Hi,

Please see the following thread https://www.nitrc.org/forum/forum.php?th... In general if you have your data fully preprocessed in FSL you should be able to simply import the Gray/White/CSF masks directly in Setup.ROIs, and, assuming that those masks are in the same space as your functional data, they should show up without a problem later in the Denoising step to be used as potential confounder effects for aCompCor. One potential reason why they may not be showing up in your case may perhaps be if the WM/CSF masks are defined in subject-space while the functional data is defined in MNI-space. 

Hope this helps

Alfonso

Originally posted by Nam Kap:

Hello, 

We are preprocessing our data externally using FSL and importing the preprocessed data into CONN. As one part of this, we have existing WM/CSF subject-specific structural masks  (not TPMs) such as 'sub-XX_whitematter.nii', and 'sub-XX_cerebrospinalfluid.nii'. We would like to use these masks to extract the CSF/WM timecourses for denoising. Is there a way to do that using batchscript? Do we need to add any prefixes before importing them as ROI in the Setup.ROI? Our imported structural and functional data have undergone all the preprocessing steps in FSL, except for slice-time correction. Our primary goal is to perfrom denoising and functional connectivity analysis in CONN on this preprocessed data. 

 

If we don't run any preproc segmentation after importing the data, the WM/CSF variables in Denoising look wrong/nonexistnt. We tried running functional segmentation, but got the error message "mean functional file not found" (details below). How would we create the mean functional file? There doesn't seem to be a preprocessing step for that. Or is this all the wrong approach, and we need to be doing something different to get out those aCompCor variables from WM/CSF tissue masks? 

 

Error using conn_setup_preproc

Error preparing files for normalization. Mean functional file not found (associated with functional data

/Volumes/backup/fMRI/conn/sub-XX/sub-XX_task_run-1_preproc_bold.nii ; run either

realignment or ART first, or select the option "first functional volume as reference" -#coregtomean field- if you prefer to use the first

functional volume instead of the mean functional volume as reference)

 

Error in conn (line 1443)

 ok=conn_setup_preproc('',varargin{2:end});

 

Error in conn_menumanager (line 125)

 feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end}); 

CONN22.v2407

SPM12 + DAiSS DEM FieldMap MEEGtools

Matlab v.2023b

project: CONN22.v2407

spm @ /Users/Shared/MATLAB/spm12-maint

conn @ /Users/Shared/MATLAB/conn