Hi all,
I keep running into this error and I am at my wit's end. I'm not sure what I'm doing wrong, but it seems like no matter what I do, this error won't leave me alone.

I am trying to use the batch script example to spatially preprocess my data. In the current structure (see attached image), whenever I try to run my batch script, I get the error seen below. However, when I move the script to the save level as the *.nii files (without changing anything else), the script works. That leads me to believe that the data itself is acceptable as is. Unfortunately, it would only work on one subject and therefore defeats the purpose of batch scripting.

I've also tried dumping all the *nii files into one giant folder, with the script, but that doesn't work either.

Any ideas?

Thanks,
Katherine


ERROR:
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Initialising SPM.........done

SPM present working directory:
M:\shared\Nicolas\ADNI_rsfMRI_complexity\inprocess_katherine_2_batchscript

>> conn
>> run('M:\shared\Nicolas\ADNI_rsfMRI_complexity\inprocess_katherine_2_batchscript\ExampleDataset_BatchScript_kw_spatial.m')

73 subjects
1 sessions

??? Error using ==> conn_getinfo at 26
File type not implemented

Error in ==> conn_file at 3
[V,str,icon,filename]=conn_getinfo(filename);

Error in ==> conn_batch at 306
CONN_x.Setup.structural{nsub}{nses}=conn_file(temp{min(numel(temp),nses)});

Error in ==> conn_setup_wizard at 124
conn_batch(batch);

Error in ==> conn_batch at 222
conn_setup_wizard(OPTIONS);

Error in ==> ExampleDataset_BatchScript_kw_spatial at 34
conn_batch(batch);

Error in ==> run at 57
evalin('caller', [s ';']);
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My script:
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%% FIND functional/structural files
cwd=pwd;
FUNCTIONAL_FILE=cellstr(conn_dir('*rsfmri*.nii'));
STRUCTURAL_FILE=cellstr(conn_dir('*t1*.nii'));
NSUBJECTS=73; % Number of subjects for analyses
if rem(length(FUNCTIONAL_FILE),NSUBJECTS),error('mismatch number of functional files');end
if rem(length(STRUCTURAL_FILE),NSUBJECTS),error('mismatch number of anatomical files');end
nsessions=length(FUNCTIONAL_FILE)/NSUBJECTS;
FUNCTIONAL_FILE=reshape(FUNCTIONAL_FILE,[NSUBJECTS,nsessions]);
STRUCTURAL_FILE={STRUCTURAL_FILE {1:NSUBJECTS}};
disp([num2str(size(FUNCTIONAL_FILE,1)),' subjects']);
disp([num2str(size(FUNCTIONAL_FILE,2)),' sessions']);
TR=3; % Repetition time = 3 seconds

%% PREPARES connectivity analyses (using default values for all parameters, see help conn_batch to define non-default values)
clear batch;
% CONN New experiment (realignment/coregistration/segmentation/normalization/smoothing)
batch.filename=fullfile(cwd,'adniFMRI_batchscript.mat'); % New conn_*.mat experiment name
batch.New.FWHM=6; % 6mm FWHM smoothing
batch.New.VOX=2; % 2mm voxel size for analyses
batch.New.functionals=repmat({{}},[NSUBJECTS,1]); % Point to functional volumes for each subject/session
for nsub=1:NSUBJECTS,for nses=1:nsessions,batch.New.functionals{nsub}{nses}{1}=FUNCTIONAL_FILE{nsub,nses};end; end %note: each subject's data is defined by three sessions and one single (4d) file per session
batch.New.structurals=STRUCTURAL_FILE; % Point to anatomical volumes for each subject
% CONN Setup % Default options (uses all ROIs in conn/rois/ directory); see conn_batch for additional options
batch.Setup.RT=TR; % TR (seconds)
nconditions=nsessions; % treats each session as a different condition (comment the following three lines and lines 84-86 below if you do not wish to analyze between-session differences)
batch.Setup.conditions.names=cellstr([repmat('Session',[nconditions,1]),num2str((1:nconditions)')]);
for ncond=1:nconditions,for nsub=1:NSUBJECTS,for nses=1:nsessions, batch.Setup.conditions.onsets{ncond}{nsub}{nses}=[];batch.Setup.conditions.durations{ncond}{nsub}{nses}=[]; end;end;end
for ncond=1:nconditions,for nsub=1:NSUBJECTS,for nses=ncond, batch.Setup.conditions.onsets{ncond}{nsub}{nses}=0; batch.Setup.conditions.durations{ncond}{nsub}{nses}=inf;end;end;end
batch.Setup.overwrite='Yes';
batch.Setup.done=1;
%% RUNS analyses
conn_batch(batch);

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