Alfonso,

Thank you for your response.

That helps a great deal.

I have another question regarding ROI masks.

I've had some trouble running the batch script and using different white matter and csf masks as ROI's.

I can successfully use different white matter and csf masks for each subject. However, it does not work when I included them in a batch script.

Initially, I tried using the Batch.Setup.masks.White.files{nsub} and Batch.Setu.maksCSF.files{nsub} for assigning the alternative white matter and csf masks. However, they were ignored, and the resulting roi's used for denoising were the segmented grey matter and white matter files for each subject (c1 and c2 files, respectively).

I then tried the BATCH.Setup.rois.names{nrois} and BATCH.Setup.rois.names{nrois}{nsub} options for the csf and white matter masks.

But I get the following error messages for my batch script:

Step 5/6: Importing ROI data
100.0% (Subject 15 Session 2)

Bad cell reference operation.

Error in conn_process (line 841)

if length(dims)>=n1&&~isempty(dims{n1}),
CONN_x.Preproc.confounds.dimensions{end+1}=[min(dims{n1}(1),CONN_x.Preproc.variables.dimensions{idx}(1)),CONN_x.Preproc.variables.dimensions{idx}(1)];
else

Error in conn_process (line 12)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:5]);

Error in conn_batch (line 432)
conn_process Setup;

Error in batch_new_conn (line 314)
conn_batch(BATCH)

What exactly am I doing wrong here?

Your input would greatly be appreciated.

Thanks.

h.