Reproduction attempt

[cmaumet]

Hi @mselimata!

As discussed, I have tried to re-run your code, here are a few questions:

• In https://github.com/mselimata/spmbasics/blob/main/README.md?plain=1#L31 you mention that the root parameter must be updated but I did not understand what "in the first section defining the data root" is so wondering where this should be done. Can you point me to the corresponding file?

• could you update the README to include subtitles under "How to Reproduce Each Step" in order to separate the original analysis and the two reproductions (1- GUI, 2-batch, 3-script). This will make it easier to reproduce only a subpart of all the analyses you have done (here I'd like to reproduce only scripting for example)

• I am running into an error, can you help? Here is what I did: first, I moved to the spmbasics folder and then:

root = fullfile(pwd, '/data/MoAEpilot')
run src/script/preprocessing_script

I get the following error:

>> run src/script/preprocessing_script
Unrecognized function or variable 'X'.

Error in preprocessing_script (line 2)
nrun = X; % enter the number of runs here

Error in run (line 91)
evalin('caller', strcat(script, ';'));

[mselimata]

Thank you @cmaumet

* In https://github.com/mselimata/spmbasics/blob/main/README.md?plain=1#L31 you mention that the `root` parameter must be updated but I did not understand what "in the first section defining the data root" is so wondering where this should be done. Can you point me to the corresponding file?

It is on the job_preprocessing_script_job.m the line on the pointed link below:
https://github.com/mselimata/spmbasics/blob/main/src/script/preprocessing_script_job.m#L14

* could you update the README to include subtitles under "How to Reproduce Each Step" in order to separate the original analysis and the two reproductions (1- GUI, 2-batch, 3-script). This will make it easier to reproduce only a subpart of all the analyses you have done (here I'd like to reproduce only scripting for example)

Edited to be more clear, thank you.

root = fullfile(pwd, '/data/MoAEpilot')
run src/script/preprocessing_script

I get the following error:

run src/script/preprocessing_script
Unrecognized function or variable 'X'.

Error in preprocessing_script (line 2)
nrun = X; % enter the number of runs here

Error in run (line 91)
evalin('caller', strcat(script, ';'));

Yes, because preprocessing_script.m is kept in default settings. It is redundant right now maybe it is better to remove it from the repo.
Instead run src/script/preprocessing_script_job should be used and it should work.