help > Error reading sidecar json files
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Mar 27, 2025  01:03 AM | abslab
Error reading sidecar json files

Dear sirs, 


I specify  Setup.RT=NaN and Setup.preprocessing.sliceorder='BIDS'  to read the information from sidecar json files. But I got the following error message:


Error using conn_get_rt (line 51)
error reading RepetitionTime field; cannot find .json file or timing information associated with data file
..../002_S_0413/func/sauEPIs_01.surf.nii   


(I am using default_ss)


The orginal json file EPIs_01.json was put beside the image file EPIs_01.nii. It has the RT and SliceTiming fields. 


Should I specify the path of the json files somewhere? Or should I rename it as "sauEPIs_01.surf.json" manually?


Thank you for your help in advance. 


Abslab

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Mar 28, 2025  01:03 PM | Alfonso Nieto-Castanon - Boston University
RE: Error reading sidecar json files

Dear Abslab,


Thank you for reporting this, this was a bug in the code as CONN should be able to find the associated EPIs_01.json file without the need to rename that .json file. Please use the attached patch and let me know if you still run into any issues (this patch is for the latest release of CONN -v2407-, to use it simply copy the attached file to your conn distribution folder overwriting the file with the same name there)


Best


Alfonso


Originally posted by abslab:



Dear sirs, 


I specify  Setup.RT=NaN and Setup.preprocessing.sliceorder='BIDS'  to read the information from sidecar json files. But I got the following error message:


Error using conn_get_rt (line 51)
error reading RepetitionTime field; cannot find .json file or timing information associated with data file
..../002_S_0413/func/sauEPIs_01.surf.nii   


(I am using default_ss)


The orginal json file EPIs_01.json was put beside the image file EPIs_01.nii. It has the RT and SliceTiming fields. 


Should I specify the path of the json files somewhere? Or should I rename it as "sauEPIs_01.surf.json" manually?


Thank you for your help in advance. 


Abslab



 

Attachment: conn_setup_preproc_meanimage.m
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Mar 29, 2025  05:03 AM | abslab
RE: Error reading sidecar json files

Hi Alfonso


Thank you very much for the new script. Yes I am using c2407. Yes the new script is working fine. No error message any more. 


Thank you again.


Abslab


 


Originally posted by Alfonso Nieto-Castanon:



Dear Abslab,


Thank you for reporting this, this was a bug in the code as CONN should be able to find the associated EPIs_01.json file without the need to rename that .json file. Please use the attached patch and let me know if you still run into any issues (this patch is for the latest release of CONN -v2407-, to use it simply copy the attached file to your conn distribution folder overwriting the file with the same name there)


Best


Alfonso


Originally posted by abslab:



Dear sirs, 


I specify  Setup.RT=NaN and Setup.preprocessing.sliceorder='BIDS'  to read the information from sidecar json files. But I got the following error message:


Error using conn_get_rt (line 51)
error reading RepetitionTime field; cannot find .json file or timing information associated with data file
..../002_S_0413/func/sauEPIs_01.surf.nii   


(I am using default_ss)


The orginal json file EPIs_01.json was put beside the image file EPIs_01.nii. It has the RT and SliceTiming fields. 


Should I specify the path of the json files somewhere? Or should I rename it as "sauEPIs_01.surf.json" manually?


Thank you for your help in advance. 


Abslab



 



 

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