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help > Denoising error after patch
May 2, 2026 10:05 PM | Joshua Neal - Virginia Tech
Denoising error after patch
Hello,
I have a project utilizing fmriprep preprocessed data with Conn
25b. At the denoising window I have received errors akin to the
earlier threads about patching the conn.m file. As such, I saved my
project, closed Conn, and updated the file. Upon attempted to use
the denoising tab again, I still received errors along with
warnings.
Creating QC displays. Please wait...
QC_DOF, QC_PeakFC, QC_IqrFC, QC_MeanFC, and
QC_StdFC 2nd-level covariates updated
warning: unable to create QA_COV plot
Unable to perform assignment because the size of the left side is 3-by-1 and the size of the right side is 0-by-1.
Unable to perform assignment because the size of the left side is 3-by-1 and the size of the right side is 0-by-1.
QA plots stored in folder
F:\conn_ADHD20025b\results\qa\QA_GUIrequest_DataSensitivity_2026_05_02
Creating QC displays. Please wait...
Warning! Empty correlation data
ERROR DESCRIPTION:
Index exceeds the number of array elements. Index must not exceed 1.
Error in conn (line 7641)
if ~isempty(CONN_x.Preproc.qa.folders{2})&&isfield(CONN_x.Preproc.qa,'options2')&&isequal(testoptions,CONN_x.Preproc.qa.options2),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in conn_menumanager (line 125)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Additionally, I also attempted to use the "compute scrubbing" function at setup with the fmriprep dvars and framewise displacement in order as a suggested fix for this as well. The only way I was able to do that process without errors was by listing the names of the dvars and framewise covariates separated by a comma in the options. However, the resulting scrubbing covariate appears as just a straight line, and the 2nd level covariates do not appear accurate (QC_ValidScans, QC_ProportionValidScans, QC_MeanMotion, QC_MeanGSchange lists as zero/NaN for all particpants, QC_InvalidScans lists all the scans for every participant). When I attempted to use only framewise displacement for the scrubbing calculation, I received the following error:
Index exceeds the number of array elements. Index must not exceed 1.
Error in conn (line 7641)
if ~isempty(CONN_x.Preproc.qa.folders{2})&&isfield(CONN_x.Preproc.qa,'options2')&&isequal(testoptions,CONN_x.Preproc.qa.options2),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in conn_menumanager (line 125)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Additionally, I also attempted to use the "compute scrubbing" function at setup with the fmriprep dvars and framewise displacement in order as a suggested fix for this as well. The only way I was able to do that process without errors was by listing the names of the dvars and framewise covariates separated by a comma in the options. However, the resulting scrubbing covariate appears as just a straight line, and the 2nd level covariates do not appear accurate (QC_ValidScans, QC_ProportionValidScans, QC_MeanMotion, QC_MeanGSchange lists as zero/NaN for all particpants, QC_InvalidScans lists all the scans for every participant). When I attempted to use only framewise displacement for the scrubbing calculation, I received the following error:
compute scrubbing
thr=[5 0.9]
extension=1
Input=allsessions_framewise_displacement
Output=scrubbing
thr=[5 0.9]
extension=1
Input=allsessions_framewise_displacement
Output=scrubbing
created file
F:\fmriprep1.25\fmriprep\fmriprep\sub-0010002\ses-1\func\scrubbing_sub-0010002_ses-1_task-rest_run-2_desc-confounds_regressors_framewise_displacement.mat
ERROR DESCRIPTION:
Index in position 2 is invalid. Array indices must be positive integers or logical values.
Error in conn_convertl12l1covariate (line 293)
y5(nsub)=max(y5(nsub), max(abs(data(:,end-1)),[],1) );% MaxGSchange
^^^^^^^^^^^^^
Error in conn_convertl12l1covariate (line 89)
ocov=conn_convertl12l1covariate('scrubbing',answ{:});
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in conn (line 4966)
Index in position 2 is invalid. Array indices must be positive integers or logical values.
Error in conn_convertl12l1covariate (line 293)
y5(nsub)=max(y5(nsub), max(abs(data(:,end-1)),[],1) );% MaxGSchange
^^^^^^^^^^^^^
Error in conn_convertl12l1covariate (line 89)
ocov=conn_convertl12l1covariate('scrubbing',answ{:});
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in conn (line 4966)
opt=conn_convertl12l1covariate('?',opts{:});
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
CONN25.b
SPM25 + DAiSS DEM FieldMap MEEGtools
Matlab v.2026a
project: CONN22.v2407
storage: 5942.5Gb available
spm @ C:\Users\jnnea\OneDrive\Documents\MATLAB\spm25
conn @ C:\Users\jnnea\OneDrive\Documents\MATLAB\conn25b
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
CONN25.b
SPM25 + DAiSS DEM FieldMap MEEGtools
Matlab v.2026a
project: CONN22.v2407
storage: 5942.5Gb available
spm @ C:\Users\jnnea\OneDrive\Documents\MATLAB\spm25
conn @ C:\Users\jnnea\OneDrive\Documents\MATLAB\conn25b
Assistance to navigate these errors would
be greatly appreciated.
Thanks,
Josh