Dear Alfonso, 

thank you for pointing this out - this actually brings up a possible point of confusion on my side. In this case the duplicate name came from the the CSF mask (in the ROI tab) and the CSF (including the first order derivatives) I included from fMRIprep output as a first level covariate. Did I understand correctly, that the ROI tab defines masks / labels / networks (including the different tissue types) that later can be used as sources for connectivity analysis, and it is thus valid to just adapt the naming so there is no 'duplicate name'? 

thank you as well for taking your time to explain the procedure!

Best, 

Hana

Dear Hana,

Yes, you are exactly right, the ROIs tab defines masks from where BOLD signal timeseries (e.g. average or PCA decompositions) will be extracted during the Setup step (which can then be used for anything you want, e.g. timeseries from WM/CSF tissue classes are typically used during denoising, while other ROIs are typically used as seeds for SBC or as sources for RRC analyses), so in your scenario simply renaming the fMRIprep variable to avoid that duplicate name should fix that. 

Best

Alfonso

Originally posted by Hana Adolphi:

 

Dear Alfonso, 

thank you for pointing this out - this actually brings up a possible point of confusion on my side. In this case the duplicate name came from the the CSF mask (in the ROI tab) and the CSF (including the first order derivatives) I included from fMRIprep output as a first level covariate. Did I understand correctly, that the ROI tab defines masks / labels / networks (including the different tissue types) that later can be used as sources for connectivity analysis, and it is thus valid to just adapt the naming so there is no 'duplicate name'? 

thank you as well for taking your time to explain the procedure!

Best, 

Hana

As I am using fMRIprep preprocessed data I am wondering ho

Originally posted by Alfonso Nieto-Castanon:

Dear Hana, The error seems to indicate some sort of "duplicate name" condition regarding either different ROIs or different 1st-level covariates that share the same name. That said, regarding the question about sessions, yes, different subjects may have different number of functional runs/sessions, but those runs/sessions are always numbered from 1 to the number of sessions for each subject (e.g. if subject 1 was scanned twice, no matter "when" that happened, that data will be entered as session #1 and session #2 for subject 1, if subject 2 was scanned once, that data will be entered as session #1 for subject 2, etc.). Later, when you define your "conditions of interest" (in Setup.Conditions) that is where you define the association between these arbitrary session numbers for each subject, and your conditions of interest. For example, in the example above, if you had "pre-intervention" and "post-intervention" scans for subject 1, while a single "post-intervention" scan for subject 2, you would indicate in Setup.Conditions that the condition "pre-intervention" is associated with Session #1 for subject 1 and it is missing in subject 2, while the condition "post-intervention" is associated with Session #2 for subject 1 and with Session #1 for subject 2. Hope this helps Alfonso Originally posted by Hana Adolphi:

Dear all,  I am receiving the error message below when trying to set up my script with unequal session numbers. Different debugging attempts have not yielded a working solution, so I would be very glad for some support.  What do I have to take into account when I want to be able to analyze different session numbers ? I have set the allow missing data to true (although I think this only refers to the condition setup right?). The script is supposed to be able to denoise and run first level analysis with all available sessions for each subject. while some subjects will have scans for all three sessions, some have missing sessions from either sessions (so that not necessarily all sessions are available incrementally). Do you think this is feasible?  My original version of the script with equal session numbers had worked fine so I assume there is something I am missing to take into account for unequal number of sessions.  CONN: RUNNING SETUP STEP Step 1/7: Checking data completeness ....  Step 7/7: Updating Denoising variables 50.0% Intermediate brace '{}' indexing produced a comma-separated list with 2 values, but it must produce a single value when followed by subsequent indexing operations. Error in conn_process (line 1211) if length(dims)>=n1&&~isempty(dims{n1}), CONN_x.Preproc.confounds.dimensions{end+1}=[dims{n1}(1),CONN_x.Preproc.variables.dimensions{idx}(1)]; Error in conn_process (line 55) case 'setup', conn_disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]); Error in conn_batch (line 1322) conn_process Setup; Thank you in advance,  Hana

 

Dear Alfonso, 

thank you for your explanation!

I came across two threads (links below) that suggest that the naming of files that are generated outsite conn matters for the denoising step for SPM or FSL output. As I am using fMRIprep preprocessed data, I have now created following .txt files that I load into CONN through scripting:

1) "realignment" file that includes the 24 head motion parameters  (translation, rotation; their derivatives & quadratic terms)

2) "tissue_regressor" - file for all csf and white matter values (including their derivatives and quadratic terms) 

3) "motion_outlier" file -  files with all outliers detected by fMRIprep. 

As I have observed, that when loading the files through batch scripting the denoising tab looks different from loading the data through the gui, I have following questions:

1.       do I have to follow a specific file convention for CONN to load the files correctly?

2.       does it matter, whether the files inlcude column names or not?

3.       edit: I just found an (partial) answer to the following question: is it even okay to concatenate the regressors into one file, given that the # of compounds to be extracted will also be defined? Is CONN then able to derive the correct # of compounds as defined by confound.dimensions? (is it be okay to indicate for the tissue files 10 compounds (as in 5 for CSF and WM each) or is this invalid, since the files also contain the derivatives and squared values? 

p.s. the threads I was referring to are those two: 

NITRC: CONN : functional connectivity toolbox: RE: Problems preprocessing imported data unwarped with fsl topup

NITRC: CONN : functional connectivity toolbox: RE: Problems preprocessing imported data unwarped with fsl topup

Thank you in advance for you response!

Best,

Hana

A slight movement is normal, but if it's too loose, double-check the installation. Usually, one side is active when the flap is closed, both sides when open. Refer to your system's design. Excessive vibrations may indicate an installation or exhaust issue. Have it inspected by a professional.