Dear Alice,

That's a good point, I will add an explicit option to disregard structural and segmentation volumes for the case that you describe. In the meantime you may avoid this error simply entering as structural volumes any T1 image (e.g. the file referenceT1_icbm.nii  in the folder conn/utils/surf/) and in the Gray/White/CSF ROIs any mask files (e.g. the files referenceT1_icbm_gm.nii, referenceT1_icbm_wm.nii, and referenceT1_icbm_csf.nii, respectively).

That said, just a general warning here to make sure you do include quality control steps aimed at evaluating the quality of your denoised data before computing functional connectivity matrices. Even if your data is already denoised, evaluating the quality of your data specifically for functional connectivity analyses (e.g. in CONN you may use the provided data quality, validity, and sensitivity scores) can help identify and resolve problems in the FC data soon, and avoid any self-reinforcing biases (e.g. those arising when one comes back to quality control only after first analyzing the data and possibly not finding some expected results)

Hope this helps

Alfonso

Originally posted by Alice Pirastru:

Hello,

I want to use the conn tool purely to extract functional connectivity matrices from already preprocessed, denoised and normalized 4D functional data. Therefore I'm not uploading structural data for any subject and directly performing the ROI-to-ROI analysis by setting this option. I've included an atlas to do so (Brainnettome atlas). However, after clicking the Done button the process immediatly stops at "Step 2/7 segmentation" for missing structural data (the details of the error are reported below). I don't want to perform gm signal regression or other similar option since my data have been already denoised. How can I skip this part and go straighforward to the matrices extraction?

Thank you,

alpi

ERROR DESCRIPTION:
 
Error using conn_setup_preproc
No structural file defined for Subject 1 Session 1. Please select a structural file

Error in conn_process (line 339)
 conn_setup_preproc('run_structural_segment','subjects',nsub);

Error in conn_process (line 55)
 case 'setup', conn_disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);

Error in conn (line 6392)
 conn_process(processname); ispending=false;

Error in conn_menumanager (line 124)
 feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end}); 
CONN22.a
SPM12 + AAL3 ArtRepair Beamforming DEM FieldMap LI LST MEEGtools aal cat12 wfupickatlas xjview
Matlab v.2023b
project: CONN22.a
storage: 628.2Gb available