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Homer-fNIRS and AtlasViewer Community

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NEW POSTS SUBMITTED AT

https://openfnirs.org/community/homer3-forum/

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Welcome to the Homer-fNIRS Community. We use this forum to discuss usage of the Homer and AtlasViewer software packages for analyzing fNIRS measurements of brain activity.

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David Boas, Shannon Lim2

4/27/20

Homer3 and AtlasViewer Video Tutorials

Thanks David! Video tutorials would be very helpful. I would like some tutorials or a wikipage on

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Homer3 and AtlasViewer Video Tutorials

Thanks David! Video tutorials would be very helpful. I would like some tutorials or a wikipage on

4/27/20

4/27/20

Homer3 wiki manual

The homer3 wiki manual can be found at https://github.com/BUNPC/Homer3/wiki It is coming together

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Homer3 wiki manual

The homer3 wiki manual can be found at https://github.com/BUNPC/Homer3/wiki It is coming together

4/27/20

11/25/20

Homer forum moved to openfnirs.org

NEW POSTS SUBMITTED AT https://openfnirs.org/community/homer3-forum/ Please join with a free or homer

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Homer forum moved to openfnirs.org

NEW POSTS SUBMITTED AT https://openfnirs.org/community/homer3-forum/ Please join with a free or homer

11/25/20

Guy Perkins, Boas, David2

11/24/20

HRF not saving to group.procStream.output

Take a look at the homer3 wiki page. This describes the format https://github.com/BUNPC/Homer3/wiki/

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HRF not saving to group.procStream.output

Take a look at the homer3 wiki page. This describes the format https://github.com/BUNPC/Homer3/wiki/

11/24/20

Asger L. Christiansen, Asger L. Christiansen5

11/23/20

Too many trigger markers prevents loading data into Homer3

David, Thanks for working on this issue! I plan to use Homer3 to process and analyze our pilot data

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Too many trigger markers prevents loading data into Homer3

David, Thanks for working on this issue! I plan to use Homer3 to process and analyze our pilot data

11/23/20

Verena Schäfer, Yucel, Meryem6

11/19/20

Problem with Bandpass_Filter_Auxiliary and Prune Channels

Hi Verena, The bandpass function expects all elements (time points) of the data to be finite. The OD

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Problem with Bandpass_Filter_Auxiliary and Prune Channels

Hi Verena, The bandpass function expects all elements (time points) of the data to be finite. The OD

11/19/20

nicop...@gmail.com, Boas, David2

11/18/20

AtlasViewer not loading digpts correctly?

Most likely you are using centimeter units when atlasviewer is expected millimeter units From: homer-

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AtlasViewer not loading digpts correctly?

Most likely you are using centimeter units when atlasviewer is expected millimeter units From: homer-

11/18/20

Jordan Borrell, Stephen Tucker7

11/18/20

Problem with mhrR_GLM

Thanks for your correspondence about this-- you are right: the issue arose because a recent update

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Problem with mhrR_GLM

Thanks for your correspondence about this-- you are right: the issue arose because a recent update

11/18/20

Paweł Augustynowicz

11/18/20

fluence profile serial number

Hello, I have a basic technical question with installing pre-calculated high resolution fluence

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fluence profile serial number

Hello, I have a basic technical question with installing pre-calculated high resolution fluence

11/18/20

Sabrina Brigadoi, … Stephen Tucker6

11/18/20

mlActMan instead of mlActAuto in hmrR_MotionArtifactByChannel?

Hi Adam, Try deleting the generated .mat files and creating a new processing stream. Some used

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mlActMan instead of mlActAuto in hmrR_MotionArtifactByChannel?

Hi Adam, Try deleting the generated .mat files and creating a new processing stream. Some used

11/18/20

Joel Licea, Boas, David2

11/11/20

Probe Window on HOMER3

Good idea This zoom feature doesn't exist on the probe display window… but it is a good idea. I

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Probe Window on HOMER3

Good idea This zoom feature doesn't exist on the probe display window… but it is a good idea. I

11/11/20

Shannon Lim, … Boas, David7

11/6/20

How are trials combined within a block/condition?

The GLM in Homer3 will very soon properly handle trials of different lengths as you can include stim

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How are trials combined within a block/condition?

The GLM in Homer3 will very soon properly handle trials of different lengths as you can include stim

11/6/20

11/2/20

Our 2020 fNIRS Training Workshop was a great success the last 2 weeks. All of the lectures and

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Our 2020 fNIRS Training Workshop was a great success the last 2 weeks. All of the lectures and

11/2/20

shann...@gmail.com, Boas, David4

10/26/20

Length of trange resulting in "inaccurate" results

Hi David, Thanks for your initial thoughts. 1. Yes, I have short separation channels (8 of them) 2. I

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Length of trange resulting in "inaccurate" results

Hi David, Thanks for your initial thoughts. 1. Yes, I have short separation channels (8 of them) 2. I

10/26/20

adam.v....@gmail.com, … Boas, David11

10/25/20

Error processing GLM (homer 3)

For analyzing lots of data in a non-interactive way, you want to run the analysis script in matlab

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Error processing GLM (homer 3)

For analyzing lots of data in a non-interactive way, you want to run the analysis script in matlab

10/25/20

Meenakshi Siddharthan, Boas, David2

10/23/20

AtlasViewer Channel Exclusion

Meena, AtlasViewer does an image reconstruction using the HRF output from Homer. If this HRF output

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AtlasViewer Channel Exclusion

