error running ds001168 demo

[marcobarilari]

while running

bidsCreateVDM(opt); I got this error

Options are locked & loaded.

FOR TASK: rest
WILL WORK ON SUBJECTS
    '01'

 FIELDMAP WORKFLOW
 PROCESSING GROUP: SUBJECT No.: 1 SUBJECT ID : 01 
 FIELDMAP WORKFLOW: COREGISTERING FIELD MAPS TO FIRST FUNC IMAGE


------------------------------------------------------------------------
01-Nov-2020 22:55:42 - Running job #1
------------------------------------------------------------------------
01-Nov-2020 22:55:42 - Running 'Coregister: Estimate'

SPM12: spm_coreg (v7320)                           22:55:42 - 01/11/2020
========================================================================
Completed                               :          22:55:57 - 01/11/2020
01-Nov-2020 22:55:57 - Done    'Coregister: Estimate'
01-Nov-2020 22:55:57 - Running 'Coregister: Estimate'

SPM12: spm_coreg (v7320)                           22:55:57 - 01/11/2020
========================================================================
Completed                               :          22:56:11 - 01/11/2020
01-Nov-2020 22:56:11 - Done    'Coregister: Estimate'
01-Nov-2020 22:56:11 - Running 'Coregister: Estimate'

SPM12: spm_coreg (v7320)                           22:56:11 - 01/11/2020
========================================================================
Completed                               :          22:56:28 - 01/11/2020
01-Nov-2020 22:56:28 - Done    'Coregister: Estimate'
01-Nov-2020 22:56:28 - Running 'Coregister: Estimate'

SPM12: spm_coreg (v7320)                           22:56:28 - 01/11/2020
========================================================================
Completed                               :          22:56:47 - 01/11/2020
01-Nov-2020 22:56:47 - Done    'Coregister: Estimate'
01-Nov-2020 22:56:47 - Done

 FIELDMAP WORKFLOW: CREATING VDMs 
Error using getMetadataFromIntendedForFunc (line 58)
Voxel displacement map creation requires a non empty valuefor the TotalReadoutTime of the bold sequence they are
matched to.

Error in setBatchCreateVDMs>getMetadataForVDM (line 94)
  [totalReadoutTime, blipDir] = getMetadataFromIntendedForFunc(BIDS, fmapMetadata);

Error in setBatchCreateVDMs (line 59)
      [echotimes, isEPI, totReadTime, blipDir] = getMetadataForVDM(BIDS, ...

Error in bidsCreateVDM (line 39)
        matlabbatch = setBatchCreateVDMs(BIDS, opt, subID);

[Remi-Gau]

Yup I know that one.

I have added some comments in this file.

https://github.com/cpp-lln-lab/CPP_SPM/blob/1530a1642a5213e0657646690b80a0c6f3a51cd9/src/fieldmaps/getTotalReadoutTime.m#L25

I had "very quickly" added a mention in this issue: #144

In a nutshell, the info we need to create a VDM in SPM (see calculate VDM module in SPM batch):

• blip direction
• echo time
• total EPI readout time

I am fairly sure about to get the ones from that dataset. But total EPI readout time is not mentioned, so maybe there is a way to compute it from the information we have, but I am not sure how (see the comments with a lot of ??? in the file above).

We want to cross-check:

• can we make it easy for us by having BIDSme give us the total EPI readout time during BIDS conversion?
• is it actually possible to compute total EPI readout time from the info in ds001168? If it is not then that is an issue because it means some BIDS dataset are not usable with SPM. I tend to think that this has been thought of so there must be a way out.

Things to keep an eye on:

• the code from this repo from the fMRIprep gang could have answers for us: https://github.com/nipreps/sdcflows