topup error when running prisma_preproc.py on BIDS subjects with extra fmap data

[noahbenson]

Details below all assume that you have the winawerlab server mounted in /Volumes/server.

Command:

> cd /Volumes/server/Projects/Retinotopy/CMag/data/BIDS
> python prisma_preproc.py -dir_structure bids -bids_task prf -datadir $PWD/sub-wlsubj090/ses-nyu3t01 -subject wlsubj90

This produces a topup error reported to stdout as:

RuntimeError: Command:
topup --config=b02b0.cnf --datain=/Volumes/server/Projects/Retinotopy/CMag/data/BIDS/derivatives/preprocessed/sub-wlsubj090/ses-nyu3t01/workflow/unwarp_distort/distortion_merged_encfile.txt --fwhm=0.000000 --imain=/Volumes/server/Projects/Retinotopy/CMag/data/BIDS/derivatives/preprocessed/sub-wlsubj090/ses-nyu3t01/workflow/merge_distort/distortion_merged.nii.gz --out=distortion_merged_base --iout=distortion_merged_corrected.nii.gz --fout=distortion_merged_field.nii.gz --jacout=jac --logout=distortion_merged_topup.log --rbmout=xfm --dfout=warpfield
Standard output:

Standard error:

Part of FSL (ID: 5.0.10)
topup

Usage: 
topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --out=my_topup_results


Compulsory arguments (You MUST set one or more of):
        --imain         name of 4D file with images
        --datain        name of text file with PE directions/times

Optional arguments (You may optionally specify one or more of):
        --out           base-name of output files (spline coefficients (Hz) and movement parameters)
        --fout          name of image file with field (Hz)
        --iout          name of 4D image file with unwarped images
        --logout        Name of log-file
        --warpres       (approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10
        --subsamp       sub-sampling scheme, default 1
        --fwhm          FWHM (in mm) of gaussian smoothing kernel, default 8
        --config        Name of config file specifying command line arguments
        --miter         Max # of non-linear iterations, default 5
        --lambda        Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
        --ssqlambda     If set (=1), lambda is weighted by current ssq, default 1
        --regmod        Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
        --estmov        Estimate movements if set, default 1 (true)
        --minmet        Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
        --splineorder   Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
        --numprec       Precision for representing Hessian, double or float. Default double
        --interp        Image interpolation model, linear or spline. Default spline
        --scale         If set (=1), the images are individually scaled to a common mean, default 0 (false)
        --regrid                If set (=1), the calculations are done in a different grid, default 1 (true)
        -h,--help       display help info
        -v,--verbose    Print diagonostic information while running
        -h,--help       display help info

This error does not happen for other subjects in the directory (e.g., wlsubj092). As far as I can tell, the differentiating factor between subjects that work and subjects that don't is the contents of the subject's fmap directory:

> ls sub-wlsubj090/ses-nyu3t01/fmap
sub-wlsubj090_ses-nyu3t01_acq-dwi_dir-AP_run-01_epi.json
sub-wlsubj090_ses-nyu3t01_acq-dwi_dir-AP_run-01_epi.nii.gz
sub-wlsubj090_ses-nyu3t01_acq-dwi_dir-PA_run-01_epi.json
sub-wlsubj090_ses-nyu3t01_acq-dwi_dir-PA_run-01_epi.nii.gz
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-AP_run-01_epi.json
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-AP_run-01_epi.nii.gz
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-AP_run-02_epi.json
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-AP_run-02_epi.nii.gz
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-PA_run-01_epi.json
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-PA_run-01_epi.nii.gz
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-PA_run-02_epi.json
sub-wlsubj090_ses-nyu3t01_acq-fMRI_dir-PA_run-02_epi.nii.gz
> ls sub-wlsubj092/ses-nyu3t01/fmap
sub-wlsubj092_ses-nyu3t01_acq-fMRI_dir-AP_run-01_epi.json
sub-wlsubj092_ses-nyu3t01_acq-fMRI_dir-AP_run-01_epi.nii.gz
sub-wlsubj092_ses-nyu3t01_acq-fMRI_dir-PA_run-01_epi.json
sub-wlsubj092_ses-nyu3t01_acq-fMRI_dir-PA_run-01_epi.nii.gz

I'm assuming that the issue is related to the extra distortion scans and the diffusion scans. Is there a way to tell prisma_preproc to use a specific run of the distortion scans? (The second run of distrotion scans, in this case, was for the diffusion scan.)