The HRF estimation seems to be quite fast (particularly with microtime resolution 1 and AR off), but the "deconvolving HRF" step always takes very very long, even for just 300 volumes.

Is there a way to make this step faster?

I hope to get some help!
I've tried Job1 of the demo jobs, but failed. The error messages are shown below.
I just followed the rsHRF_manual_Matlab and don’t know how to solve the problem.
Thank you for any help !

Error use rsHRF_estimation_temporal_basis (line 34)
The source code for the parfor loop that attempted to execute the worker process could not be found (D:\MATLAB\toolbox\spm12\toolbox\rsHRF\rsHRF_estimation_temporal_basis.m)
In file "D:\MATLAB\toolbox\spm12\toolbox\rsHRF\rsHRF_estimation_temporal_basis.m" (v4473), function "rsHRF_estimation_temporal_basis" at line 34.
In file "D:\MATLAB\toolbox\spm12\toolbox\rsHRF\rsHRF_deconv_job.m" (???), function "rsHRF_deconv_job" at line 41.
In file "D:\MATLAB\toolbox\spm12\toolbox\rsHRF\rsHRF.m" (???), function "rsHRF" at line 113.
In file "D:\MATLAB\toolbox\spm12\toolbox\rsHRF\tbx_cfg_rsHRF.m" (???), function "wgr_vox_ROI_rsHRF_conn" at line 884.
The following modules did not run:
Failed: Voxel-wise HRF deconvolution

We would need to create an automatic testing environment. We have some services that can help us to do this (CircleCI, Travis...). Let's explore possibilities and decide.

It would be great to have a test case with the same data for Matlab and Python, so we can test if results are the same in both cases. Programming tests for Python won't be an issue, but for Matlab it is probable that we have to get an standalone executable for the rsHRF (other option is to execute the scripts in Octave).

Finally, we will create the BIDSapp using Docker. The handling of BIDS structure will be through pyBIDS.

It is important (although not mandatory) to create a standalone Python package, we would need the package to have some input parameters and checks. This process also can be automatized.

With this, it will be much easier to build the Docker.

Hello

hope to get some help

I have Matlab R2015a, and try to install HRF, the install script works fine, no errors, however, loading SPM comes with this message and the toolbox does not appear in tools from the batch mode. Thank you for any help !

SPM12: v7771 20:45:33 - 05/03/2021

Initialising SPM : ..
Warning: Loading of older CAT12 segmentation versions was not successful and will be skipped.
Loading of toolbox /Applications/spm12/toolbox/rsHRF/tbx_cfg_rsHRF.m failed.
......done

SPM present working directory:
/Users/

Hi @sofievdbos and @guorongwu , I don't remember if we changed this. In the master branch of the python implementation this is allowed, on the other hand it's not here.
thanks!

The link for the IOS-LFP rat data in the tutorial (rsHRF/demo_codes/rsHRF_tutorials.md) is not available.

Hi
I need some help. I'm confused by these parameters. I have learned the manual. In the manual, different jobs have different parameters. I don't know how to changes these parameters to get a best result.
Can you tell me how to set them? Thanks a lot

Dear experts,

I installed your toolbox and I've encountered some issues setting the parameters.
First, is there a way to choose the best HRF basis function based on my data?
Could be a correct approach to estimate both canonical and gamma functions and then compare them? If so, how should I do it operatively?

Then, in the case of gamma function, how can I estimate the number of basis functions?

In Threshold (SD) for event detection should I change the value (i.e 1)? (considering both the options: canonical and gamma function). I read here in the solved issues that your advice is to do not change if I don't know what parameter set.

Also, what is K (local peak)? How is it calculated?

Many thanks in advance

Beatrice

When I applied rsHRF for my data, the event number of some voxels is 0.
How are voxels without an event processed?

Hi Daniele,

I am trying to run the Voxel-wise HRF estimation. I get the following error:

#----------------------------------------------------------------
27-Apr-2021 18:31:43 - Failed 'Voxel-wise HRF deconvolution'
Undefined function 'wavedec' for input arguments of type 'double'.
In file "C:\Users\lloydb\surfdrive\ExperimentData\toolbox\spm12\spm12\toolbox\rsHRF\rsHRF_iterative_wiener_deconv.m" (???), function "rsHRF_iterative_wiener_deconv" at line 22.
In file "C:\Users\lloydb\surfdrive\ExperimentData\toolbox\spm12\spm12\toolbox\rsHRF\rsHRF_deconv_job.m" (???), function "rsHRF_deconv_job" at line 107.
In file "C:\Users\lloydb\surfdrive\ExperimentData\toolbox\spm12\spm12\toolbox\rsHRF\rsHRF.m" (???), function "rsHRF" at line 113.
In file "C:\Users\lloydb\surfdrive\ExperimentData\toolbox\spm12\spm12\toolbox\rsHRF\tbx_cfg_rsHRF.m" (???), function "wgr_vox_ROI_rsHRF_conn" at line 884.

The following modules did not run:
Failed: Voxel-wise HRF deconvolution
#----------------------------------------------------------------

I changed the flag_parfor to 0 in rsHRF_estimation_temporal_basis.m (line 20) just in case the issue was with parfor, but the error remains.
(by the way I am running it on Matlab version R2020a)

I had a look for the function 'wavedec' and it seems you have to buy it with the toolbox wavelet... Do you think that is the cause of the error? And do you suggest to purchase wavelet?

Thank you for your help!
Beth

We need a proper structure of folders. The python files should be inside a folder called rsHRF in different modular folders according to their functionality.

Take a look to this template example:

https://github.com/uwescience/shablona

this example is also useful to prepare the package's testing environment, continuous integration and documentation.