Hi CONN developers
I’m struggling with an error during the denoising step.
Specifically, I’m analyzing resting-state functional connectivity changes between pre-treatment and post-treatment conditions in 51 patients using paired-t test.
I divided my job into 16 parallel tasks, and found no error during the default preprocessing and set-up procedures.
I also used 16 parallel jobs in the denoising step, and the following error message came out !!
It seems so weird that 14 jobs completed without an error, while 2 jobs resulted in the following error.
I have repeated this job again and again, however the same error occurred during the denoising step (error jobs ranged from 1 to 4 each time the same denoising steps were conducted).
I’m currently using Matlab 2022b and CONN 22a on Window 11.
This message did not occur when analyzing the same data using Matlab 2020b and CONN 22a upon Window 10 system.
How can I solve this?
Thank you in advance for your advice.
Best regards
MJ
MATLAB is running in headless mode. Figure windows will not be displayed.
To get started, type doc.
For product information, visit http://www.mathworks.com.
H:\AD_FCfmri\conn_project01_acute_recovery.qlog\231210171327627\node.0004231210171327627.bat running
Processing H:\AD_FCfmri\conn_project01_acute_recovery.mat?id=0004231210171327627,subjects=[10 11 12],partition=4-16 job 1/1
saved H:\AD_FCfmri\conn_project01_acute_recovery.0004231210171327627.dmat
CONN: RUNNING DENOISING STEP
Step 1/6: Expanding conditions
100.0% (Condition recovery)
Step 2/6: Importing conditions/covariates
100.0% (Subject 12 Session 2)
Step 3/6: Denoising functional data
Regression : White Matter (5P) (5 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : CSF (5P) (5 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : realignment (12P) (6 dimensions; no polynomial expansion; added first-order derivative; non-filtered)
Regression : scrubbing (40P) (40 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : Effect of acute (2P) (1 dimensions; no polynomial expansion; added first-order derivative; non-filtered)
Regression : Effect of recovery (2P) (1 dimensions; no polynomial expansion; added first-order derivative; non-filtered)
Order : Regression followed by filtering (RegBP)
Detrending : 1
Despiking : 0
Bandpass : [0.01 0.08]
66.7% (Subject 11)H:\ AD_FCfmri \conn_project01_acute_recovery.qlog\231210171327627\node.0004231210171327627.bat error
ERROR DESCRIPTION:
Error using fwrite
Invalid file identifier. Use fopen to generate a valid file identifier.
Error in conn_init_vol (line 27)
fwrite(handle,[0],'float',4*(sum(V.size.Nv)*V.size.Nt));
Error in conn_process (line 1391)
Yout{ncondition}=conn_init_vol(Yout{ncondition},[],[],softlink,softlinkoverwrite(ncondition));
Error in conn_process (line 69)
case {'preprocessing_gui','denoising_gui'}, conn_disp(['CONN: RUNNING DENOISING STEP']); conn_process([1.5,2,6:9],varargin{:});
Error in conn_jobmanager (line 892)
conn_process(job(n).fcn,job(n).args{2:end});
CONN v.22.a
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2022b
storage: 6130.1Gb available
spm @ F:\programs_utilities\SPM_related_2023\spm12\spm12
conn @ F:\programs_utilities\SPM_related_2023\conn22a\conn
Hi,
That fwrite error typically indicates either a hard-disk issue (e.g. your drive may be full) or a permissions issue (CONN may be trying to overwrite a file of a different user without write permissions). In your case, if it is none of the above, I imagine this could also indicate that two processes are trying to write simultaneously to the same file. Typically that never happens in normal CONN parallelization operations as each process handles a different subset of subejcts, but I imagine this issue may arise if you have some processes from a previous attempt that are still running on your computer or cluster (if that is the case then simply killing those processes and/or restarting your computer and/or just waiting until all processes from a previous attempt have finished should work to avoid these issues)
Hope this helps
Alfonso
Originally posted by Min Joong Kim:
Hi CONN developers
I’m struggling with an error during the denoising step.
Specifically, I’m analyzing resting-state functional connectivity changes between pre-treatment and post-treatment conditions in 51 patients using paired-t test.
I divided my job into 16 parallel tasks, and found no error during the default preprocessing and set-up procedures.
I also used 16 parallel jobs in the denoising step, and the following error message came out !!
It seems so weird that 14 jobs completed without an error, while 2 jobs resulted in the following error.
I have repeated this job again and again, however the same error occurred during the denoising step (error jobs ranged from 1 to 4 each time the same denoising steps were conducted).
I’m currently using Matlab 2022b and CONN 22a on Window 11.
This message did not occur when analyzing the same data using Matlab 2020b and CONN 22a upon Window 10 system.
How can I solve this?
Thank you in advance for your advice.
Best regards
MJ
MATLAB is running in headless mode. Figure windows will not be displayed.
To get started, type doc.
For product information, visit http://www.mathworks.com.
H:\AD_FCfmri\conn_project01_acute_recovery.qlog\231210171327627\node.0004231210171327627.bat running
Processing H:\AD_FCfmri\conn_project01_acute_recovery.mat?id=0004231210171327627,subjects=[10 11 12],partition=4-16 job 1/1
saved H:\AD_FCfmri\conn_project01_acute_recovery.0004231210171327627.dmat
CONN: RUNNING DENOISING STEP
Step 1/6: Expanding conditions
100.0% (Condition recovery)
Step 2/6: Importing conditions/covariates
100.0% (Subject 12 Session 2)
Step 3/6: Denoising functional data
Regression : White Matter (5P) (5 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : CSF (5P) (5 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : realignment (12P) (6 dimensions; no polynomial expansion; added first-order derivative; non-filtered)
Regression : scrubbing (40P) (40 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : Effect of acute (2P) (1 dimensions; no polynomial expansion; added first-order derivative; non-filtered)
Regression : Effect of recovery (2P) (1 dimensions; no polynomial expansion; added first-order derivative; non-filtered)
Order : Regression followed by filtering (RegBP)
Detrending : 1
Despiking : 0
Bandpass : [0.01 0.08]
66.7% (Subject 11)H:\ AD_FCfmri \conn_project01_acute_recovery.qlog\231210171327627\node.0004231210171327627.bat error
ERROR DESCRIPTION:
Error using fwrite
Invalid file identifier. Use fopen to generate a valid file identifier.
Error in conn_init_vol (line 27)
fwrite(handle,[0],'float',4*(sum(V.size.Nv)*V.size.Nt));
Error in conn_process (line 1391)
Yout{ncondition}=conn_init_vol(Yout{ncondition},[],[],softlink,softlinkoverwrite(ncondition));
Error in conn_process (line 69)
case {'preprocessing_gui','denoising_gui'}, conn_disp(['CONN: RUNNING DENOISING STEP']); conn_process([1.5,2,6:9],varargin{:});
Error in conn_jobmanager (line 892)
conn_process(job(n).fcn,job(n).args{2:end});
CONN v.22.a
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2022b
storage: 6130.1Gb available
spm @ F:\programs_utilities\SPM_related_2023\spm12\spm12
conn @ F:\programs_utilities\SPM_related_2023\conn22a\conn