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hmrR_tCCA unable to run

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Posts: 11
Topic starter
(@nehohmee)
Active Member
Joined: 1 year ago

Hi everyone,

I have been unable to run hmrR_tCCA for my dataset with both short channels and accelerometer. This error appears:

"Function hmrR_tCCA generated error at line 129: The product of the downsample factor Q and the upsample factor P must be less than 2^31."

I am unable to figure out what is causing the problem, and would really appreciate any help I could get!

My processing pipeline and dataset can be found here: https://drive.google.com/drive/folders/1iV0PKjJZ8YSReRqfa0GpeevrJ81RfVqF?usp=share_link

Thank you so much!

I am running Homer3 v1.58.0, R2021a on Mac.

5 Replies
Meryem Yücel
Posts: 198
(@mayucel)
Joined: 4 years ago

@nehohmee,

 

You need your resting run and functional run(s) under the same subject folder to be able to run tcca. I only see one file there.

 

Meryem

 

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2 Replies
(@nehohmee)
Joined: 1 year ago

Active Member
Posts: 11

Hi @mayucel ,

Thank you for your reply. I have two questions as I encountered a problem despite adding my resting file:

1) I am aware it was suggested in the tCCA document that "We recommend to position your resting state data as the first run and set runIdxResting = 1". However, since my resting data was part of my functional data, I had to resort to segmenting out the resting data into another file. As such, this resting data becomes the second run within my folder. I then set runIdxResting = 2. Is this correct? Or do I have to rename all of my files such that my functional data becomes run 2 and my resting file becomes run 1?

2) Moving forward from what I did in Point 1, I received the error "Function hmIR_tCCA generated error at line 165: Index in position 2 exceeds array bounds (must not exceed 2)." Are there any potential reasons as to why this error appears, and how I could overcome this and run tCCA successfully? 

I have attached my dataset and processing pipeline here for reference: https://drive.google.com/drive/folders/1RvyipxGF_00mFHxyCO-OaDApPrJ-OkVn?usp=share_link

Thank you so much for your time and help!

Naomi

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(@nehohmee)
Joined: 1 year ago

Active Member
Posts: 11

Hi @mayucel ,

As a follow-up, I tried to rename my functional files to run 2 (002), and my segmented resting files to run 1 (001). However, this only caused MATLAB to stop responding. It looks like this is not a viable option.

Would really appreciate any help I can get. Thank you so much!

Naomi

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Meryem Yücel
Posts: 198
(@mayucel)
Joined: 4 years ago

@nehohmee, I see that the channel info don't show up for the resting run you put on gdrive (see attached figure). How did you cut the data? I resegment it using the homer segment tool, then renamed the files as 1resting and 2functional, then tcca worked. Also looking at your config file, you have kept the default [1 2 3 4] for tcca_aux_ind, however you only have two auxiliary channels in the file you send. This will break the code. If you want to use those aux channels as your regressors, you need to put [1 2]. (Since I do not know their content, I cannot say whether to use them or not.)

Hope this helps.

Meryem

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1 Reply
(@nehohmee)
Joined: 1 year ago

Active Member
Posts: 11

Hi @mayucel ,

I really appreciate your help thus far. I decided to try on a Windows laptop as somehow MATLAB kept freezing on my Mac during segmenting and loading of files.

I segmented my file using the Homer3 segment tool, and renamed both snirf files to 1resting and 2functional. Channel info appeared intact after doing so, and I proceeded with tcca with aux channels [1 2]. It seems the learning run was successful, as I obtained a tCCAfilter matrix (attached for reference). However, I was unable to obtain any HRF data output. The following error pops up when the pipeline runs on the functional file:

"Function hmrR_tCCA generated error at line 68: The product of the downsample factor Q and the upsample factor P must be less than 2^31."

My goal is to extract HRF data. Am I doing something wrong? I have checked and made sure I followed the steps correctly. I am unsure what else could be causing this error.

My data and the error message can be found here for reference: https://drive.google.com/drive/folders/1ZOu5tdPGrw4NUV03gcU_H4IHj_gdO0VC?usp=share_link

Just a note that I have tried running the pipeline as an entire session and file by file, but the same error persists.

Any help would mean a lot to me. Thank you so much!

Naomi

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