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help > Issue with aCompCor variables when importing already preprocessed data
Sep 3, 2024 08:09 PM | Nam Kap
Issue with aCompCor variables when importing already preprocessed data
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
Threaded View
Title | Author | Date |
---|---|---|
Nam Kap | Sep 3, 2024 | |
Alfonso Nieto-Castanon | Sep 3, 2024 | |