Hello!
I am new to CONN and I using the compiled version.
I am trying to complete a preprocessing step using the preprocessing pipeline for volume-based analysis (direct normalization to MNI-space) when FieldMaps are available. When entering functional data, for each subject I am including two resting state scan files in separate sessions as my primary data set. I created a secondary data set, independent from the primary data set, where for each subject I add their .img fieldmap file (in Hz) to each session.
When asked about slice order, I chose interleaved (Siemens). When entering VDM settings, I select the secondary data set as my fieldmap location and pre-computed fieldmap file as my fieldmap type. I then enter my EPI total readout time. All other parameters are left unchanged.
When I set up the pipeline, I receive this error following a prompt that says "Preparing functional Creation of voxel-displacement map (VDM) for Susceptibility Distortion Correction":
ERROR DESCRIPTION:
Error using spm_jsonread Invalid or incomplete JSON.
Error in conn_jsonread (line 29)
Error in conn_setup_preproc (line 2804)
Error in conn (line 1105)
Error in conn_menumanager (line 120)
CONN19.b
SPM compiled
Matlab v.2019b
project: CONN19.b
storage: 848.8Gb available
Following the error message chain above, in conn_setup_preproc (line 2804) I found
if nses==1&&isempty(BLIP), conn_disp('fprintf','warning: unable to find PhaseEncodingDirection information in %s\n',filename); end
However, it looks like the issue may begin earlier on line 2771, it is not recognizing what we enter for vdm_type, and not registering that we entered a number for BLIP.
Does anyone see an obvious error, or perhaps have a suggestion on how I can resolve this issue. As far as I am aware, I do not need a JSON file here, so I am curious why this error keeps appearing and how the number entered into the BLIP field relates to the error?
Thanks,
Ted
I am new to CONN and I using the compiled version.
I am trying to complete a preprocessing step using the preprocessing pipeline for volume-based analysis (direct normalization to MNI-space) when FieldMaps are available. When entering functional data, for each subject I am including two resting state scan files in separate sessions as my primary data set. I created a secondary data set, independent from the primary data set, where for each subject I add their .img fieldmap file (in Hz) to each session.
When asked about slice order, I chose interleaved (Siemens). When entering VDM settings, I select the secondary data set as my fieldmap location and pre-computed fieldmap file as my fieldmap type. I then enter my EPI total readout time. All other parameters are left unchanged.
When I set up the pipeline, I receive this error following a prompt that says "Preparing functional Creation of voxel-displacement map (VDM) for Susceptibility Distortion Correction":
ERROR DESCRIPTION:
Error using spm_jsonread Invalid or incomplete JSON.
Error in conn_jsonread (line 29)
Error in conn_setup_preproc (line 2804)
Error in conn (line 1105)
Error in conn_menumanager (line 120)
CONN19.b
SPM compiled
Matlab v.2019b
project: CONN19.b
storage: 848.8Gb available
Following the error message chain above, in conn_setup_preproc (line 2804) I found
if nses==1&&isempty(BLIP), conn_disp('fprintf','warning: unable to find PhaseEncodingDirection information in %s\n',filename); end
However, it looks like the issue may begin earlier on line 2771, it is not recognizing what we enter for vdm_type, and not registering that we entered a number for BLIP.
Does anyone see an obvious error, or perhaps have a suggestion on how I can resolve this issue. As far as I am aware, I do not need a JSON file here, so I am curious why this error keeps appearing and how the number entered into the BLIP field relates to the error?
Thanks,
Ted