Hello,
I am a bit confused about how to import fmriprep processed data into conn. I have a derivatives folder. Inside the derivatives folder is an fmriprep folder, and the fmriprep folder contains all the subject folders. The subject folders contain the anat and func folders with the data, etc. Is this the correct file organization that conn expects? When I click on the the import new fmriprep project, and then go into the fmriprep folder and select, I get the following error message: "No matching sub-* files found in BIDs directory.
Additionally, within each func folder, I have the data for task and rest data. I only want to process two resting state runs within the func folder. How might I specify that?
Thanks!
Emily
Hi Emily,
Selecting the derivatives/fmriprep folder should automatically find all subjects data (they will appear listed in the list named 'BIDS subjects' in the GUI), you can then select in the list named 'functional' which specific runs/tasks you are interested in before clicking on 'Import' to import those to your CONN project.
Hope this helps
Alfonso
Originally posted by Emily Belleau:
Hello,
I am a bit confused about how to import fmriprep processed data into conn. I have a derivatives folder. Inside the derivatives folder is an fmriprep folder, and the fmriprep folder contains all the subject folders. The subject folders contain the anat and func folders with the data, etc. Is this the correct file organization that conn expects? When I click on the the import new fmriprep project, and then go into the fmriprep folder and select, I get the following error message: "No matching sub-* files found in BIDs directory.
Additionally, within each func folder, I have the data for task and rest data. I only want to process two resting state runs within the func folder. How might I specify that?
Thanks!
Emily
Hi Alfonso,
I'm using CONN 22.v2407 to import an old fmriprep folder (the fmriprep version is 1.5.0) as you've decribed below. When I picked the fmriprep folder containing all the subject folders, I get a message box that states 1 folders selected (4678 matching files), with the buttons 'ok' and 'undo'. After pressing 'ok', the BIDS subjects & functional boxes show up in the CONN gui, but they're empty, as though no subjects were detected (see attached screenshot). Does this mean I'm out of luck with this old dataset and should rerun fmriprep with newer version?
Thanks so much!
Jennie
Originally posted by Alfonso Nieto-Castanon:
Hi Emily,
Selecting the derivatives/fmriprep folder should automatically find all subjects data (they will appear listed in the list named 'BIDS subjects' in the GUI), you can then select in the list named 'functional' which specific runs/tasks you are interested in before clicking on 'Import' to import those to your CONN project.
Hope this helps
Alfonso
Originally posted by Emily Belleau:
Hello,
I am a bit confused about how to import fmriprep processed data into conn. I have a derivatives folder. Inside the derivatives folder is an fmriprep folder, and the fmriprep folder contains all the subject folders. The subject folders contain the anat and func folders with the data, etc. Is this the correct file organization that conn expects? When I click on the the import new fmriprep project, and then go into the fmriprep folder and select, I get the following error message: "No matching sub-* files found in BIDs directory.
Additionally, within each func folder, I have the data for task and rest data. I only want to process two resting state runs within the func folder. How might I specify that?
Thanks!
Emily