun 25, 2018 at 5:43 AM Jonathan Winawer notifications@github.com wrote:

I see that Matlab2017B introduced a built-in niftiread and niftiwrite. I wonder if it's too soon to switch over to these and eliminate our mex functions? It would make life simpler to rely on Mathworks functions and solve a lot of headaches with environment, compiling, etc.

https://www.mathworks.com/help/images/ref/niftiread.html https://www.mathworks.com/help/images/ref/niftiwrite.html

-Jon

On Tue, Jun 19, 2018 at 11:02 AM, Bruno Miguel notifications@github.com wrote:

Size arguments must be real integers.

I have a 4D single complex array in Matlab. When I try to use writeFileNifti.m and writeFileNifti.mexa64 to write the NIfTI file, the result NIfTI file is not correct. It seems the matrix is messed up.

Ps. I am using Matlab 2018a with CentOS 6.9. writeFileNifti.m and writeFileNifti.mexa64 were downloaded on 6/12/2018 from here.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/297, or mute the thread < https://github.com/notifications/unsubscribe-auth/ACBX3qFlMSlwGs_0FIM68Y3O2TqBj-J1ks5t-RJtgaJpZM4UtsGh

.

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

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[JWinawer]

I have not tested them yet, but am just starting to. If they work, I think they are preferable to Shen's tools, since they should be kept up-to-date by Mathworks, and won't require importing new functions when there are changes to either Shen's code or to compatibility with new Matlab versions.

-Jon

On Mon, Jun 25, 2018 at 11:03 AM, Ariel Rokem notifications@github.com wrote:

Out of curiosity: has anyone had a chance to try out these functions? Do they produce the same output as the Shen's toolbox?

I guess it's possible that they took the toolbox and integrated it into their code-base (it's released under a permissive license).

On Mon, Jun 25, 2018 at 5:43 AM Jonathan Winawer <notifications@github.com

wrote:

I see that Matlab2017B introduced a built-in niftiread and niftiwrite. I wonder if it's too soon to switch over to these and eliminate our mex functions? It would make life simpler to rely on Mathworks functions and solve a lot of headaches with environment, compiling, etc.

https://www.mathworks.com/help/images/ref/niftiread.html https://www.mathworks.com/help/images/ref/niftiwrite.html

-Jon

On Tue, Jun 19, 2018 at 11:02 AM, Bruno Miguel <notifications@github.com

wrote:

Size arguments must be real integers.

I have a 4D single complex array in Matlab. When I try to use writeFileNifti.m and writeFileNifti.mexa64 to write the NIfTI file, the result NIfTI file is not correct. It seems the matrix is messed up.

Ps. I am using Matlab 2018a with CentOS 6.9. writeFileNifti.m and writeFileNifti.mexa64 were downloaded on 6/12/2018 from here.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/297, or mute the thread < https://github.com/notifications/unsubscribe-auth/ACBX3qFlMSlwGs_ 0FIM68Y3O2TqBj-J1ks5t-RJtgaJpZM4UtsGh

.

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place https://maps.google.com/?q=6+Washington+Place+%0D%0A+New+York,+NY,+10003&entry=gmail&source=g New York, NY, 10003 https://maps.google.com/?q=6+Washington+Place+%0D%0A+New+York,+NY,+10003&entry=gmail&source=g (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

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-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

[arokem]

+1

On Mon, Jun 25, 2018 at 8:09 AM Jonathan Winawer notifications@github.com wrote:

I have not tested them yet, but am just starting to. If they work, I think they are preferable to Shen's tools, since they should be kept up-to-date by Mathworks, and won't require importing new functions when there are changes to either Shen's code or to compatibility with new Matlab versions.

-Jon

On Mon, Jun 25, 2018 at 11:03 AM, Ariel Rokem notifications@github.com wrote:

Out of curiosity: has anyone had a chance to try out these functions? Do they produce the same output as the Shen's toolbox?

I guess it's possible that they took the toolbox and integrated it into their code-base (it's released under a permissive license).

On Mon, Jun 25, 2018 at 5:43 AM Jonathan Winawer < notifications@github.com

wrote:

I see that Matlab2017B introduced a built-in niftiread and niftiwrite. I wonder if it's too soon to switch over to these and eliminate our mex functions? It would make life simpler to rely on Mathworks functions and solve a lot of headaches with environment, compiling, etc.

https://www.mathworks.com/help/images/ref/niftiread.html https://www.mathworks.com/help/images/ref/niftiwrite.html

-Jon

On Tue, Jun 19, 2018 at 11:02 AM, Bruno Miguel < notifications@github.com

wrote:

Size arguments must be real integers.

I have a 4D single complex array in Matlab. When I try to use writeFileNifti.m and writeFileNifti.mexa64 to write the NIfTI file, the result NIfTI file is not correct. It seems the matrix is messed up.

Ps. I am using Matlab 2018a with CentOS 6.9. writeFileNifti.m and writeFileNifti.mexa64 were downloaded on 6/12/2018 from here.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/297, or mute the thread < https://github.com/notifications/unsubscribe-auth/ACBX3qFlMSlwGs_ 0FIM68Y3O2TqBj-J1ks5t-RJtgaJpZM4UtsGh

.

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place < https://maps.google.com/?q=6+Washington+Place+%0D%0A+New+York,+NY,+10003&entry=gmail&source=g

New York, NY, 10003 < https://maps.google.com/?q=6+Washington+Place+%0D%0A+New+York,+NY,+10003&entry=gmail&source=g

(212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

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-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

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[brunodireito]

I was actually trying to follow the notes here: http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/PRF_Tutorial.

The data was downloaded from: http://white.stanford.edu/software/downloadsData/mrVistaPRFSession.zip

thank you

[JWinawer]

I'll try to look at that, but it's old. I would try the tutorials on the GutHub wiki page, which includes a pRF tutorial, as well as several others on the same data set:

https://github.com/vistalab/vistasoft/wiki/Ernie-Tutorials

On Mon, Jun 25, 2018 at 8:21 AM, Bruno Miguel notifications@github.com wrote:

I was actually trying to follow the notes here: http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/PRF_Tutorial.

The data was downloaded from: http://white.stanford.edu/software/downloadsData/mrVistaPRFSession.zip

thank you

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-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/