help > ROI-extracted from smoothed or unsmoothed data? Can't tell what happened
Nov 25, 2022  07:11 AM | Samantha Baldi
ROI-extracted from smoothed or unsmoothed data? Can't tell what happened
Dear Alfonso, 

I am trying to make sense of the analyses that I performed, particularly if CONN managed to extract ROI data from the unsmoothed functional data, as it should be by default and if not otherwise specified.
I preprocessed my functional data using the HCP pipelines, and I then put the needed functional, structural and ROI files in the folder LocalCopyData. I still performed some preprocessing steps within CONN, namely structural segmentation, ART and functional smoothing. So at the end of these steps, I can see in my LocalCopyData folder functional files both with and without 's' for each subject. 

I did not specified anything different than the default in terms of secondary dataset, and indeed when loading the conn.mat project, I can see the following relevant fields: 
CONN_x.Setup.secondarydataset.functonals_type = 2; 
CONN_x.Setup.secondarydataset.label = 'unsmoothed volume'.
And, when looking specifically at the rois field, I see the following:
CONN_x.Setup.rois.files = /data/conn_analyses/LocalCopyDataFiles/Sub0*/allBNA_MNI2mm.nii (correct file name and folder)
CONN_x.Setup.rois.unsmoothedvolumes = 1

So all seems well here. However I then look at the logfile.txt (which I am going to attach), and I see the following, after completing the above mentioned preprocessing steps: 
2022-Sep-28 00:49 : Step 5/7: Importing ROI data
warning: set-1 data for subject 1 session 1 not found
2022-Sep-28 00:51 : warning: set-1 data for subject 1 session 2 not found
2022-Sep-28 00:52 : warning: set-1 data for subject 1 session 3 not found
2022-Sep-28 00:53 : warning: set-1 data for subject 1 session 4 not found
2022-Sep-28 00:54 : warning: set-1 data for subject 1 session 5 not found
2022-Sep-28 00:55 : warning: set-1 data for subject 1 session 6 not found
2022-Sep-28 00:56 : warning: set-1 data for subject 1 session 7 not found
(...) 

After reading on another post on the forum, should I then conclude that CONN was not able to locate the unsmoothed dataset and thus proceeded to extract the ROI data from the smoothed dataset? The next step was denoising, by the way. 
Where can I see in the output or conn.mat project whether this was actually the case? 

Thanks in advance
Samantha
Attachment: logfile.txt

Threaded View

TitleAuthorDate
ROI-extracted from smoothed or unsmoothed data? Can't tell what happened
Samantha Baldi Nov 25, 2022
Samantha Baldi Nov 25, 2022