Hi Alfonso, thanks for the suggestions! I made the BATCH script based on the manual available online and think there's a few things I still have wrong. My current script reads:
clear BATCH;
BATCH.filename= '/media/nir/SharedDrive/Ben/GSPmar4.mat';
BATCH.Setup.isnew=1;
BATCH.Setup.preprocessing.steps={'default_mni'};
BATCH.Setup.functionals{1}{1}='/media/nir/SharedDrive/Ben/GSP/Sub0052_Ses1/Sub0052_Ses1_Scan_02_BOLD1.nii'
BATCH.Setup.functionals{1}{2}='/media/nir/SharedDrive/Ben/GSP/Sub0052_Ses1/Sub0052_Ses1_Scan_03_BOLD2.nii'
BATCH.Setup.functionals{2}{1}='/media/nir/SharedDrive/Ben/GSP/Sub0053_Ses1/Sub0053_Ses1_Scan_02_BOLD1.nii'
BATCH.Setup.functionals{2}{2}='/media/nir/SharedDrive/Ben/GSP/Sub0053_Ses1/Sub0053_Ses1_Scan_03_BOLD2.nii'
BATCH.Setup.structurals{1}='/media/nir/SharedDrive/Ben/GSP/Sub0052_Ses1/Sub0052_Ses1_Scan_01_ANAT1.nii'
BATCH.Setup.structurals{2}='/media/nir/SharedDrive/Ben/GSP/Sub0053_Ses1/Sub0053_Ses1_Scan_01_ANAT1.nii'
BATCH.Setup.preprocessing.fwhm=8;
BATCH.Setup.preprocessing.voxelsize_func=2;
BATCH.Setup.preprocessing.sliceorder=[1:2:47,2:2:47];
BATCH.Setup.RT=3.0;
BATCH.Setup.nsubjects=2;
BATCH.Setup.analyses=[1,2];
BATCH.Setup.voxelmask=1;
BATCH.Setup.voxelresolution=1;
BATCH.Setup.outputfiles=[0,1,0];
BATCH.Setup.roi.names={'LeftVentralStriatum','RightVentralStriatum', 'LeftDorsalPutamen', 'RightDorsalPutamen', 'LeftMedialDorsalThalamus', 'RightMedialDorsalThalamus', 'LeftVentralPutamen', 'RightVentralPutamen', 'LeftDorsalStriatum', 'RightDorsalStriatum'};

