Dear Besim,

Sorry but the explicit analysis mask is expected to be a single file (the same mask across all subjects). Currently only the "implicit mask" option considers the possibility of using a different analysis mask for each subject (but note that this precludes the possibility of running voxel-level analyses at the group level). I would probably suggest to simply enter the normalized functionals and structurals in CONN instead of the subject-space files in order to avoid these issues. You can always enter the subject-space functionals as additional data (e.g. as a secondary dataset) if you have subject-space ROIs defined for your data (and in that case you would not need to worry about analysis masks, since those only apply when computing voxel-level timeseries, not when computing ROI-level timeseries)

Hope this helps

Alfonso

Originally posted by Besim Prenaj:

Dear Conn users

I use data from dHCP that has already been preprocessed. The data has been normalized, but then brought back to its native form. So I have subject-specific masks that I would like to upload to CONN. The GUI does not seem to have an option for this. I then tried the following with the CONN batch (as described in the "CONN batch manual"):

MASK_FILE = cellstr(conn_dir('sub-*_ses-*_desc-brain_mask.nii'));
batch.Setup.voxelmask = 1;
for nsub = 1:NSUBJECTS
    for nses = 1:nsessions
        batch.Setup.voxelmaskfile{nsub}{nses} = MASK_FILE{nsub};
    end
end

However, this does not seem to work. Error message: 

Error using char Cell elements must be character arrays. Error in conn_file (line 10) filename=char(filename); Error in conn_batch (line 773) CONN_x.Setup.explicitmask=conn_file(batch.Setup.voxelmaskfile); Error in VV_Analysis (line 111) conn_batch(batch); % runs Preprocessing and Setup steps only

Can anyone help?

Thank You, Besim