[FIX] display error when impossible slice timing values are given

[Remi-Gau]

fixes #967

[JacMatu]

Running the script produced an error

[14:07:39] bidspm - INFO				getAndCheckSliceOrder
 SLICE TIMING INFORMATION EXTRACTED FROM METADATA.

[14:07:39] bidspm - INFO				

[14:07:39] bidspm - ERROR				getAcquisitionTime
Acquisition time cannot be < to any slice timing value:

Current values:
- acquisition time: 1.942857
- slice timing 
	-      0
	- 0.0575
	-  0.115
	- 0.1725
	-   0.23
	- 0.2875
	-  0.345
	- 0.4025
	-   0.46
	- 0.5175
	-  0.575
	- 0.6325
	-   0.69
	-  0.745
	- 0.8025
	-   0.86
	- 0.9175
	-  0.975
	- 1.0325
	-   1.09
	- 1.1475
	-  1.205
	- 1.2625
	-   1.32
	- 1.3775
	-  1.435
	- 1.4925
	-   1.55
	- 1.6075
	-  1.665
	- 1.7225
	- 1.7775
	-  1.835
	- 1.8925
	-   1.95


 Error getAcquisitionTime:sliceTimingSuperiorToAcqTime occurred:
	- Error in errorHandling
		line 57 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/src/messages/errorHandling.m
	- Error in logger
		line 70 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/src/messages/logger.m
	- Error in getAcquisitionTime
		line 31 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/src/preproc/utils/getAcquisitionTime.m
	- Error in setBatchSTC
		line 66 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/src/batches/preproc/setBatchSTC.m
	- Error in bidsSTC
		line 47 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/src/workflows/preproc/bidsSTC.m
	- Error in preprocess
		line 247 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/bidspm.m
	- Error in executeAction
		line 147 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/bidspm.m
	- Error in bidspm
		line 79 in /Users/jacekmatuszewski/Documents/Language_MVPA/bidspm/bidspm.m
	- Error in step_1_bidspm_preprocess
		line 24 in /Users/jacekmatuszewski/Documents/Language_MVPA/Data/BIDS_Nifti/code/step_1_bidspm_preprocess.m

error log attached

error_2023-03-28T14-07.log

[Remi-Gau]

OK this is a rounding error on my side

will fix that

[Remi-Gau]

I tested with values and assuming that you have a TR of 2 seconds.

It should work now.

[JacMatu]

bidspm();

results in

Unrecognized function or variable 'bugReport'.

Error in bidspm (line 85)
    bugReport(opt, ME);

Is there a quick fix for that? Is that some kind of dev debugging mode?

[Remi-Gau]

The function should be there in the version 3.0.0 you are using:

https://github.com/cpp-lln-lab/bidspm/blob/main/src/messages/bugReport.m

It is the function that will write a bug report when something fails.

If you get this error it means that bidspm may not have been properly initialised.

What command did you run?

[Remi-Gau]

wait... you just ran bidspm() and got this error?

let me check

[Remi-Gau]

@JacMatu try updating again from my branch

I could reproduce the error you are getting but at least now we should know more about why bidspm() failed to run.

[JacMatu]

Maybe I messed something up with paths and initializing. I've reset everything and it runs! THanks for help Remi, I'll be back with next errors!

…

On Tue, 28 Mar 2023 at 17:59, Remi Gau ***@***.***> wrote: wait... you just ran bidspm() and got this error? let me check — Reply to this email directly, view it on GitHub <#969 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWQTRS5X5ITEM3J3GLM7NLTW6MDE7ANCNFSM6AAAAAAWKGF3E4> . You are receiving this because you commented.Message ID: ***@***.***>

-- Ph. D. Laboratory of Brain Imaging (LOBI) Nencki Institute of Experimental Biology Polish Academy of Sciences Pasteur 3, 02-093 Warsaw, Poland Tel: +48 22 5892 551 mail: ***@***.*** ***@***.***> website: http://lobi.nencki.gov.pl/ Google Scholar profile <https://scholar.google.com/citations?user=QI1KL4wAAAAJ&hl=pl&oi=ao>

[Remi-Gau]

Cool.
Merging this then.