help > MRIcroGL - slice timing correction
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Nov 1, 2024  03:11 PM | Belina Rodrigues
MRIcroGL - slice timing correction

Hi, 


 


When I convert ima.files into nifti from an interleaved acquisition using MRIcroGL, does slice timing correction happen? When I check the output of the conversion from ima.file to nifti on AFNI, the timing of the slices seems to have been corrected. 


 


Thanks


 


 


 

Nov 1, 2024  03:11 PM | Chris Rorden
RE: MRIcroGL - slice timing correction

dcm2niix will attempt to losslessly convert DICOM to NIfTI. Therefore, it does not alter your images for motion or slice times. For many manufacturers (GE and Siemens) the slice times will be recorded in the BIDS JSON file so you can use your favorite tool to slice time correct your data. Some manufacturers (e.g. Philips) do no include slice times in the source DICOMs.

Nov 1, 2024  05:11 PM | Belina Rodrigues
RE: MRIcroGL - slice timing correction

Originally posted by Chris Rorden:



dcm2niix will attempt to losslessly convert DICOM to NIfTI. Therefore, it does not alter your images for motion or slice times. For many manufacturers (GE and Siemens) the slice times will be recorded in the BIDS JSON file so you can use your favorite tool to slice time correct your data. Some manufacturers (e.g. Philips) do no include slice times in the source DICOMs.



Thank you for your quick reply. How would you recommend I check that the slice timing correction has adequately been done?


 


thanks 

Nov 4, 2024  06:11 PM | Chris Rorden
RE: MRIcroGL - slice timing correction

I would contact the message forums of the tool you used for the slice time correction - AFNI, FSL and SPM all have their own mechanisms and contact methods (e.g. jiscmail). dcm2niix is for image conversion, not processing, so this question is out of scope for this forum.

Nov 4, 2024  10:11 PM | Belina Rodrigues
RE: MRIcroGL - slice timing correction

Thank you.