Hi Asena,

Could you please try entering in the Setup.Structural tab just a template T1 image (the same for every subject), e.g. the one in CONN's distribution folder utils/surf/referenceT1.nii. After modifying the preprocessing pipeline as you described one typically still needs to enter "some" image in the structural tab simply because CONN will use those images as background images when displaying results for each subject.

Hope this helps

Alfonso

Originally posted by Asena Kocan:

Hi Alfonso,

I'm working on a CONN project (v22.v2407) where I only have functional scans available — no anatomical (structural) scans. I understand that CONN can be run without structural images if the preprocessing pipeline is adjusted accordingly.

Here's what I did so far:

• In the Preprocessing pipeline, I removed all steps involving structural data (e.g., segmentation, normalization using structural).


• The Structural tab in SETUP is currently left blank for all subjects.

However, during denoising or setup, I get this error:

Index exceeds the number of array elements (0).

Error in conn (line 6901)

CONN_h.menus.m_preproc.Xs=conn_fileutils('spm_get_data',CONN_h.menus.m_preproc.XS(1).pinv(CONN_h.menus.m_preproc.XS(1).mat)*xyz);

Do you or anyone know why I might be getting this error and how I can avoid it?

Interestingly, it lets me run denoising and 1st-level without an issue, but I am not sure if ignoring it is a good idea.

I really appreciate any guidance you can provide here!

Best,

Asena