Meena, AtlasViewer does an image reconstruction using the HRF output from Homer. If this HRF output

10/23/20

Simina Pitur, Boas, David2

10/16/20

Taking the average of the whole time course versus taking the average of only the baseline periods

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Taking the average of the whole time course versus taking the average of only the baseline periods

10/16/20

10/15/20

AtlasViewer generate sensitivity profile missing WL2

Good afternoon, Recently I've been trying to generate the sensitivity profile using digpts only

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AtlasViewer generate sensitivity profile missing WL2

Good afternoon, Recently I've been trying to generate the sensitivity profile using digpts only

10/15/20

Yucel, Meryem, Samuel Montero2

9/24/20

using homer3 functions offline

Thanks for sharing, this is very helpful. Sam On Thu, Sep 24, 2020 at 11:32 AM Yucel, Meryem <

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using homer3 functions offline

Thanks for sharing, this is very helpful. Sam On Thu, Sep 24, 2020 at 11:32 AM Yucel, Meryem <

9/24/20

Joel Licea, … Sergio Novi5

9/17/20

Perfomance Metrics Homer3

Hi Yucel, I think this type of simulated data is what we need access to. Thank you so much for the

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Perfomance Metrics Homer3

Hi Yucel, I think this type of simulated data is what we need access to. Thank you so much for the

9/17/20

Meenakshi Siddharthan, … Yucel, Meryem11

9/15/20

[Homer3/AtlasViewerGUI] Homer3 compatibility for AtlasViewer

Dear Meryem, Thank you for the reply! So we've rearranged our .nirs files using the matlab code

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[Homer3/AtlasViewerGUI] Homer3 compatibility for AtlasViewer

Dear Meryem, Thank you for the reply! So we've rearranged our .nirs files using the matlab code

9/15/20

Shannon Lim, … Boas, David8

9/15/20

AtlasViewer: Checking if individual MRI was imported correctly

The original purpose for importing MRIs was for visualization and calculating the forward problem for

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AtlasViewer: Checking if individual MRI was imported correctly

The original purpose for importing MRIs was for visualization and calculating the forward problem for

9/15/20

9/15/20

Save the date for the next Homer3 webinar!!

Hello all, Our next installment in our webinar series were supposed to be on September 15, 2020

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Save the date for the next Homer3 webinar!!

Hello all, Our next installment in our webinar series were supposed to be on September 15, 2020

9/15/20

9/12/20

Increase Confidence and Build More Effective Email Campaigns

We have a long way to go from our clients. In the midst of dissatisfaction and difficulties that

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Increase Confidence and Build More Effective Email Campaigns

We have a long way to go from our clients. In the midst of dissatisfaction and difficulties that

9/12/20

Dharminder Singh Tejinder Singh Langri, Boas, David5

9/11/20

Custom device data processing

I am not sure if that tutorial exists at the moment. We certainly go through it in our Homer class

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Custom device data processing

I am not sure if that tutorial exists at the moment. We certainly go through it in our Homer class

9/11/20

Parya Farzam, Hila Gvirts4

9/10/20

Save the Date for virtual 2020 fNIRS course!

Thank you We'll be two ( one of my students is religious and it would be hard for him to

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Save the Date for virtual 2020 fNIRS course!

Thank you We'll be two ( one of my students is religious and it would be hard for him to

9/10/20

Shusaku Umeda, Yucel, Meryem3

9/7/20

Question on processing time series motion corrections using accelerometers

Hi Meryem, Thank you for reply! Yes, as you said, our customer wants to remove motion artifact from

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Question on processing time series motion corrections using accelerometers

Hi Meryem, Thank you for reply! Yes, as you said, our customer wants to remove motion artifact from

9/7/20

Nicollette Purcell, Stephen Tucker4

9/2/20

manually excluding data

Hi, The latest version on GitHub allows you to disable time points. Sorry for the delay! We are in

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manually excluding data

Hi, The latest version on GitHub allows you to disable time points. Sorry for the delay! We are in

9/2/20

Sagar K V, Simina Pitur2

8/27/20

Convert fNIRsoft (.nir) to Homer2 (.nirs)

Hello, Hope my answer doesn't come too late, bu these scripts here convert from .nir and .mrk to

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Convert fNIRsoft (.nir) to Homer2 (.nirs)

Hello, Hope my answer doesn't come too late, bu these scripts here convert from .nir and .mrk to

8/27/20

Franziska Klein, … shann...@gmail.com4

8/20/20

AtlasViewer: Sensitivity Map Problem

Hi Franziska, Would you be willing to share your adapted code? or guide me to which code you adapted

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AtlasViewer: Sensitivity Map Problem

Hi Franziska, Would you be willing to share your adapted code? or guide me to which code you adapted

8/20/20

Franziska Klein, … shann...@gmail.com5

8/20/20

AtlasViewer: 'Warning: No cortical anatomical labels provided for this anatomy'

Hi Franziska, Did you find a solution for your issue? Are you able to project the probe coordinate

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AtlasViewer: 'Warning: No cortical anatomical labels provided for this anatomy'

Hi Franziska, Did you find a solution for your issue? Are you able to project the probe coordinate

8/20/20

Aleksandra Dopierała, Yucel, Meryem2

8/4/20

Manually excluding channels in Homer3

Hi Aleksandra, Unfortunately, none of the three are there yet in homer3, but they are in our to-do

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Manually excluding channels in Homer3

Hi Aleksandra, Unfortunately, none of the three are there yet in homer3, but they are in our to-do

8/4/20

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