hello !
i'm in the midst of running fmriprep on my pilot data for a new two-session experiment.
i noticed an issue at my BIDS validation step regarding the storage of information on Phase Encoding direction and Total Readout Time. the specific errors: [ERR] You have to define 'PhaseEncodingDirection' for this file. (code: 18 - PHASE_ENCODING_DIRECTION_MUST_DEFINE)[ERR] You have to define 'TotalReadoutTime' for this file. (code: 19 - TOTAL_READOUT_TIME_MUST_DEFINE)
this information for the nifty files is meant to be pulled from the corresponding jsons, which have input fields for both that are either not being read or are being incorrectly read. more importantly i noticed that the phase encoding direction input may be reversed. all of my AP jsons have "j-" as the direction, and the PA jsons have "j". according to the documentation this should be the other way around, so i am worried that the wrong info might be coming in when it's transferred from the scanner.
if you have any advice on either of these issues (1, bids not reading the phase encoding/readout value and 2. the reversed encoding direction) please let me know
thanks !
hello !
i'm in the midst of running fmriprep on my pilot data for a new two-session experiment.
i noticed an issue at my BIDS validation step regarding the storage of information on Phase Encoding direction and Total Readout Time. the specific errors: [ERR] You have to define 'PhaseEncodingDirection' for this file. (code: 18 - PHASE_ENCODING_DIRECTION_MUST_DEFINE)[ERR] You have to define 'TotalReadoutTime' for this file. (code: 19 - TOTAL_READOUT_TIME_MUST_DEFINE)
this information for the nifty files is meant to be pulled from the corresponding jsons, which have input fields for both that are either not being read or are being incorrectly read. more importantly i noticed that the phase encoding direction input may be reversed. all of my AP jsons have "j-" as the direction, and the PA jsons have "j". according to the documentation this should be the other way around, so i am worried that the wrong info might be coming in when it's transferred from the scanner.
if you have any advice on either of these issues (1, bids not reading the phase encoding/readout value and 2. the reversed encoding direction) please let me know
thanks !