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[FIX] display error when impossible slice timing values are given #969

Merged
merged 7 commits into from
Mar 29, 2023
Merged

[FIX] display error when impossible slice timing values are given #969

merged 7 commits into from
Mar 29, 2023

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Remi-Gau
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fixes #967

@JacMatu
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JacMatu commented Mar 28, 2023 •
edited by Remi-Gau

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
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OK this is a rounding error on my side

will fix that

@Remi-Gau
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I tested with values and assuming that you have a TR of 2 seconds.

It should work now.

@JacMatu
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JacMatu commented Mar 28, 2023 •
edited by Remi-Gau

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

let me check

@Remi-Gau
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@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
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JacMatu commented Mar 28, 2023 via email

@Remi-Gau
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Cool.
Merging this then.

@Remi-Gau Remi-Gau merged commit d29096c into cpp-lln-lab:main Mar 29, 2023
13 checks passed
@Remi-Gau Remi-Gau deleted the fix-acq_time_error branch March 29, 2023 09:09
@JacMatu JacMatu mentioned this pull request Apr 18, 2023
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Successfully merging this pull request may close these issues.

[BUG] 'pattern' error during BUILDING JOB: slice timing correction
2 participants
@Remi-Gau @JacMatu