%works this far
BATCH.Setup.rois.names={'LeftVentralStriatum','RightVentralStriatum', 'LeftDorsalPutamen', 'RightDorsalPutamen', 'LeftMedialDorsalThalamus', 'RightMedialDorsalThalamus', 'LeftVentralPutamen', 'RightVentralPutamen', 'LeftDorsalStriatum', 'RightDorsalStriatum'}
BATCH.Setup.rois.dimensions={1,1,1,1,1,1,1,1,1,1}
BATCH.Setup.rois.files{1}='/media/nir/SharedDrive/Ben/ROIs/binLeftVentralStriatum.nii';
BATCH.Setup.rois.files{2}='/media/nir/SharedDrive/Ben/ROIs/binRightVentralStriatum.nii';
BATCH.Setup.rois.files{3}='/media/nir/SharedDrive/Ben/ROIs/binLeftDorsalPutamen.nii';
BATCH.Setup.rois.files{4}='/media/nir/SharedDrive/Ben/ROIs/binRightDorsalPutamen.nii';
BATCH.Setup.rois.files{5}='/media/nir/SharedDrive/Ben/ROIs/binLeftMedialDorsalThalamus.nii';
BATCH.Setup.rois.files{6}='/media/nir/SharedDrive/Ben/ROIs/binRightMedialDorsalThalamus.nii';
BATCH.Setup.rois.files{7}='/media/nir/SharedDrive/Ben/ROIs/binLeftVentralPutamen.nii';
BATCH.Setup.rois.files{8}='/media/nir/SharedDrive/Ben/ROIs/binRightVentralPutamen.nii';
BATCH.Setup.rois.files{9}='/media/nir/SharedDrive/Ben/ROIs/binLeftDorsalStriatum.nii';
BATCH.Setup.rois.files{10}='/media/nir/SharedDrive/Ben/ROIs/binRightDorsalStriatum.nii';
BATCH.Setup.conditions.names={'preop'};
BATCH.Setup.conditions.onsets{1}{1}{1}=[6];
BATCH.Setup.conditions.onsets{1}{1}{2}=[6];
BATCH.Setup.conditions.onsets{1}{2}{1}=[6];
BATCH.Setup.conditions.onsets{1}{2}{2}=[6];
BATCH.Setup.conditions.durations{1}{1}{1}=[inf];
BATCH.Setup.conditions.durations{1}{1}{2}=[inf];
BATCH.Setup.conditions.durations{1}{2}{1}=[inf];
BATCH.Setup.conditions.durations{1}{2}{2}=[inf];
%BATCH.Setup.covariates.names={'realignment'};
%BATCH.Setup.covariates.files{1}{1}{1}='/media/nir/SharedDrive/Ben/GSP/Sub0052_Ses1/rp_aSub0052_Ses1_Scan_02_BOLD1.txt';
%BATCH.Setup.covariates.files{1}{1}{2}='/media/nir/SharedDrive/Ben/GSP/Sub0052_Ses1/rp_aSub0052_Ses1_Scan_03_BOLD2.txt';
%BATCH.Setup.covariates.files{1}{2}{1}='/media/nir/SharedDrive/Ben/GSP/Sub0053_Ses1/rp_aSub0053_Ses1_Scan_02_BOLD1.txt';
%BATCH.Setup.covariates.files{1}{2}{2}='/media/nir/SharedDrive/Ben/GSP/Sub0053_Ses1/rp_aSub0053_Ses1_Scan_03_BOLD2.txt';
BATCH.Setup.subjects.effect_names{1}={'ANYresponse'};
BATCH.Setup.subjects.effects{1}=[-1;1];
BATCH.Setup.done=1;
BATCH.Setup.overwrite='No';
BATCH.Preprocessing.filter=[.01,.1];
%BATCH.Preprocessing.confounds.names={'White','CSF','realignment'};
%BATCH.Preprocessing.confounds.dimensions={3,3,6};
%BATCH.Preprocessing.confounds.deriv={0,0,1};
BATCH.Preprocessing.done=1;
BATCH.Preprocessing.overwrite='No';
BATCH.Analysis.type=1;
BATCH.Analysis.measure=1;
BATCH.Analysis.weight=2;
BATCH.Analysis.sources.names={'LeftVentralStriatum','RightVentralStriatum', 'LeftDorsalPutamen', 'RightDorsalPutamen', 'LeftMedialDorsalThalamus', 'RightMedialDorsalThalamus', 'LeftVentralPutamen', 'RightVentralPutamen', 'LeftDorsalStriatum', 'RightDorsalStriatum'};
BATCH.Analysis.sources.dimensions={1,1,1,1,1,1,1,1,1,1};
BATCH.Analysis.sources.deriv={0,0,0,0,0,0,0,0,0,0};
BATCH.Analysis.done=1;
BATCH.Analysis.overwrite='No';
BATCH.Results.between_subjects.effect_names={'All'};
BATCH.Results.between_subjects.contrast=[1];
%BATCH.Results.between_conditions.effect_names={task1','task2'};
%BATCH.Results.between_conditions.contrast=[1,-1];
BATCH.Results.between_sources.effect_names={'RightVentralStriatum'};
BATCH.Results.between_sources.contrast=[1];
%BATCH.Results.analysis_number=2;
BATCH.Results.done=1;
conn_batch(BATCH);

and it seems to go farther, but now I'm getting this error:
Error using cell/strmatch (line 19)
Requires character array or cell array of character vectors as inputs.

Error in conn_batch (line 1289)
idx=strmatch(batch.Results.between_subjects.effect_names{neffect},CONN_x.Setup.l2covariates.names,'exact');
Error in CONNbatch (line 77)
conn_batch(BATCH);
I'm guessing I need to comment out line 19?
Ben